Euclidean_distances.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "e8a2c3e3-1865-4d05-a82d-fcc32c0a6677",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "7d8755c1-c683-457f-a3e0-8a96122369d6",
   "metadata": {},
   "outputs": [],
   "source": [
    "from micom.workflows import GrowthResults"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f9d5d100-2452-41c0-8cf0-c4f2c5055199",
   "metadata": {},
   "source": [
    "first step \n",
    "- find the most abundant taxa (the taxa with more than 1% relative abundance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "4d40f89b-40ab-4883-959c-0e6fad026b73",
   "metadata": {},
   "outputs": [],
   "source": [
    "annotations = pd.read_csv(\"/proj/gibbons/sswegle_micom/Res_Saves/annotations_swegle.csv\")\n",
    "exchanges = pd.read_csv(\"/proj/gibbons/sswegle_micom/Res_Saves/exchanges_swegle.csv\")\n",
    "growth_rates = pd.read_csv(\"/proj/gibbons/sswegle_micom/Res_Saves/growth_rates_swegle.csv\")\n",
    "growth_rates = pd.read_csv(\"/proj/gibbons/sswegle_micom/Res_Saves/growth_rates_swegle.csv\")\n",
    "res = GrowthResults(growth_rates, exchanges, annotations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "01adfabc-72fd-4021-856b-02d1b455d0f2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>taxon</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>tolerance</th>\n",
       "      <th>reaction</th>\n",
       "      <th>flux</th>\n",
       "      <th>abundance</th>\n",
       "      <th>metabolite</th>\n",
       "      <th>direction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>SRR15032086</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_h(e)</td>\n",
       "      <td>-89.997588</td>\n",
       "      <td>0.120313</td>\n",
       "      <td>h[e]</td>\n",
       "      <td>import</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>9</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>SRR15032086</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_malt(e)</td>\n",
       "      <td>-0.024506</td>\n",
       "      <td>0.120313</td>\n",
       "      <td>malt[e]</td>\n",
       "      <td>import</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>SRR15032086</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_pi(e)</td>\n",
       "      <td>70.317187</td>\n",
       "      <td>0.120313</td>\n",
       "      <td>pi[e]</td>\n",
       "      <td>export</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>17</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>SRR15032086</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_gly(e)</td>\n",
       "      <td>-32.664068</td>\n",
       "      <td>0.120313</td>\n",
       "      <td>gly[e]</td>\n",
       "      <td>import</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>26</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>SRR15032086</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_ade(e)</td>\n",
       "      <td>11.025896</td>\n",
       "      <td>0.120313</td>\n",
       "      <td>ade[e]</td>\n",
       "      <td>export</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648745</th>\n",
       "      <td>3058276</td>\n",
       "      <td>Veillonella</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_succ(e)</td>\n",
       "      <td>169.919386</td>\n",
       "      <td>0.001058</td>\n",
       "      <td>succ[e]</td>\n",
       "      <td>export</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648746</th>\n",
       "      <td>3058278</td>\n",
       "      <td>Veillonella</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_metsox_S_L(e)</td>\n",
       "      <td>-0.000146</td>\n",
       "      <td>0.001058</td>\n",
       "      <td>metsox_S_L[e]</td>\n",
       "      <td>import</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648747</th>\n",
       "      <td>3058282</td>\n",
       "      <td>Veillonella</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_pyr(e)</td>\n",
       "      <td>-31.651654</td>\n",
       "      <td>0.001058</td>\n",
       "      <td>pyr[e]</td>\n",
       "      <td>import</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648748</th>\n",
       "      <td>3058288</td>\n",
       "      <td>Veillonella</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_isoprene(e)</td>\n",
       "      <td>5.508882</td>\n",
       "      <td>0.001058</td>\n",
       "      <td>ispre[e]</td>\n",
       "      <td>export</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>648749</th>\n",
       "      <td>3058289</td>\n",
       "      <td>Veillonella</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>0.000001</td>\n",
       "      <td>EX_oaa(e)</td>\n",
       "      <td>4.876942</td>\n",
       "      <td>0.001058</td>\n",
       "      <td>oaa[e]</td>\n",
       "      <td>export</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>648750 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Unnamed: 0        taxon    sample_id  tolerance          reaction  \\\n",
       "0                2    Alistipes  SRR15032086   0.000001           EX_h(e)   \n",
       "1                9    Alistipes  SRR15032086   0.000001        EX_malt(e)   \n",
       "2               10    Alistipes  SRR15032086   0.000001          EX_pi(e)   \n",
       "3               17    Alistipes  SRR15032086   0.000001         EX_gly(e)   \n",
       "4               26    Alistipes  SRR15032086   0.000001         EX_ade(e)   \n",
       "...            ...          ...          ...        ...               ...   \n",
       "648745     3058276  Veillonella  SRR15032514   0.000001        EX_succ(e)   \n",
       "648746     3058278  Veillonella  SRR15032514   0.000001  EX_metsox_S_L(e)   \n",
       "648747     3058282  Veillonella  SRR15032514   0.000001         EX_pyr(e)   \n",
       "648748     3058288  Veillonella  SRR15032514   0.000001    EX_isoprene(e)   \n",
       "648749     3058289  Veillonella  SRR15032514   0.000001         EX_oaa(e)   \n",
       "\n",
       "              flux  abundance     metabolite direction  \n",
       "0       -89.997588   0.120313           h[e]    import  \n",
       "1        -0.024506   0.120313        malt[e]    import  \n",
       "2        70.317187   0.120313          pi[e]    export  \n",
       "3       -32.664068   0.120313         gly[e]    import  \n",
       "4        11.025896   0.120313         ade[e]    export  \n",
       "...            ...        ...            ...       ...  \n",
       "648745  169.919386   0.001058        succ[e]    export  \n",
       "648746   -0.000146   0.001058  metsox_S_L[e]    import  \n",
       "648747  -31.651654   0.001058         pyr[e]    import  \n",
       "648748    5.508882   0.001058       ispre[e]    export  \n",
       "648749    4.876942   0.001058         oaa[e]    export  \n",
       "\n",
       "[648750 rows x 9 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exchanges"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bad7a78c-08f4-4b79-b64d-07aa03f9a580",
   "metadata": {},
   "source": [
    "next step = find the average abundance of each microbe across samples "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "0b6fc5a6-8dc1-46a1-b853-1c8b4eed010b",
   "metadata": {},
   "outputs": [],
   "source": [
    "grouped_microbes = exchanges.groupby(['taxon'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f4eab59e-0e2e-4038-a2d1-b7a095a2aab0",
   "metadata": {},
   "outputs": [],
   "source": [
    "grouped_means = grouped_microbes['abundance'].mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "aaae914b-c671-4a7b-bd21-6935abc32e17",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "taxon\n",
       "Acidaminococcus     0.011517\n",
       "Actinomyces         0.000621\n",
       "Adlercreutzia       0.001168\n",
       "Akkermansia         0.058139\n",
       "Alistipes           0.075543\n",
       "                      ...   \n",
       "Terrisporobacter    0.014781\n",
       "Varibaculum         0.006495\n",
       "Veillonella         0.004449\n",
       "Weissella           0.004379\n",
       "medium                   NaN\n",
       "Name: abundance, Length: 85, dtype: float64"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grouped_means"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "5ef59391-ebda-45b7-bf0c-990530196ebd",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "taxon\n",
       "Bacteroides         0.302967\n",
       "Prevotella          0.124266\n",
       "Faecalibacterium    0.107079\n",
       "Roseburia           0.087074\n",
       "Blautia             0.082805\n",
       "Alistipes           0.075543\n",
       "Ruminococcus        0.058961\n",
       "Akkermansia         0.058139\n",
       "Paraprevotella      0.045048\n",
       "Megamonas           0.033435\n",
       "Name: abundance, dtype: float64"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ten_most_abundant_taxa = grouped_means.nlargest(10)\n",
    "ten_most_abundant_taxa"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dca4ca79-0f42-4ff0-ae2b-654a372248f2",
   "metadata": {},
   "source": [
    "- this shows the ten most abundant microbes in my sample \n",
    "- but, needs to be in table format again"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "ab3b57a7-ed21-4a7b-9833-743715adeb7b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartments</th>\n",
       "      <th>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.064537</td>\n",
       "      <td>0.210478</td>\n",
       "      <td>2650</td>\n",
       "      <td>1613</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.203834</td>\n",
       "      <td>0.506204</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.129073</td>\n",
       "      <td>0.262992</td>\n",
       "      <td>2808</td>\n",
       "      <td>1732</td>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.051118</td>\n",
       "      <td>0.101162</td>\n",
       "      <td>2073</td>\n",
       "      <td>1577</td>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6294</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.105515</td>\n",
       "      <td>0.203996</td>\n",
       "      <td>2808</td>\n",
       "      <td>1732</td>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032514</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6296</th>\n",
       "      <td>Coprococcus</td>\n",
       "      <td>0.093003</td>\n",
       "      <td>0.179806</td>\n",
       "      <td>2188</td>\n",
       "      <td>1591</td>\n",
       "      <td>Coprococcus</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032514</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6301</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.133591</td>\n",
       "      <td>0.258274</td>\n",
       "      <td>1986</td>\n",
       "      <td>1472</td>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032514</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6307</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>0.087276</td>\n",
       "      <td>0.168734</td>\n",
       "      <td>2357</td>\n",
       "      <td>1567</td>\n",
       "      <td>Roseburia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032514</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6308</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>0.038845</td>\n",
       "      <td>0.075099</td>\n",
       "      <td>2779</td>\n",
       "      <td>1788</td>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032514</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2256 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          compartments  abundance  growth_rate  reactions  metabolites  \\\n",
       "1          Akkermansia   0.133546     0.077366       2274         1386   \n",
       "2            Alistipes   0.064537     0.210478       2650         1613   \n",
       "3          Bacteroides   0.203834     0.506204       3293         1883   \n",
       "5              Blautia   0.129073     0.262992       2808         1732   \n",
       "6          Eubacterium   0.051118     0.101162       2073         1577   \n",
       "...                ...        ...          ...        ...          ...   \n",
       "6294           Blautia   0.105515     0.203996       2808         1732   \n",
       "6296       Coprococcus   0.093003     0.179806       2188         1591   \n",
       "6301  Faecalibacterium   0.133591     0.258274       1986         1472   \n",
       "6307         Roseburia   0.087276     0.168734       2357         1567   \n",
       "6308      Ruminococcus   0.038845     0.075099       2779         1788   \n",
       "\n",
       "                 taxon  tradeoff    sample_id  \n",
       "1          Akkermansia       0.7  SRR15032081  \n",
       "2            Alistipes       0.7  SRR15032081  \n",
       "3          Bacteroides       0.7  SRR15032081  \n",
       "5              Blautia       0.7  SRR15032081  \n",
       "6          Eubacterium       0.7  SRR15032081  \n",
       "...                ...       ...          ...  \n",
       "6294           Blautia       0.7  SRR15032514  \n",
       "6296       Coprococcus       0.7  SRR15032514  \n",
       "6301  Faecalibacterium       0.7  SRR15032514  \n",
       "6307         Roseburia       0.7  SRR15032514  \n",
       "6308      Ruminococcus       0.7  SRR15032514  \n",
       "\n",
       "[2256 rows x 8 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "only_top_ten = growth_rates.loc[growth_rates['abundance'] >= .035445]\n",
    "only_top_ten"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "4bcf9763-9bb1-43af-98be-2081359269cf",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "      <th>medium</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032079.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>0.840000</td>\n",
       "      <td>0.942212</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032080</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032080.pickle</td>\n",
       "      <td>16.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>0.592593</td>\n",
       "      <td>0.855661</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032082.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.696970</td>\n",
       "      <td>0.908204</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>306</td>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032510.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>0.881483</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>307</th>\n",
       "      <td>307</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032511.pickle</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>0.799526</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>308</th>\n",
       "      <td>308</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>309</td>\n",
       "      <td>SRR15032513</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032513.pickle</td>\n",
       "      <td>19.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>0.633333</td>\n",
       "      <td>0.839063</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>310</th>\n",
       "      <td>310</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>311 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Unnamed: 0    sample_id               description  time_point  \\\n",
       "0             0  SRR15032078           High fiber diet           8   \n",
       "1             1  SRR15032079           High fiber diet           4   \n",
       "2             2  SRR15032080  High fermented food diet           3   \n",
       "3             3  SRR15032081  High fermented food diet           2   \n",
       "4             4  SRR15032082           High fiber diet           7   \n",
       "..          ...          ...                       ...         ...   \n",
       "306         306  SRR15032510  High fermented food diet           2   \n",
       "307         307  SRR15032511           High fiber diet           6   \n",
       "308         308  SRR15032512  High fermented food diet           7   \n",
       "309         309  SRR15032513  High fermented food diet           6   \n",
       "310         310  SRR15032514           High fiber diet           9   \n",
       "\n",
       "                   file  found_taxa  total_taxa  found_fraction  \\\n",
       "0    SRR15032078.pickle        24.0        37.0        0.648649   \n",
       "1    SRR15032079.pickle        21.0        25.0        0.840000   \n",
       "2    SRR15032080.pickle        16.0        27.0        0.592593   \n",
       "3    SRR15032081.pickle        11.0        17.0        0.647059   \n",
       "4    SRR15032082.pickle        23.0        33.0        0.696970   \n",
       "..                  ...         ...         ...             ...   \n",
       "306  SRR15032510.pickle        21.0        28.0        0.750000   \n",
       "307  SRR15032511.pickle        22.0        32.0        0.687500   \n",
       "308  SRR15032512.pickle        23.0        37.0        0.621622   \n",
       "309  SRR15032513.pickle        19.0        30.0        0.633333   \n",
       "310  SRR15032514.pickle        24.0        37.0        0.648649   \n",
       "\n",
       "     found_abundance_fraction      medium  \n",
       "0                    0.889586  high_fiber  \n",
       "1                    0.942212  high_fiber  \n",
       "2                    0.855661   fermented  \n",
       "3                    0.898909     western  \n",
       "4                    0.908204  high_fiber  \n",
       "..                        ...         ...  \n",
       "306                  0.881483     western  \n",
       "307                  0.799526  high_fiber  \n",
       "308                  0.843232   fermented  \n",
       "309                  0.839063   fermented  \n",
       "310                  0.740106     western  \n",
       "\n",
       "[311 rows x 10 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata = pd.read_csv(\"/proj/gibbons/sswegle_micom/All the Steps/metadata_swegle.csv\")\n",
    "metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "95c79cad-21d6-461e-a102-65de9e720d9e",
   "metadata": {},
   "outputs": [],
   "source": [
    "filtered_meta = metadata[metadata.time_point < 8]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "4e0ced87-a468-420b-a433-69608fc6566e",
   "metadata": {},
   "outputs": [],
   "source": [
    "top_ten_merged = only_top_ten.merge(filtered_meta, on=\"sample_id\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "8dc5dfe5-2855-48ef-9bad-fbce8307d50d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartments</th>\n",
       "      <th>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "      <th>medium</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>7.736626e-02</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
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       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.064537</td>\n",
       "      <td>2.104784e-01</td>\n",
       "      <td>2650</td>\n",
       "      <td>1613</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.203834</td>\n",
       "      <td>5.062036e-01</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.129073</td>\n",
       "      <td>2.629917e-01</td>\n",
       "      <td>2808</td>\n",
       "      <td>1732</td>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.051118</td>\n",
       "      <td>1.011622e-01</td>\n",
       "      <td>2073</td>\n",
       "      <td>1577</td>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1788</th>\n",
       "      <td>Anaerostipes</td>\n",
       "      <td>0.047938</td>\n",
       "      <td>1.497117e-02</td>\n",
       "      <td>2034</td>\n",
       "      <td>1491</td>\n",
       "      <td>Anaerostipes</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1789</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.488549</td>\n",
       "      <td>3.029477e-01</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1790</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.094856</td>\n",
       "      <td>3.214070e-06</td>\n",
       "      <td>2808</td>\n",
       "      <td>1732</td>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1791</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.120583</td>\n",
       "      <td>3.149052e-11</td>\n",
       "      <td>1986</td>\n",
       "      <td>1472</td>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1792</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>6.170115e-02</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1793 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          compartments  abundance   growth_rate  reactions  metabolites  \\\n",
       "0          Akkermansia   0.133546  7.736626e-02       2274         1386   \n",
       "1            Alistipes   0.064537  2.104784e-01       2650         1613   \n",
       "2          Bacteroides   0.203834  5.062036e-01       3293         1883   \n",
       "3              Blautia   0.129073  2.629917e-01       2808         1732   \n",
       "4          Eubacterium   0.051118  1.011622e-01       2073         1577   \n",
       "...                ...        ...           ...        ...          ...   \n",
       "1788      Anaerostipes   0.047938  1.497117e-02       2034         1491   \n",
       "1789       Bacteroides   0.488549  3.029477e-01       3293         1883   \n",
       "1790           Blautia   0.094856  3.214070e-06       2808         1732   \n",
       "1791  Faecalibacterium   0.120583  3.149052e-11       1986         1472   \n",
       "1792   Parabacteroides   0.057953  6.170115e-02       2879         1747   \n",
       "\n",
       "                 taxon  tradeoff    sample_id  Unnamed: 0  \\\n",
       "0          Akkermansia       0.7  SRR15032081           3   \n",
       "1            Alistipes       0.7  SRR15032081           3   \n",
       "2          Bacteroides       0.7  SRR15032081           3   \n",
       "3              Blautia       0.7  SRR15032081           3   \n",
       "4          Eubacterium       0.7  SRR15032081           3   \n",
       "...                ...       ...          ...         ...   \n",
       "1788      Anaerostipes       0.7  SRR15032512         308   \n",
       "1789       Bacteroides       0.7  SRR15032512         308   \n",
       "1790           Blautia       0.7  SRR15032512         308   \n",
       "1791  Faecalibacterium       0.7  SRR15032512         308   \n",
       "1792   Parabacteroides       0.7  SRR15032512         308   \n",
       "\n",
       "                   description  time_point                file  found_taxa  \\\n",
       "0     High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "1     High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "2     High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "3     High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "4     High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "...                        ...         ...                 ...         ...   \n",
       "1788  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "1789  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "1790  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "1791  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "1792  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "\n",
       "      total_taxa  found_fraction  found_abundance_fraction     medium  \n",
       "0           17.0        0.647059                  0.898909    western  \n",
       "1           17.0        0.647059                  0.898909    western  \n",
       "2           17.0        0.647059                  0.898909    western  \n",
       "3           17.0        0.647059                  0.898909    western  \n",
       "4           17.0        0.647059                  0.898909    western  \n",
       "...          ...             ...                       ...        ...  \n",
       "1788        37.0        0.621622                  0.843232  fermented  \n",
       "1789        37.0        0.621622                  0.843232  fermented  \n",
       "1790        37.0        0.621622                  0.843232  fermented  \n",
       "1791        37.0        0.621622                  0.843232  fermented  \n",
       "1792        37.0        0.621622                  0.843232  fermented  \n",
       "\n",
       "[1793 rows x 17 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top_ten_merged"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "c09620c1-3d2a-4e16-a38a-f984bfbfa77a",
   "metadata": {},
   "outputs": [],
   "source": [
    "#merged.rename(columns={\"compartments\": \"taxon\"}, inplace=True)\n",
    "#merged\n",
    "small_ex = exchanges[['taxon', 'sample_id', 'direction', 'metabolite', 'flux']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "88d1e1d1-0996-4a48-9665-3b5d48a5f517",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartments</th>\n",
       "      <th>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "      <th>medium</th>\n",
       "      <th>direction</th>\n",
       "      <th>metabolite</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>export</td>\n",
       "      <td>MGlcn148[e]</td>\n",
       "      <td>0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>export</td>\n",
       "      <td>h[e]</td>\n",
       "      <td>149.145825</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>export</td>\n",
       "      <td>MGlcn46[e]</td>\n",
       "      <td>0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>export</td>\n",
       "      <td>MGlcn23_rl[e]</td>\n",
       "      <td>0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>export</td>\n",
       "      <td>MGlcn59[e]</td>\n",
       "      <td>0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184977</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>pydxn[e]</td>\n",
       "      <td>-0.000189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184978</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>ura[e]</td>\n",
       "      <td>-22.903380</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184979</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>export</td>\n",
       "      <td>etoh[e]</td>\n",
       "      <td>10.690341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184980</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>fe3[e]</td>\n",
       "      <td>-0.000499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184981</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>export</td>\n",
       "      <td>succ[e]</td>\n",
       "      <td>8.352195</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>184982 rows × 20 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           compartments  abundance  growth_rate  reactions  metabolites  \\\n",
       "0           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "1           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "2           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "3           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "4           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "...                 ...        ...          ...        ...          ...   \n",
       "184977  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184978  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184979  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184980  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184981  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "\n",
       "                  taxon  tradeoff    sample_id  Unnamed: 0  \\\n",
       "0           Akkermansia       0.7  SRR15032081           3   \n",
       "1           Akkermansia       0.7  SRR15032081           3   \n",
       "2           Akkermansia       0.7  SRR15032081           3   \n",
       "3           Akkermansia       0.7  SRR15032081           3   \n",
       "4           Akkermansia       0.7  SRR15032081           3   \n",
       "...                 ...       ...          ...         ...   \n",
       "184977  Parabacteroides       0.7  SRR15032512         308   \n",
       "184978  Parabacteroides       0.7  SRR15032512         308   \n",
       "184979  Parabacteroides       0.7  SRR15032512         308   \n",
       "184980  Parabacteroides       0.7  SRR15032512         308   \n",
       "184981  Parabacteroides       0.7  SRR15032512         308   \n",
       "\n",
       "                     description  time_point                file  found_taxa  \\\n",
       "0       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "1       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "2       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "3       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "4       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "...                          ...         ...                 ...         ...   \n",
       "184977  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184978  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184979  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184980  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184981  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "\n",
       "        total_taxa  found_fraction  found_abundance_fraction     medium  \\\n",
       "0             17.0        0.647059                  0.898909    western   \n",
       "1             17.0        0.647059                  0.898909    western   \n",
       "2             17.0        0.647059                  0.898909    western   \n",
       "3             17.0        0.647059                  0.898909    western   \n",
       "4             17.0        0.647059                  0.898909    western   \n",
       "...            ...             ...                       ...        ...   \n",
       "184977        37.0        0.621622                  0.843232  fermented   \n",
       "184978        37.0        0.621622                  0.843232  fermented   \n",
       "184979        37.0        0.621622                  0.843232  fermented   \n",
       "184980        37.0        0.621622                  0.843232  fermented   \n",
       "184981        37.0        0.621622                  0.843232  fermented   \n",
       "\n",
       "       direction     metabolite        flux  \n",
       "0         export    MGlcn148[e]    0.000002  \n",
       "1         export           h[e]  149.145825  \n",
       "2         export     MGlcn46[e]    0.000003  \n",
       "3         export  MGlcn23_rl[e]    0.000001  \n",
       "4         export     MGlcn59[e]    0.000002  \n",
       "...          ...            ...         ...  \n",
       "184977    import       pydxn[e]   -0.000189  \n",
       "184978    import         ura[e]  -22.903380  \n",
       "184979    export        etoh[e]   10.690341  \n",
       "184980    import         fe3[e]   -0.000499  \n",
       "184981    export        succ[e]    8.352195  \n",
       "\n",
       "[184982 rows x 20 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged_including_direction_and_metabolite = pd.merge(top_ten_merged, small_ex, how=\"left\", left_on= ['taxon', 'sample_id'], right_on = ['taxon', 'sample_id'])\n",
    "merged_including_direction_and_metabolite"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "950d9fc2-6afe-4e7d-90cb-4544cdd39bef",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartments</th>\n",
       "      <th>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "      <th>medium</th>\n",
       "      <th>direction</th>\n",
       "      <th>metabolite</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>import</td>\n",
       "      <td>MGlcn144[e]</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>import</td>\n",
       "      <td>MGlcn68_rl[e]</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>import</td>\n",
       "      <td>pi[e]</td>\n",
       "      <td>-0.137294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>import</td>\n",
       "      <td>acnam[e]</td>\n",
       "      <td>-5.706658</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>0.077366</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "      <td>import</td>\n",
       "      <td>gly[e]</td>\n",
       "      <td>-40.258076</td>\n",
       "    </tr>\n",
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       "      <th>184975</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
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       "      <td>High fermented food diet</td>\n",
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       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
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       "      <td>fermented</td>\n",
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       "      <td>met_L[e]</td>\n",
       "      <td>-22.584343</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184976</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>sheme[e]</td>\n",
       "      <td>-0.000072</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184977</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>pydxn[e]</td>\n",
       "      <td>-0.000189</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184978</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>ura[e]</td>\n",
       "      <td>-22.903380</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>184980</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.057953</td>\n",
       "      <td>0.061701</td>\n",
       "      <td>2879</td>\n",
       "      <td>1747</td>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>308</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "      <td>import</td>\n",
       "      <td>fe3[e]</td>\n",
       "      <td>-0.000499</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>104846 rows × 20 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           compartments  abundance  growth_rate  reactions  metabolites  \\\n",
       "5           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "6           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "7           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "8           Akkermansia   0.133546     0.077366       2274         1386   \n",
       "10          Akkermansia   0.133546     0.077366       2274         1386   \n",
       "...                 ...        ...          ...        ...          ...   \n",
       "184975  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184976  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184977  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184978  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "184980  Parabacteroides   0.057953     0.061701       2879         1747   \n",
       "\n",
       "                  taxon  tradeoff    sample_id  Unnamed: 0  \\\n",
       "5           Akkermansia       0.7  SRR15032081           3   \n",
       "6           Akkermansia       0.7  SRR15032081           3   \n",
       "7           Akkermansia       0.7  SRR15032081           3   \n",
       "8           Akkermansia       0.7  SRR15032081           3   \n",
       "10          Akkermansia       0.7  SRR15032081           3   \n",
       "...                 ...       ...          ...         ...   \n",
       "184975  Parabacteroides       0.7  SRR15032512         308   \n",
       "184976  Parabacteroides       0.7  SRR15032512         308   \n",
       "184977  Parabacteroides       0.7  SRR15032512         308   \n",
       "184978  Parabacteroides       0.7  SRR15032512         308   \n",
       "184980  Parabacteroides       0.7  SRR15032512         308   \n",
       "\n",
       "                     description  time_point                file  found_taxa  \\\n",
       "5       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "6       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "7       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "8       High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "10      High fermented food diet           2  SRR15032081.pickle        11.0   \n",
       "...                          ...         ...                 ...         ...   \n",
       "184975  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184976  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184977  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184978  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "184980  High fermented food diet           7  SRR15032512.pickle        23.0   \n",
       "\n",
       "        total_taxa  found_fraction  found_abundance_fraction     medium  \\\n",
       "5             17.0        0.647059                  0.898909    western   \n",
       "6             17.0        0.647059                  0.898909    western   \n",
       "7             17.0        0.647059                  0.898909    western   \n",
       "8             17.0        0.647059                  0.898909    western   \n",
       "10            17.0        0.647059                  0.898909    western   \n",
       "...            ...             ...                       ...        ...   \n",
       "184975        37.0        0.621622                  0.843232  fermented   \n",
       "184976        37.0        0.621622                  0.843232  fermented   \n",
       "184977        37.0        0.621622                  0.843232  fermented   \n",
       "184978        37.0        0.621622                  0.843232  fermented   \n",
       "184980        37.0        0.621622                  0.843232  fermented   \n",
       "\n",
       "       direction     metabolite       flux  \n",
       "5         import    MGlcn144[e]  -0.000001  \n",
       "6         import  MGlcn68_rl[e]  -0.000001  \n",
       "7         import          pi[e]  -0.137294  \n",
       "8         import       acnam[e]  -5.706658  \n",
       "10        import         gly[e] -40.258076  \n",
       "...          ...            ...        ...  \n",
       "184975    import       met_L[e] -22.584343  \n",
       "184976    import       sheme[e]  -0.000072  \n",
       "184977    import       pydxn[e]  -0.000189  \n",
       "184978    import         ura[e] -22.903380  \n",
       "184980    import         fe3[e]  -0.000499  \n",
       "\n",
       "[104846 rows x 20 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "only_imports = merged_including_direction_and_metabolite.loc[merged_including_direction_and_metabolite.direction == 'import']\n",
    "only_imports "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "cefb1382-4930-435c-b29c-3e243638e2c8",
   "metadata": {},
   "outputs": [],
   "source": [
    "annotations = pd.read_csv(\"/proj/gibbons/sswegle_micom/Res_Saves/annotations_swegle.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "e642ecb6-f004-4254-8ba1-9048eea6c9cf",
   "metadata": {},
   "outputs": [],
   "source": [
    "merged_with_annotations = only_imports.merge(annotations, on=\"metabolite\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "27780963-35cc-41fb-8bf3-b099e0a1ec2a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['compartments', 'abundance', 'growth_rate', 'reactions', 'metabolites',\n",
       "       'taxon', 'tradeoff', 'sample_id', 'Unnamed: 0', 'description',\n",
       "       'time_point', 'file', 'found_taxa', 'total_taxa', 'found_fraction',\n",
       "       'found_abundance_fraction', 'medium', 'direction', 'metabolite', 'flux',\n",
       "       'reaction', 'name', 'molecular_weight', 'C_number', 'N_number', 'hmdb',\n",
       "       'inchi', 'kegg.compound', 'pubchem.compound', 'reaction.1'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged_with_annotations.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "16623055-92c4-4ed1-951c-9574ff2849ee",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compartments</th>\n",
       "      <th>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>description</th>\n",
       "      <th>...</th>\n",
       "      <th>reaction</th>\n",
       "      <th>name</th>\n",
       "      <th>molecular_weight</th>\n",
       "      <th>C_number</th>\n",
       "      <th>N_number</th>\n",
       "      <th>hmdb</th>\n",
       "      <th>inchi</th>\n",
       "      <th>kegg.compound</th>\n",
       "      <th>pubchem.compound</th>\n",
       "      <th>reaction.1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.133546</td>\n",
       "      <td>7.736626e-02</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>NaN</td>\n",
       "      <td>28</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.051118</td>\n",
       "      <td>1.011622e-01</td>\n",
       "      <td>2073</td>\n",
       "      <td>1577</td>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>NaN</td>\n",
       "      <td>28</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.038339</td>\n",
       "      <td>7.753369e-02</td>\n",
       "      <td>1986</td>\n",
       "      <td>1472</td>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>3</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>NaN</td>\n",
       "      <td>28</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>0.060697</td>\n",
       "      <td>1.373560e-01</td>\n",
       "      <td>3108</td>\n",
       "      <td>1734</td>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>21</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>NaN</td>\n",
       "      <td>28</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.267677</td>\n",
       "      <td>5.714096e-01</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>78</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>NaN</td>\n",
       "      <td>28</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>EX_MGlcn144(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104841</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.066253</td>\n",
       "      <td>9.328558e-02</td>\n",
       "      <td>2650</td>\n",
       "      <td>1613</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>295</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>515.703</td>\n",
       "      <td>26</td>\n",
       "      <td>1</td>\n",
       "      <td>HMDB00036</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>440567.0</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104842</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.562325</td>\n",
       "      <td>2.644783e-01</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>295</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>515.703</td>\n",
       "      <td>26</td>\n",
       "      <td>1</td>\n",
       "      <td>HMDB00036</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>440567.0</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104843</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.051763</td>\n",
       "      <td>8.718740e-07</td>\n",
       "      <td>2808</td>\n",
       "      <td>1732</td>\n",
       "      <td>Blautia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>295</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>515.703</td>\n",
       "      <td>26</td>\n",
       "      <td>1</td>\n",
       "      <td>HMDB00036</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>440567.0</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104844</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.081267</td>\n",
       "      <td>1.323349e-02</td>\n",
       "      <td>1986</td>\n",
       "      <td>1472</td>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>295</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>515.703</td>\n",
       "      <td>26</td>\n",
       "      <td>1</td>\n",
       "      <td>HMDB00036</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>440567.0</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104845</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>0.076292</td>\n",
       "      <td>1.347324e-02</td>\n",
       "      <td>2357</td>\n",
       "      <td>1567</td>\n",
       "      <td>Roseburia</td>\n",
       "      <td>0.7</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>295</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>...</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>515.703</td>\n",
       "      <td>26</td>\n",
       "      <td>1</td>\n",
       "      <td>HMDB00036</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>440567.0</td>\n",
       "      <td>EX_tchola(e)</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>104846 rows × 30 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            compartments  abundance   growth_rate  reactions  metabolites  \\\n",
       "0            Akkermansia   0.133546  7.736626e-02       2274         1386   \n",
       "1            Eubacterium   0.051118  1.011622e-01       2073         1577   \n",
       "2       Faecalibacterium   0.038339  7.753369e-02       1986         1472   \n",
       "3        Bifidobacterium   0.060697  1.373560e-01       3108         1734   \n",
       "4            Bacteroides   0.267677  5.714096e-01       3293         1883   \n",
       "...                  ...        ...           ...        ...          ...   \n",
       "104841         Alistipes   0.066253  9.328558e-02       2650         1613   \n",
       "104842       Bacteroides   0.562325  2.644783e-01       3293         1883   \n",
       "104843           Blautia   0.051763  8.718740e-07       2808         1732   \n",
       "104844  Faecalibacterium   0.081267  1.323349e-02       1986         1472   \n",
       "104845         Roseburia   0.076292  1.347324e-02       2357         1567   \n",
       "\n",
       "                   taxon  tradeoff    sample_id  Unnamed: 0  \\\n",
       "0            Akkermansia       0.7  SRR15032081           3   \n",
       "1            Eubacterium       0.7  SRR15032081           3   \n",
       "2       Faecalibacterium       0.7  SRR15032081           3   \n",
       "3        Bifidobacterium       0.7  SRR15032099          21   \n",
       "4            Bacteroides       0.7  SRR15032282          78   \n",
       "...                  ...       ...          ...         ...   \n",
       "104841         Alistipes       0.7  SRR15032499         295   \n",
       "104842       Bacteroides       0.7  SRR15032499         295   \n",
       "104843           Blautia       0.7  SRR15032499         295   \n",
       "104844  Faecalibacterium       0.7  SRR15032499         295   \n",
       "104845         Roseburia       0.7  SRR15032499         295   \n",
       "\n",
       "                     description  ...        reaction  \\\n",
       "0       High fermented food diet  ...  EX_MGlcn144(e)   \n",
       "1       High fermented food diet  ...  EX_MGlcn144(e)   \n",
       "2       High fermented food diet  ...  EX_MGlcn144(e)   \n",
       "3       High fermented food diet  ...  EX_MGlcn144(e)   \n",
       "4       High fermented food diet  ...  EX_MGlcn144(e)   \n",
       "...                          ...  ...             ...   \n",
       "104841  High fermented food diet  ...    EX_tchola(e)   \n",
       "104842  High fermented food diet  ...    EX_tchola(e)   \n",
       "104843  High fermented food diet  ...    EX_tchola(e)   \n",
       "104844  High fermented food diet  ...    EX_tchola(e)   \n",
       "104845  High fermented food diet  ...    EX_tchola(e)   \n",
       "\n",
       "                              name  molecular_weight  C_number  N_number  \\\n",
       "0       mucin-type O-glycan No 144               NaN        28         2   \n",
       "1       mucin-type O-glycan No 144               NaN        28         2   \n",
       "2       mucin-type O-glycan No 144               NaN        28         2   \n",
       "3       mucin-type O-glycan No 144               NaN        28         2   \n",
       "4       mucin-type O-glycan No 144               NaN        28         2   \n",
       "...                            ...               ...       ...       ...   \n",
       "104841                taurocholate           515.703        26         1   \n",
       "104842                taurocholate           515.703        26         1   \n",
       "104843                taurocholate           515.703        26         1   \n",
       "104844                taurocholate           515.703        26         1   \n",
       "104845                taurocholate           515.703        26         1   \n",
       "\n",
       "             hmdb inchi kegg.compound pubchem.compound      reaction.1  \n",
       "0             NaN   NaN           NaN              NaN  EX_MGlcn144(e)  \n",
       "1             NaN   NaN           NaN              NaN  EX_MGlcn144(e)  \n",
       "2             NaN   NaN           NaN              NaN  EX_MGlcn144(e)  \n",
       "3             NaN   NaN           NaN              NaN  EX_MGlcn144(e)  \n",
       "4             NaN   NaN           NaN              NaN  EX_MGlcn144(e)  \n",
       "...           ...   ...           ...              ...             ...  \n",
       "104841  HMDB00036   NaN           NaN         440567.0    EX_tchola(e)  \n",
       "104842  HMDB00036   NaN           NaN         440567.0    EX_tchola(e)  \n",
       "104843  HMDB00036   NaN           NaN         440567.0    EX_tchola(e)  \n",
       "104844  HMDB00036   NaN           NaN         440567.0    EX_tchola(e)  \n",
       "104845  HMDB00036   NaN           NaN         440567.0    EX_tchola(e)  \n",
       "\n",
       "[104846 rows x 30 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "only_imports = merged_with_annotations\n",
    "only_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "3888d86c-6978-4ce6-a41c-8178ce881f7e",
   "metadata": {},
   "outputs": [],
   "source": [
    "taxon_imports_table = only_imports[[\"taxon\", \"direction\", \"sample_id\", \"medium\", \"name\", \"flux\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "e56916fd-3204-4c7f-a610-f4d59e8333f6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104841</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>fermented</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>-0.000139</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104842</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>fermented</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>-0.000017</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104843</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>fermented</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>-0.000177</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104844</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>fermented</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>-0.000113</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104845</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032499</td>\n",
       "      <td>fermented</td>\n",
       "      <td>taurocholate</td>\n",
       "      <td>-0.000120</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>104846 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id     medium  \\\n",
       "0            Akkermansia    import  SRR15032081    western   \n",
       "1            Eubacterium    import  SRR15032081    western   \n",
       "2       Faecalibacterium    import  SRR15032081    western   \n",
       "3        Bifidobacterium    import  SRR15032099    western   \n",
       "4            Bacteroides    import  SRR15032282    western   \n",
       "...                  ...       ...          ...        ...   \n",
       "104841         Alistipes    import  SRR15032499  fermented   \n",
       "104842       Bacteroides    import  SRR15032499  fermented   \n",
       "104843           Blautia    import  SRR15032499  fermented   \n",
       "104844  Faecalibacterium    import  SRR15032499  fermented   \n",
       "104845         Roseburia    import  SRR15032499  fermented   \n",
       "\n",
       "                              name      flux  \n",
       "0       mucin-type O-glycan No 144 -0.000001  \n",
       "1       mucin-type O-glycan No 144 -0.000003  \n",
       "2       mucin-type O-glycan No 144 -0.000001  \n",
       "3       mucin-type O-glycan No 144 -0.000002  \n",
       "4       mucin-type O-glycan No 144 -0.000004  \n",
       "...                            ...       ...  \n",
       "104841                taurocholate -0.000139  \n",
       "104842                taurocholate -0.000017  \n",
       "104843                taurocholate -0.000177  \n",
       "104844                taurocholate -0.000113  \n",
       "104845                taurocholate -0.000120  \n",
       "\n",
       "[104846 rows x 6 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "taxon_imports_table"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "478ab947-07c2-47b8-b5de-cd104200431e",
   "metadata": {},
   "source": [
    "next step \n",
    "- comparing the metabolite imports of the most abundant taxa before and after diet intervention"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3d0b3e98-5885-4d9d-aed8-6198861791d9",
   "metadata": {},
   "source": [
    "# bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "0cd9a800-10d6-4c55-b3e6-300674c4ba49",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "46a27275-cb89-4b0a-80f0-d20dc36de257",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-18.557204</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>121</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-37.953074</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>151</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032112</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-18.938989</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>163</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032115</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-17.728793</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104813</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104823</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6543 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              taxon direction    sample_id   medium  \\\n",
       "4       Bacteroides    import  SRR15032282  western   \n",
       "63      Bacteroides    import  SRR15032081  western   \n",
       "121     Bacteroides    import  SRR15032099  western   \n",
       "151     Bacteroides    import  SRR15032112  western   \n",
       "163     Bacteroides    import  SRR15032115  western   \n",
       "...             ...       ...          ...      ...   \n",
       "104813  Bacteroides    import  SRR15032439  western   \n",
       "104823  Bacteroides    import  SRR15032392  western   \n",
       "104834  Bacteroides    import  SRR15032344  western   \n",
       "104836  Bacteroides    import  SRR15032439  western   \n",
       "104838  Bacteroides    import  SRR15032392  western   \n",
       "\n",
       "                                                name       flux  \n",
       "4                         mucin-type O-glycan No 144  -0.000004  \n",
       "63                                 hydrogenphosphate -18.557204  \n",
       "121                                hydrogenphosphate -37.953074  \n",
       "151                                hydrogenphosphate -18.938989  \n",
       "163                                hydrogenphosphate -17.728793  \n",
       "...                                              ...        ...  \n",
       "104813           released mucin-type O-glycan No 135  -0.000007  \n",
       "104823                                      Nitrogen  -0.000001  \n",
       "104834                    mucin-type O-glycan No 135  -0.000001  \n",
       "104836                    mucin-type O-glycan No 135  -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc)  -0.000049  \n",
       "\n",
       "[6543 rows x 6 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_bacteroides_only = western_only.loc[western_only['taxon'] == 'Bacteroides']\n",
    "western_bacteroides_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "5bfefd9f-b17a-45e9-9946-921d1f5da8b3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-13.464623429376656"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_bacteroides = western_bacteroides_only[\"flux\"].mean()\n",
    "mean_import_of_western_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "6e490b08-b316-4a73-9ba3-336ee140c706",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                                         -50.622811\n",
       "(S)-lactaldehyde                                    -35.421978\n",
       "(S)-lactate                                         -46.299493\n",
       "(S)-propane-1,2-diol                                -29.994424\n",
       "2-Demethylmenaquinone 8                              -0.000001\n",
       "                                                       ...    \n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})    -0.000002\n",
       "sulfate                                              -0.141754\n",
       "tetradecanoate (n-C14:0)                            -14.568705\n",
       "thiosulfate(2-)                                      -0.024979\n",
       "uracil                                              -58.118870\n",
       "Name: flux, Length: 396, dtype: float64"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_bacteroides = western_bacteroides_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "75942627-2ab8-4845-9f1a-17759e42fb3d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "392e6ea6-081f-4463-8c03-6147acb5e278",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>87</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032089</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-14.936859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032083</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-44.994203</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>105</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-60.547483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104353</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032475</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.073540</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104354</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032482</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.027590</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>6016 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              taxon direction    sample_id      medium  \\\n",
       "68      Bacteroides    import  SRR15032094  high_fiber   \n",
       "76      Bacteroides    import  SRR15032095  high_fiber   \n",
       "87      Bacteroides    import  SRR15032089  high_fiber   \n",
       "103     Bacteroides    import  SRR15032083  high_fiber   \n",
       "105     Bacteroides    import  SRR15032082  high_fiber   \n",
       "...             ...       ...          ...         ...   \n",
       "104353  Bacteroides    import  SRR15032475  high_fiber   \n",
       "104354  Bacteroides    import  SRR15032482  high_fiber   \n",
       "104355  Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357  Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363  Bacteroides    import  SRR15032503  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "87               hydrogenphosphate -14.936859  \n",
       "103              hydrogenphosphate -44.994203  \n",
       "105              hydrogenphosphate -60.547483  \n",
       "...                            ...        ...  \n",
       "104353  3-Dehydrochenodeoxycholate  -0.073540  \n",
       "104354  3-Dehydrochenodeoxycholate  -0.027590  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "\n",
       "[6016 rows x 6 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_bacteroides_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Bacteroides']\n",
    "high_fiber_bacteroides_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "564d3dd5-c9b3-4e67-af2e-1f86202278a0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-18.370876588894085"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_bacteroides = high_fiber_bacteroides_only[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "21bb358a-b810-4309-b4d5-735dde5615c8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                -49.809350\n",
       "(S)-lactaldehyde           -35.490875\n",
       "(S)-lactate                -42.909849\n",
       "(S)-malate(2-)             -15.413889\n",
       "(S)-propane-1,2-diol       -40.039460\n",
       "                              ...    \n",
       "proton                     -90.675300\n",
       "sulfate                     -0.387960\n",
       "tetradecanoate (n-C14:0)   -15.639674\n",
       "thiosulfate(2-)             -0.030674\n",
       "uracil                     -57.194970\n",
       "Name: flux, Length: 108, dtype: float64"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_bacteroides = high_fiber_bacteroides_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "caa3bdb7-5e94-49ad-8ad4-fcb8633e6839",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                                         -50.622811\n",
       "(S)-lactaldehyde                                    -35.421978\n",
       "(S)-lactate                                         -46.299493\n",
       "(S)-propane-1,2-diol                                -29.994424\n",
       "2-Demethylmenaquinone 8                              -0.000001\n",
       "                                                       ...    \n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})    -0.000002\n",
       "sulfate                                              -0.141754\n",
       "tetradecanoate (n-C14:0)                            -14.568705\n",
       "thiosulfate(2-)                                      -0.024979\n",
       "uracil                                              -58.118870\n",
       "Name: flux, Length: 396, dtype: float64"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "cc4c4f63-994b-4544-975f-af60fb6e09ea",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                -49.809350\n",
       "(S)-lactaldehyde           -35.490875\n",
       "(S)-lactate                -42.909849\n",
       "(S)-malate(2-)             -15.413889\n",
       "(S)-propane-1,2-diol       -40.039460\n",
       "                              ...    \n",
       "proton                     -90.675300\n",
       "sulfate                     -0.387960\n",
       "tetradecanoate (n-C14:0)   -15.639674\n",
       "thiosulfate(2-)             -0.030674\n",
       "uracil                     -57.194970\n",
       "Name: flux, Length: 108, dtype: float64"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_bacteroides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "4f1e6c87-766d-4471-91f9-3c181071aed0",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_bacteroides_imports = pd.DataFrame (mean_import_of_western_bacteroides, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "d017ab15-97f3-45c3-a0b2-82a5967e905b",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_bacteroides_imports.rename(columns={\"flux\": \"western_flux\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "a20c41cb-4a34-46f2-8c52-f8a1100ff204",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>(R)-lactate</th>\n",
       "      <td>-50.622811</td>\n",
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       "    <tr>\n",
       "      <th>(S)-lactaldehyde</th>\n",
       "      <td>-35.421978</td>\n",
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       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-46.299493</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-29.994424</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Demethylmenaquinone 8</th>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.141754</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-14.568705</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.024979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-58.118870</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>396 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                   western_flux\n",
       "name                                                           \n",
       "(R)-lactate                                          -50.622811\n",
       "(S)-lactaldehyde                                     -35.421978\n",
       "(S)-lactate                                          -46.299493\n",
       "(S)-propane-1,2-diol                                 -29.994424\n",
       "2-Demethylmenaquinone 8                               -0.000001\n",
       "...                                                         ...\n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})     -0.000002\n",
       "sulfate                                               -0.141754\n",
       "tetradecanoate (n-C14:0)                             -14.568705\n",
       "thiosulfate(2-)                                       -0.024979\n",
       "uracil                                               -58.118870\n",
       "\n",
       "[396 rows x 1 columns]"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_bacteroides_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "1c977ac2-0997-4246-a99a-2b96955b3d56",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_bacteroides_imports = pd.DataFrame (mean_import_of_high_fiber_bacteroides, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "7eb9a25c-450f-42c6-829b-9161e6a42176",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_bacteroides_imports.rename(columns={\"flux\": \"high_fiber_flux\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "1f2ffdbc-6421-4b4f-bd96-e27a12d9607b",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>high_fiber_flux</th>\n",
       "    </tr>\n",
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       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <td>-35.490875</td>\n",
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       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-40.039460</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-90.675300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.387960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-15.639674</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
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       "      <th>uracil</th>\n",
       "      <td>-57.194970</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>108 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux\n",
       "name                                     \n",
       "(R)-lactate                    -49.809350\n",
       "(S)-lactaldehyde               -35.490875\n",
       "(S)-lactate                    -42.909849\n",
       "(S)-malate(2-)                 -15.413889\n",
       "(S)-propane-1,2-diol           -40.039460\n",
       "...                                   ...\n",
       "proton                         -90.675300\n",
       "sulfate                         -0.387960\n",
       "tetradecanoate (n-C14:0)       -15.639674\n",
       "thiosulfate(2-)                 -0.030674\n",
       "uracil                         -57.194970\n",
       "\n",
       "[108 rows x 1 columns]"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_bacteroides_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "603656d6-5539-407f-b604-d890b94f6a08",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes = pd.concat([western_bacteroides_imports['western_flux'], high_fiber_bacteroides_imports['high_fiber_flux']], axis=1, keys= ['western_bacteroides_imports', 'high_fiber_bacteroides_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "d02c1394-a84a-4c12-a7ac-1c4cadf729e0",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_bacteroides_imports</th>\n",
       "      <th>high_fiber_bacteroides_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-50.622811</td>\n",
       "      <td>-49.809350</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactaldehyde</th>\n",
       "      <td>-35.421978</td>\n",
       "      <td>-35.490875</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-46.299493</td>\n",
       "      <td>-42.909849</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-29.994424</td>\n",
       "      <td>-40.039460</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Demethylmenaquinone 8</th>\n",
       "      <td>-0.000001</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Isochenodeoxycholate</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.046474</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Isocholate</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.046431</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>chondroitin sulfate B / dermatan sulfate (IdoA2S-GalNAc4S) proteoglycan</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.000221</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ethanol</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-8.498090</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>heparan sulfate proteoglycan</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.002250</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>403 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_bacteroides_imports  \\\n",
       "name                                                                              \n",
       "(R)-lactate                                                          -50.622811   \n",
       "(S)-lactaldehyde                                                     -35.421978   \n",
       "(S)-lactate                                                          -46.299493   \n",
       "(S)-propane-1,2-diol                                                 -29.994424   \n",
       "2-Demethylmenaquinone 8                                               -0.000001   \n",
       "...                                                                         ...   \n",
       "Isochenodeoxycholate                                                        NaN   \n",
       "Isocholate                                                                  NaN   \n",
       "chondroitin sulfate B / dermatan sulfate (IdoA2...                          NaN   \n",
       "ethanol                                                                     NaN   \n",
       "heparan sulfate proteoglycan                                                NaN   \n",
       "\n",
       "                                                    high_fiber_bacteroides_imports  \n",
       "name                                                                                \n",
       "(R)-lactate                                                             -49.809350  \n",
       "(S)-lactaldehyde                                                        -35.490875  \n",
       "(S)-lactate                                                             -42.909849  \n",
       "(S)-propane-1,2-diol                                                    -40.039460  \n",
       "2-Demethylmenaquinone 8                                                        NaN  \n",
       "...                                                                            ...  \n",
       "Isochenodeoxycholate                                                     -0.046474  \n",
       "Isocholate                                                               -0.046431  \n",
       "chondroitin sulfate B / dermatan sulfate (IdoA2...                       -0.000221  \n",
       "ethanol                                                                  -8.498090  \n",
       "heparan sulfate proteoglycan                                             -0.002250  \n",
       "\n",
       "[403 rows x 2 columns]"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "id": "268fe58c-4380-417a-9e6b-85d1076c6cdd",
   "metadata": {},
   "outputs": [],
   "source": [
    "bacteroides_imports_for_both_diets = combined_diet_fluxes.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "id": "7199d55b-b0ff-4635-9552-db486bb965fe",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_bacteroides_imports</th>\n",
       "      <th>high_fiber_bacteroides_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-50.622811</td>\n",
       "      <td>-49.809350</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactaldehyde</th>\n",
       "      <td>-35.421978</td>\n",
       "      <td>-35.490875</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-46.299493</td>\n",
       "      <td>-42.909849</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-29.994424</td>\n",
       "      <td>-40.039460</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-42.282852</td>\n",
       "      <td>-45.545415</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-87.202176</td>\n",
       "      <td>-90.675300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.141754</td>\n",
       "      <td>-0.387960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-14.568705</td>\n",
       "      <td>-15.639674</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.024979</td>\n",
       "      <td>-0.030674</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-58.118870</td>\n",
       "      <td>-57.194970</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>101 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_bacteroides_imports  \\\n",
       "name                                                    \n",
       "(R)-lactate                                -50.622811   \n",
       "(S)-lactaldehyde                           -35.421978   \n",
       "(S)-lactate                                -46.299493   \n",
       "(S)-propane-1,2-diol                       -29.994424   \n",
       "2-Oxobutanoate                             -42.282852   \n",
       "...                                               ...   \n",
       "proton                                     -87.202176   \n",
       "sulfate                                     -0.141754   \n",
       "tetradecanoate (n-C14:0)                   -14.568705   \n",
       "thiosulfate(2-)                             -0.024979   \n",
       "uracil                                     -58.118870   \n",
       "\n",
       "                          high_fiber_bacteroides_imports  \n",
       "name                                                      \n",
       "(R)-lactate                                   -49.809350  \n",
       "(S)-lactaldehyde                              -35.490875  \n",
       "(S)-lactate                                   -42.909849  \n",
       "(S)-propane-1,2-diol                          -40.039460  \n",
       "2-Oxobutanoate                                -45.545415  \n",
       "...                                                  ...  \n",
       "proton                                        -90.675300  \n",
       "sulfate                                        -0.387960  \n",
       "tetradecanoate (n-C14:0)                      -15.639674  \n",
       "thiosulfate(2-)                                -0.030674  \n",
       "uracil                                        -57.194970  \n",
       "\n",
       "[101 rows x 2 columns]"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bacteroides_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "66d0a8e6-0565-4b76-92e8-7a91abc6e419",
   "metadata": {},
   "source": [
    "finding the euclidean distance: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "id": "74cdb7ea-cb88-456f-b59c-7aa86f9f6503",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "63.35243012853294"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bacteroides_euclidean_distance = ((bacteroides_imports_for_both_diets.western_bacteroides_imports - bacteroides_imports_for_both_diets.high_fiber_bacteroides_imports)**2).sum()**(1/2)\n",
    "\n",
    "bacteroides_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "976533f4-852a-4f0d-9a2b-b2f751962659",
   "metadata": {},
   "source": [
    "# prevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "id": "862d0efb-e470-4710-b87c-d23786ab7a8d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 44,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "id": "7ae52ba2-312b-4813-a0f3-891bfd565aed",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>276</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032195</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-47.939886</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>359</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032287</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-36.087967</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>608</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032334</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-66.619241</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>698</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032384</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-81.096947</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104752</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 173</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104763</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 140</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104779</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104782</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104820</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032351</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1300 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             taxon direction    sample_id   medium  \\\n",
       "12      Prevotella    import  SRR15032323  western   \n",
       "276     Prevotella    import  SRR15032195  western   \n",
       "359     Prevotella    import  SRR15032287  western   \n",
       "608     Prevotella    import  SRR15032334  western   \n",
       "698     Prevotella    import  SRR15032384  western   \n",
       "...            ...       ...          ...      ...   \n",
       "104752  Prevotella    import  SRR15032324  western   \n",
       "104763  Prevotella    import  SRR15032324  western   \n",
       "104779  Prevotella    import  SRR15032323  western   \n",
       "104782  Prevotella    import  SRR15032324  western   \n",
       "104820  Prevotella    import  SRR15032351  western   \n",
       "\n",
       "                                       name       flux  \n",
       "12               mucin-type O-glycan No 144  -0.000002  \n",
       "276                       hydrogenphosphate -47.939886  \n",
       "359                       hydrogenphosphate -36.087967  \n",
       "608                       hydrogenphosphate -66.619241  \n",
       "698                       hydrogenphosphate -81.096947  \n",
       "...                                     ...        ...  \n",
       "104752  released mucin-type O-glycan No 173  -0.000003  \n",
       "104763  released mucin-type O-glycan No 140  -0.000001  \n",
       "104779  released mucin-type O-glycan No 145  -0.000003  \n",
       "104782  released mucin-type O-glycan No 145  -0.000002  \n",
       "104820                             Nitrogen  -0.000001  \n",
       "\n",
       "[1300 rows x 6 columns]"
      ]
     },
     "execution_count": 45,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_prevotella_only = western_only.loc[western_only['taxon'] == 'Prevotella']\n",
    "western_prevotella_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "id": "a34ab485-d752-473a-b319-3be69c88c240",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-Pantothenate            -0.002098\n",
       "(R)-lactate                 -5.248603\n",
       "(S)-lactate                -10.586181\n",
       "(S)-malate(2-)             -39.995879\n",
       "2-Oxobutanoate             -95.079619\n",
       "                              ...    \n",
       "sialyl-Tn antigen           -0.000002\n",
       "sulfate                     -0.132139\n",
       "tetradecanoate (n-C14:0)    -0.729384\n",
       "thiosulfate(2-)             -0.155418\n",
       "uracil                     -83.207332\n",
       "Name: flux, Length: 214, dtype: float64"
      ]
     },
     "execution_count": 46,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_prevotella = western_prevotella_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_prevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "ba869732-1855-4b60-b2f6-9f31d7623368",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "id": "7d7b73fe-f9b3-4c2d-9630-18f641de7561",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>79</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-64.707708</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-46.533284</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>118</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032103</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-33.397910</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>206</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032136</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-58.256250</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>272</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032184</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-51.883256</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102223</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032352</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.219051</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102389</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.037240</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102435</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032136</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.031265</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102572</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032339</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.034172</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102641</th>\n",
       "      <td>Prevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032403</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.012738</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1223 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             taxon direction    sample_id      medium  \\\n",
       "79      Prevotella    import  SRR15032095  high_fiber   \n",
       "99      Prevotella    import  SRR15032079  high_fiber   \n",
       "118     Prevotella    import  SRR15032103  high_fiber   \n",
       "206     Prevotella    import  SRR15032136  high_fiber   \n",
       "272     Prevotella    import  SRR15032184  high_fiber   \n",
       "...            ...       ...          ...         ...   \n",
       "102223  Prevotella    import  SRR15032352  high_fiber   \n",
       "102389  Prevotella    import  SRR15032095  high_fiber   \n",
       "102435  Prevotella    import  SRR15032136  high_fiber   \n",
       "102572  Prevotella    import  SRR15032339  high_fiber   \n",
       "102641  Prevotella    import  SRR15032403  high_fiber   \n",
       "\n",
       "                           name       flux  \n",
       "79            hydrogenphosphate -64.707708  \n",
       "99            hydrogenphosphate -46.533284  \n",
       "118           hydrogenphosphate -33.397910  \n",
       "206           hydrogenphosphate -58.256250  \n",
       "272           hydrogenphosphate -51.883256  \n",
       "...                         ...        ...  \n",
       "102223          thiosulfate(2-)  -0.219051  \n",
       "102389  octadecanoate (n-C18:0)  -0.037240  \n",
       "102435  octadecanoate (n-C18:0)  -0.031265  \n",
       "102572  octadecanoate (n-C18:0)  -0.034172  \n",
       "102641  octadecanoate (n-C18:0)  -0.012738  \n",
       "\n",
       "[1223 rows x 6 columns]"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_prevotella_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Prevotella']\n",
    "high_fiber_prevotella_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "id": "1b410194-e182-488c-a5e3-59a1c56d24b9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                 -9.813017\n",
       "(S)-lactate                -10.087787\n",
       "(S)-malate(2-)             -25.544395\n",
       "2-Oxobutanoate             -89.468921\n",
       "2-Oxoglutarate              -4.665738\n",
       "                              ...    \n",
       "proton                     -91.799223\n",
       "sulfate                     -0.240655\n",
       "tetradecanoate (n-C14:0)    -0.065293\n",
       "thiosulfate(2-)             -0.077733\n",
       "uracil                     -81.512629\n",
       "Name: flux, Length: 82, dtype: float64"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_prevotella = high_fiber_prevotella_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_prevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "3fe1ca49-3b8e-4d37-9cf7-bcbeb9a5534b",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_prevotella_imports = pd.DataFrame (mean_import_of_western_prevotella, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "id": "266dd58f-5771-41ac-b79f-d6004c4c3406",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_prevotella_imports.rename(columns={\"flux\": \"western_flux_prevotella\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "id": "40be7631-4bb0-42cb-8038-89e5ea08f9bb",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_prevotella</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.002098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-5.248603</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-10.586181</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-malate(2-)</th>\n",
       "      <td>-39.995879</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-95.079619</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.132139</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.729384</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.155418</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-83.207332</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>214 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_flux_prevotella\n",
       "name                                             \n",
       "(R)-Pantothenate                        -0.002098\n",
       "(R)-lactate                             -5.248603\n",
       "(S)-lactate                            -10.586181\n",
       "(S)-malate(2-)                         -39.995879\n",
       "2-Oxobutanoate                         -95.079619\n",
       "...                                           ...\n",
       "sialyl-Tn antigen                       -0.000002\n",
       "sulfate                                 -0.132139\n",
       "tetradecanoate (n-C14:0)                -0.729384\n",
       "thiosulfate(2-)                         -0.155418\n",
       "uracil                                 -83.207332\n",
       "\n",
       "[214 rows x 1 columns]"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_prevotella_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "id": "b99996a7-7ec0-4e11-97eb-b4c67b4e0172",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_prevotella_imports = pd.DataFrame (mean_import_of_high_fiber_prevotella, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "id": "f6d5525a-adc0-4394-9d16-6a05b0844482",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_prevotella_imports.rename(columns={\"flux\": \"high_fiber_flux_prevotella\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "id": "2070ff6f-eae7-43e6-a36e-cc8f33c821fe",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>high_fiber_flux_prevotella</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-9.813017</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-10.087787</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-malate(2-)</th>\n",
       "      <td>-25.544395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-89.468921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-4.665738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-91.799223</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.240655</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.065293</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.077733</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-81.512629</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>82 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_prevotella\n",
       "name                                                \n",
       "(R)-lactate                                -9.813017\n",
       "(S)-lactate                               -10.087787\n",
       "(S)-malate(2-)                            -25.544395\n",
       "2-Oxobutanoate                            -89.468921\n",
       "2-Oxoglutarate                             -4.665738\n",
       "...                                              ...\n",
       "proton                                    -91.799223\n",
       "sulfate                                    -0.240655\n",
       "tetradecanoate (n-C14:0)                   -0.065293\n",
       "thiosulfate(2-)                            -0.077733\n",
       "uracil                                    -81.512629\n",
       "\n",
       "[82 rows x 1 columns]"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_prevotella_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "id": "a834544b-6216-413e-a865-5fa6165160bc",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_prevotella = pd.concat([western_prevotella_imports['western_flux_prevotella'], high_fiber_prevotella_imports['high_fiber_flux_prevotella']], axis=1, keys= ['western_prevotella_imports', 'high_fiber_prevotella_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "id": "cca50de2-7184-49bb-9eb7-bd949e2a2478",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_prevotella_imports</th>\n",
       "      <th>high_fiber_prevotella_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.002098</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-5.248603</td>\n",
       "      <td>-9.813017</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-10.586181</td>\n",
       "      <td>-10.087787</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-malate(2-)</th>\n",
       "      <td>-39.995879</td>\n",
       "      <td>-25.544395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-95.079619</td>\n",
       "      <td>-89.468921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.132139</td>\n",
       "      <td>-0.240655</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.729384</td>\n",
       "      <td>-0.065293</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.155418</td>\n",
       "      <td>-0.077733</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-83.207332</td>\n",
       "      <td>-81.512629</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-asparagine</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-2.658086</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>215 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_prevotella_imports  \\\n",
       "name                                                   \n",
       "(R)-Pantothenate                           -0.002098   \n",
       "(R)-lactate                                -5.248603   \n",
       "(S)-lactate                               -10.586181   \n",
       "(S)-malate(2-)                            -39.995879   \n",
       "2-Oxobutanoate                            -95.079619   \n",
       "...                                              ...   \n",
       "sulfate                                    -0.132139   \n",
       "tetradecanoate (n-C14:0)                   -0.729384   \n",
       "thiosulfate(2-)                            -0.155418   \n",
       "uracil                                    -83.207332   \n",
       "L-asparagine                                     NaN   \n",
       "\n",
       "                          high_fiber_prevotella_imports  \n",
       "name                                                     \n",
       "(R)-Pantothenate                                    NaN  \n",
       "(R)-lactate                                   -9.813017  \n",
       "(S)-lactate                                  -10.087787  \n",
       "(S)-malate(2-)                               -25.544395  \n",
       "2-Oxobutanoate                               -89.468921  \n",
       "...                                                 ...  \n",
       "sulfate                                       -0.240655  \n",
       "tetradecanoate (n-C14:0)                      -0.065293  \n",
       "thiosulfate(2-)                               -0.077733  \n",
       "uracil                                       -81.512629  \n",
       "L-asparagine                                  -2.658086  \n",
       "\n",
       "[215 rows x 2 columns]"
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_prevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "id": "f8ca73a3-a137-40fa-9b16-64c745bb1a0d",
   "metadata": {},
   "outputs": [],
   "source": [
    "prevotella_imports_for_both_diets = combined_diet_fluxes_prevotella.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "id": "97ad95be-abc1-4102-946d-1819b92d8392",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_prevotella_imports</th>\n",
       "      <th>high_fiber_prevotella_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-5.248603</td>\n",
       "      <td>-9.813017</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-10.586181</td>\n",
       "      <td>-10.087787</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-malate(2-)</th>\n",
       "      <td>-39.995879</td>\n",
       "      <td>-25.544395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-95.079619</td>\n",
       "      <td>-89.468921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-9.265928</td>\n",
       "      <td>-4.665738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-89.080654</td>\n",
       "      <td>-91.799223</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.132139</td>\n",
       "      <td>-0.240655</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.729384</td>\n",
       "      <td>-0.065293</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.155418</td>\n",
       "      <td>-0.077733</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-83.207332</td>\n",
       "      <td>-81.512629</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>81 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_prevotella_imports  \\\n",
       "name                                                   \n",
       "(R)-lactate                                -5.248603   \n",
       "(S)-lactate                               -10.586181   \n",
       "(S)-malate(2-)                            -39.995879   \n",
       "2-Oxobutanoate                            -95.079619   \n",
       "2-Oxoglutarate                             -9.265928   \n",
       "...                                              ...   \n",
       "proton                                    -89.080654   \n",
       "sulfate                                    -0.132139   \n",
       "tetradecanoate (n-C14:0)                   -0.729384   \n",
       "thiosulfate(2-)                            -0.155418   \n",
       "uracil                                    -83.207332   \n",
       "\n",
       "                          high_fiber_prevotella_imports  \n",
       "name                                                     \n",
       "(R)-lactate                                   -9.813017  \n",
       "(S)-lactate                                  -10.087787  \n",
       "(S)-malate(2-)                               -25.544395  \n",
       "2-Oxobutanoate                               -89.468921  \n",
       "2-Oxoglutarate                                -4.665738  \n",
       "...                                                 ...  \n",
       "proton                                       -91.799223  \n",
       "sulfate                                       -0.240655  \n",
       "tetradecanoate (n-C14:0)                      -0.065293  \n",
       "thiosulfate(2-)                               -0.077733  \n",
       "uracil                                       -81.512629  \n",
       "\n",
       "[81 rows x 2 columns]"
      ]
     },
     "execution_count": 59,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prevotella_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b3cd111c-6f7e-48f2-b65b-a8be2bab047d",
   "metadata": {},
   "source": [
    "finding euclidean distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "id": "ba087415-6b53-419c-b96c-63e38ba5dfd3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "64.56405495878849"
      ]
     },
     "execution_count": 60,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prevotella_euclidean_distance = ((prevotella_imports_for_both_diets.western_prevotella_imports - prevotella_imports_for_both_diets.high_fiber_prevotella_imports)**2).sum()**(1/2)\n",
    "\n",
    "prevotella_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0bb27b51-8aad-4626-8c6c-176e74e0a282",
   "metadata": {},
   "source": [
    "# faecalibacterium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 61,
   "id": "212d8bad-c259-422f-aba1-23b79b4dab5a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 61,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "id": "52db1551-ed02-4da6-9247-1b80b79507cc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000011</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104757</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032363</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 173</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104762</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 140</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104792</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104795</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104800</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>Biotin</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4720 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "11      Faecalibacterium    import  SRR15032323  western   \n",
       "22      Faecalibacterium    import  SRR15032081  western   \n",
       "25      Faecalibacterium    import  SRR15032099  western   \n",
       "30      Faecalibacterium    import  SRR15032293  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104757  Faecalibacterium    import  SRR15032363  western   \n",
       "104762  Faecalibacterium    import  SRR15032293  western   \n",
       "104792  Faecalibacterium    import  SRR15032392  western   \n",
       "104795  Faecalibacterium    import  SRR15032439  western   \n",
       "104800  Faecalibacterium    import  SRR15032392  western   \n",
       "\n",
       "                                                     name      flux  \n",
       "2                              mucin-type O-glycan No 144 -0.000001  \n",
       "11                             mucin-type O-glycan No 144 -0.000001  \n",
       "22                     released mucin-type O-glycan No 68 -0.000006  \n",
       "25                     released mucin-type O-glycan No 68 -0.000002  \n",
       "30                     released mucin-type O-glycan No 68 -0.000011  \n",
       "...                                                   ...       ...  \n",
       "104757                released mucin-type O-glycan No 173 -0.000001  \n",
       "104762                released mucin-type O-glycan No 140 -0.000002  \n",
       "104792  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000006  \n",
       "104795  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000002  \n",
       "104800                                             Biotin -0.000001  \n",
       "\n",
       "[4720 rows x 6 columns]"
      ]
     },
     "execution_count": 62,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_faecalibacterium_only = western_only.loc[western_only['taxon'] == 'Faecalibacterium']\n",
    "western_faecalibacterium_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 63,
   "id": "0d0e6c95-051f-487a-8b72-0c457734f3fc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-Pantothenate                                     -0.003295\n",
       "(R)-lactate                                          -6.205649\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)     -0.000002\n",
       "12-Dehydrocholate                                    -8.623386\n",
       "3-methyl-2-oxopentanoate                             -7.946322\n",
       "                                                        ...   \n",
       "released mucin-type O-glycan No 97                   -0.000002\n",
       "released mucin-type O-glycan No 98                   -0.000002\n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})   -0.000004\n",
       "sulfate                                              -0.195368\n",
       "tetradecanoate (n-C14:0)                             -1.986389\n",
       "Name: flux, Length: 269, dtype: float64"
      ]
     },
     "execution_count": 63,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_faecalibacterium = western_faecalibacterium_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_faecalibacterium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "id": "1367d10e-606f-44af-aa06-30b798170554",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 64,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 65,
   "id": "21d0e8d5-7354-41a0-97b8-b906b507d8bd",
   "metadata": {},
   "outputs": [
    {
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>78</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.056395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>89</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032089</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.030137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.034618</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.112814</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>116</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032103</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.047895</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102424</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032121</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.004820</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102479</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032288</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.001636</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103081</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032119</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Dimer GalNAc-GlcA</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103088</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032428</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Dimer GalNAc-GlcA</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104129</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032119</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Dimer GalNAc-IdoA2S</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3739 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id      medium  \\\n",
       "78      Faecalibacterium    import  SRR15032095  high_fiber   \n",
       "89      Faecalibacterium    import  SRR15032089  high_fiber   \n",
       "97      Faecalibacterium    import  SRR15032079  high_fiber   \n",
       "107     Faecalibacterium    import  SRR15032082  high_fiber   \n",
       "116     Faecalibacterium    import  SRR15032103  high_fiber   \n",
       "...                  ...       ...          ...         ...   \n",
       "102424  Faecalibacterium    import  SRR15032121  high_fiber   \n",
       "102479  Faecalibacterium    import  SRR15032288  high_fiber   \n",
       "103081  Faecalibacterium    import  SRR15032119  high_fiber   \n",
       "103088  Faecalibacterium    import  SRR15032428  high_fiber   \n",
       "104129  Faecalibacterium    import  SRR15032119  high_fiber   \n",
       "\n",
       "                           name      flux  \n",
       "78            hydrogenphosphate -0.056395  \n",
       "89            hydrogenphosphate -0.030137  \n",
       "97            hydrogenphosphate -0.034618  \n",
       "107           hydrogenphosphate -0.112814  \n",
       "116           hydrogenphosphate -0.047895  \n",
       "...                         ...       ...  \n",
       "102424  octadecanoate (n-C18:0) -0.004820  \n",
       "102479  octadecanoate (n-C18:0) -0.001636  \n",
       "103081        Dimer GalNAc-GlcA -0.000003  \n",
       "103088        Dimer GalNAc-GlcA -0.000001  \n",
       "104129      Dimer GalNAc-IdoA2S -0.000004  \n",
       "\n",
       "[3739 rows x 6 columns]"
      ]
     },
     "execution_count": 65,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_faecalibacterium_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Faecalibacterium']\n",
    "high_fiber_faecalibacterium_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "id": "6aba069a-56b8-446d-b6c7-d4b3d3416792",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                -28.348469\n",
       "12-Dehydrocholate          -10.630604\n",
       "3-methyl-2-oxopentanoate    -3.415913\n",
       "Ammonium                   -12.138403\n",
       "Chloride                    -0.000566\n",
       "                              ...    \n",
       "potassium                   -0.000545\n",
       "proton                     -34.049277\n",
       "sulfate                     -0.093502\n",
       "tetradecanoate (n-C14:0)    -2.057449\n",
       "uracil                     -22.182488\n",
       "Name: flux, Length: 80, dtype: float64"
      ]
     },
     "execution_count": 66,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_faecalibacterium = high_fiber_faecalibacterium_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_faecalibacterium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "id": "9e5cfb91-5c6b-46fc-9c20-149bc1340e39",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_faecalibacterium_imports = pd.DataFrame (mean_import_of_western_faecalibacterium, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "id": "6b0e0a74-0906-4928-89a5-c2ff4a7591ab",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_faecalibacterium_imports.rename(columns={\"flux\": \"western_flux_faecalibacterium\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "id": "92e06bcc-76ac-41ac-9131-53c8226d2b9f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_faecalibacterium</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.003295</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-6.205649</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-8.623386</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3-methyl-2-oxopentanoate</th>\n",
       "      <td>-7.946322</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released mucin-type O-glycan No 97</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released mucin-type O-glycan No 98</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})</th>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.195368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.986389</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>269 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_flux_faecalibacterium\n",
       "name                                                                             \n",
       "(R)-Pantothenate                                                        -0.003295\n",
       "(R)-lactate                                                             -6.205649\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                        -0.000002\n",
       "12-Dehydrocholate                                                       -8.623386\n",
       "3-methyl-2-oxopentanoate                                                -7.946322\n",
       "...                                                                           ...\n",
       "released mucin-type O-glycan No 97                                      -0.000002\n",
       "released mucin-type O-glycan No 98                                      -0.000002\n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                      -0.000004\n",
       "sulfate                                                                 -0.195368\n",
       "tetradecanoate (n-C14:0)                                                -1.986389\n",
       "\n",
       "[269 rows x 1 columns]"
      ]
     },
     "execution_count": 69,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_faecalibacterium_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "id": "b571877e-3272-440a-b413-2b940ade2950",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_faecalibacterium_imports = pd.DataFrame (mean_import_of_high_fiber_faecalibacterium, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "id": "e12f0f00-6303-4810-9c74-888c0e0a5c40",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_faecalibacterium_imports.rename(columns={\"flux\": \"high_fiber_flux_faecalibacterium\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "id": "86399780-2a2b-44d2-85be-7842b60cb2d0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>high_fiber_flux_faecalibacterium</th>\n",
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       "    <tr>\n",
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       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>(R)-lactate</th>\n",
       "      <td>-28.348469</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-10.630604</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3-methyl-2-oxopentanoate</th>\n",
       "      <td>-3.415913</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-12.138403</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.000566</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000545</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-34.049277</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.093502</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.057449</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-22.182488</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>80 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_faecalibacterium\n",
       "name                                                      \n",
       "(R)-lactate                                     -28.348469\n",
       "12-Dehydrocholate                               -10.630604\n",
       "3-methyl-2-oxopentanoate                         -3.415913\n",
       "Ammonium                                        -12.138403\n",
       "Chloride                                         -0.000566\n",
       "...                                                    ...\n",
       "potassium                                        -0.000545\n",
       "proton                                          -34.049277\n",
       "sulfate                                          -0.093502\n",
       "tetradecanoate (n-C14:0)                         -2.057449\n",
       "uracil                                          -22.182488\n",
       "\n",
       "[80 rows x 1 columns]"
      ]
     },
     "execution_count": 72,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_faecalibacterium_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "id": "41e3477c-7734-40b0-aa93-352a5e4d21d6",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_faecalibacterium = pd.concat([western_faecalibacterium_imports['western_flux_faecalibacterium'], high_fiber_faecalibacterium_imports['high_fiber_flux_faecalibacterium']], axis=1, keys= ['western_faecalibacterium_imports', 'high_fiber_faecalibacterium_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "id": "e1e8eeb2-6e80-4ae8-a924-7b55507f2abf",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_faecalibacterium_imports</th>\n",
       "      <th>high_fiber_faecalibacterium_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.003295</td>\n",
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       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-6.205649</td>\n",
       "      <td>-28.348469</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-8.623386</td>\n",
       "      <td>-10.630604</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3-methyl-2-oxopentanoate</th>\n",
       "      <td>-7.946322</td>\n",
       "      <td>-3.415913</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})</th>\n",
       "      <td>-0.000004</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.195368</td>\n",
       "      <td>-0.093502</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.986389</td>\n",
       "      <td>-2.057449</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>chondroitin sulfate B / dermatan sulfate (IdoA2S-GalNAc4S) proteoglycan</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.000592</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-22.182488</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>271 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_faecalibacterium_imports  \\\n",
       "name                                                                                   \n",
       "(R)-Pantothenate                                                           -0.003295   \n",
       "(R)-lactate                                                                -6.205649   \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                           -0.000002   \n",
       "12-Dehydrocholate                                                          -8.623386   \n",
       "3-methyl-2-oxopentanoate                                                   -7.946322   \n",
       "...                                                                              ...   \n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                         -0.000004   \n",
       "sulfate                                                                    -0.195368   \n",
       "tetradecanoate (n-C14:0)                                                   -1.986389   \n",
       "chondroitin sulfate B / dermatan sulfate (IdoA2...                               NaN   \n",
       "uracil                                                                           NaN   \n",
       "\n",
       "                                                    high_fiber_faecalibacterium_imports  \n",
       "name                                                                                     \n",
       "(R)-Pantothenate                                                                    NaN  \n",
       "(R)-lactate                                                                  -28.348469  \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                                    NaN  \n",
       "12-Dehydrocholate                                                            -10.630604  \n",
       "3-methyl-2-oxopentanoate                                                      -3.415913  \n",
       "...                                                                                 ...  \n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                                  NaN  \n",
       "sulfate                                                                       -0.093502  \n",
       "tetradecanoate (n-C14:0)                                                      -2.057449  \n",
       "chondroitin sulfate B / dermatan sulfate (IdoA2...                            -0.000592  \n",
       "uracil                                                                       -22.182488  \n",
       "\n",
       "[271 rows x 2 columns]"
      ]
     },
     "execution_count": 74,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_faecalibacterium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "id": "3c2ac2e0-13af-4ddc-b59b-4eb56338c41e",
   "metadata": {},
   "outputs": [],
   "source": [
    "faecalibacterium_imports_for_both_diets = combined_diet_fluxes_faecalibacterium.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "id": "9ab8fda8-ef1d-4443-8229-fc3afb2bf379",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_faecalibacterium_imports</th>\n",
       "      <th>high_fiber_faecalibacterium_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-6.205649</td>\n",
       "      <td>-28.348469</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-8.623386</td>\n",
       "      <td>-10.630604</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3-methyl-2-oxopentanoate</th>\n",
       "      <td>-7.946322</td>\n",
       "      <td>-3.415913</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-22.634971</td>\n",
       "      <td>-12.138403</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.002003</td>\n",
       "      <td>-0.000566</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.005237</td>\n",
       "      <td>-0.003228</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.001969</td>\n",
       "      <td>-0.000545</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-43.267503</td>\n",
       "      <td>-34.049277</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.195368</td>\n",
       "      <td>-0.093502</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.986389</td>\n",
       "      <td>-2.057449</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>78 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_faecalibacterium_imports  \\\n",
       "name                                                         \n",
       "(R)-lactate                                      -6.205649   \n",
       "12-Dehydrocholate                                -8.623386   \n",
       "3-methyl-2-oxopentanoate                         -7.946322   \n",
       "Ammonium                                        -22.634971   \n",
       "Chloride                                         -0.002003   \n",
       "...                                                    ...   \n",
       "octadecanoate (n-C18:0)                          -0.005237   \n",
       "potassium                                        -0.001969   \n",
       "proton                                          -43.267503   \n",
       "sulfate                                          -0.195368   \n",
       "tetradecanoate (n-C14:0)                         -1.986389   \n",
       "\n",
       "                          high_fiber_faecalibacterium_imports  \n",
       "name                                                           \n",
       "(R)-lactate                                        -28.348469  \n",
       "12-Dehydrocholate                                  -10.630604  \n",
       "3-methyl-2-oxopentanoate                            -3.415913  \n",
       "Ammonium                                           -12.138403  \n",
       "Chloride                                            -0.000566  \n",
       "...                                                       ...  \n",
       "octadecanoate (n-C18:0)                             -0.003228  \n",
       "potassium                                           -0.000545  \n",
       "proton                                             -34.049277  \n",
       "sulfate                                             -0.093502  \n",
       "tetradecanoate (n-C14:0)                            -2.057449  \n",
       "\n",
       "[78 rows x 2 columns]"
      ]
     },
     "execution_count": 76,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "faecalibacterium_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "id": "facc1466-2bcb-4995-ad33-8bb80e23480e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "48.68283693595469"
      ]
     },
     "execution_count": 77,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "faecalibacterium_euclidean_distance = ((faecalibacterium_imports_for_both_diets.western_faecalibacterium_imports - faecalibacterium_imports_for_both_diets.high_fiber_faecalibacterium_imports)**2).sum()**(1/2)\n",
    "\n",
    "faecalibacterium_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b2cac446-f4e4-4291-8827-24d824d121c6",
   "metadata": {},
   "source": [
    "# Roseburia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "id": "891afcb0-ff72-4964-911e-8d0060ee2330",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 78,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "id": "c639b7c0-e8b7-4f7b-b9cf-2af41941d0e3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000011</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104772</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 149</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104780</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104786</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104793</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104797</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4729 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            taxon direction    sample_id   medium  \\\n",
       "6       Roseburia    import  SRR15032293  western   \n",
       "13      Roseburia    import  SRR15032323  western   \n",
       "14      Roseburia    import  SRR15032344  western   \n",
       "23      Roseburia    import  SRR15032081  western   \n",
       "26      Roseburia    import  SRR15032099  western   \n",
       "...           ...       ...          ...      ...   \n",
       "104772  Roseburia    import  SRR15032323  western   \n",
       "104780  Roseburia    import  SRR15032323  western   \n",
       "104786  Roseburia    import  SRR15032439  western   \n",
       "104793  Roseburia    import  SRR15032392  western   \n",
       "104797  Roseburia    import  SRR15032439  western   \n",
       "\n",
       "                                                     name      flux  \n",
       "6                              mucin-type O-glycan No 144 -0.000003  \n",
       "13                             mucin-type O-glycan No 144 -0.000011  \n",
       "14                             mucin-type O-glycan No 144 -0.000001  \n",
       "23                     released mucin-type O-glycan No 68 -0.000004  \n",
       "26                     released mucin-type O-glycan No 68 -0.000004  \n",
       "...                                                   ...       ...  \n",
       "104772                released mucin-type O-glycan No 149 -0.000008  \n",
       "104780                released mucin-type O-glycan No 145 -0.000009  \n",
       "104786                released mucin-type O-glycan No 145 -0.000002  \n",
       "104793  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000008  \n",
       "104797  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000002  \n",
       "\n",
       "[4729 rows x 6 columns]"
      ]
     },
     "execution_count": 79,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_roseburia_only = western_only.loc[western_only['taxon'] == 'Roseburia']\n",
    "western_roseburia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "id": "5a8eb201-8831-4a27-b872-ca692893b4ef",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-Pantothenate                                      -0.002982\n",
       "(R)-lactate                                          -51.907105\n",
       "(S)-propane-1,2-diol                                  -0.006050\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)      -0.000002\n",
       "Adenosylcobalamin                                     -0.000007\n",
       "                                                        ...    \n",
       "released mucin-type O-glycan No 99                    -0.000004\n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})    -0.000005\n",
       "sulfate                                               -0.001865\n",
       "tetradecanoate (n-C14:0)                              -1.982845\n",
       "uracil                                                -2.370423\n",
       "Name: flux, Length: 389, dtype: float64"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_roseburia = western_roseburia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_roseburia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "id": "6fb99cae-a69f-40d4-9a7d-c3b320d398a5",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "id": "c218919e-cf9a-4cbd-b647-a33f2e427288",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>80</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.047411</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>109</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.064923</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>131</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032104</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.078176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>161</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032119</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.060464</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>207</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032136</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.038690</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99435</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032461</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>O2</td>\n",
       "      <td>-1.337319</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99448</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032472</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>O2</td>\n",
       "      <td>-0.000047</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101762</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032119</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>L-lysinium(1+)</td>\n",
       "      <td>-0.001871</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101962</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032494</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>L-lysinium(1+)</td>\n",
       "      <td>-0.009683</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102684</th>\n",
       "      <td>Roseburia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032458</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.001911</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2911 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            taxon direction    sample_id      medium                     name  \\\n",
       "80      Roseburia    import  SRR15032095  high_fiber        hydrogenphosphate   \n",
       "109     Roseburia    import  SRR15032082  high_fiber        hydrogenphosphate   \n",
       "131     Roseburia    import  SRR15032104  high_fiber        hydrogenphosphate   \n",
       "161     Roseburia    import  SRR15032119  high_fiber        hydrogenphosphate   \n",
       "207     Roseburia    import  SRR15032136  high_fiber        hydrogenphosphate   \n",
       "...           ...       ...          ...         ...                      ...   \n",
       "99435   Roseburia    import  SRR15032461  high_fiber                       O2   \n",
       "99448   Roseburia    import  SRR15032472  high_fiber                       O2   \n",
       "101762  Roseburia    import  SRR15032119  high_fiber           L-lysinium(1+)   \n",
       "101962  Roseburia    import  SRR15032494  high_fiber           L-lysinium(1+)   \n",
       "102684  Roseburia    import  SRR15032458  high_fiber  octadecanoate (n-C18:0)   \n",
       "\n",
       "            flux  \n",
       "80     -0.047411  \n",
       "109    -0.064923  \n",
       "131    -0.078176  \n",
       "161    -0.060464  \n",
       "207    -0.038690  \n",
       "...          ...  \n",
       "99435  -1.337319  \n",
       "99448  -0.000047  \n",
       "101762 -0.001871  \n",
       "101962 -0.009683  \n",
       "102684 -0.001911  \n",
       "\n",
       "[2911 rows x 6 columns]"
      ]
     },
     "execution_count": 82,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_roseburia_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Roseburia']\n",
    "high_fiber_roseburia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "id": "840fb7b2-bd83-4976-86ec-bb604314724e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                -32.508383\n",
       "Ammonium                   -18.506904\n",
       "Chloride                    -0.000537\n",
       "Citrate                     -0.000550\n",
       "Co2+                        -0.000494\n",
       "                              ...    \n",
       "octadecanoate (n-C18:0)     -0.001911\n",
       "potassium                   -0.000537\n",
       "sulfate                     -0.000537\n",
       "tetradecanoate (n-C14:0)    -2.242054\n",
       "uracil                      -3.808581\n",
       "Name: flux, Length: 67, dtype: float64"
      ]
     },
     "execution_count": 83,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_roseburia = high_fiber_roseburia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_roseburia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "id": "bdb38aa2-d257-4364-ba11-7d607d842275",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_roseburia_imports = pd.DataFrame (mean_import_of_western_roseburia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "id": "61b40c92-ebf9-47cd-9d56-feec8e8da884",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_roseburia_imports.rename(columns={\"flux\": \"western_flux_roseburia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "id": "4fe43b5e-f6d8-4f71-abb2-54cd44d0d1f6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_roseburia</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.002982</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-51.907105</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-0.006050</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosylcobalamin</th>\n",
       "      <td>-0.000007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released mucin-type O-glycan No 99</th>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})</th>\n",
       "      <td>-0.000005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.001865</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.982845</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-2.370423</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>389 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_flux_roseburia\n",
       "name                                                                      \n",
       "(R)-Pantothenate                                                 -0.002982\n",
       "(R)-lactate                                                     -51.907105\n",
       "(S)-propane-1,2-diol                                             -0.006050\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                 -0.000002\n",
       "Adenosylcobalamin                                                -0.000007\n",
       "...                                                                    ...\n",
       "released mucin-type O-glycan No 99                               -0.000004\n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})               -0.000005\n",
       "sulfate                                                          -0.001865\n",
       "tetradecanoate (n-C14:0)                                         -1.982845\n",
       "uracil                                                           -2.370423\n",
       "\n",
       "[389 rows x 1 columns]"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_roseburia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "id": "f6e9be18-9c29-449c-bf5d-57e1b69c763e",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_roseburia_imports = pd.DataFrame (mean_import_of_high_fiber_roseburia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "id": "5a9a37c5-2bd1-44df-9d5b-4dbb9fdf44a1",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_roseburia_imports.rename(columns={\"flux\": \"high_fiber_flux_roseburia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "id": "d8d66e8e-bb52-4e24-8884-636acca1436f",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>high_fiber_flux_roseburia</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-32.508383</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-18.506904</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Citrate</th>\n",
       "      <td>-0.000550</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Co2+</th>\n",
       "      <td>-0.000494</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.001911</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.242054</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-3.808581</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>67 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_roseburia\n",
       "name                                               \n",
       "(R)-lactate                              -32.508383\n",
       "Ammonium                                 -18.506904\n",
       "Chloride                                  -0.000537\n",
       "Citrate                                   -0.000550\n",
       "Co2+                                      -0.000494\n",
       "...                                             ...\n",
       "octadecanoate (n-C18:0)                   -0.001911\n",
       "potassium                                 -0.000537\n",
       "sulfate                                   -0.000537\n",
       "tetradecanoate (n-C14:0)                  -2.242054\n",
       "uracil                                    -3.808581\n",
       "\n",
       "[67 rows x 1 columns]"
      ]
     },
     "execution_count": 89,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_roseburia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "id": "e902eb87-eecd-4d7f-9576-61fb14be6722",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_roseburia = pd.concat([western_roseburia_imports['western_flux_roseburia'], high_fiber_roseburia_imports['high_fiber_flux_roseburia']], axis=1, keys= ['western_roseburia_imports', 'high_fiber_roseburia_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "id": "59f69bf4-edd0-460f-9f82-615ee353bb66",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>western_roseburia_imports</th>\n",
       "      <th>high_fiber_roseburia_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.002982</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-51.907105</td>\n",
       "      <td>-32.508383</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-0.006050</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosylcobalamin</th>\n",
       "      <td>-0.000007</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})</th>\n",
       "      <td>-0.000005</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.001865</td>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.982845</td>\n",
       "      <td>-2.242054</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-2.370423</td>\n",
       "      <td>-3.808581</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Glycine</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-6.616224</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>390 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_roseburia_imports  \\\n",
       "name                                                                            \n",
       "(R)-Pantothenate                                                    -0.002982   \n",
       "(R)-lactate                                                        -51.907105   \n",
       "(S)-propane-1,2-diol                                                -0.006050   \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                    -0.000002   \n",
       "Adenosylcobalamin                                                   -0.000007   \n",
       "...                                                                       ...   \n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                  -0.000005   \n",
       "sulfate                                                             -0.001865   \n",
       "tetradecanoate (n-C14:0)                                            -1.982845   \n",
       "uracil                                                              -2.370423   \n",
       "Glycine                                                                   NaN   \n",
       "\n",
       "                                                    high_fiber_roseburia_imports  \n",
       "name                                                                              \n",
       "(R)-Pantothenate                                                             NaN  \n",
       "(R)-lactate                                                           -32.508383  \n",
       "(S)-propane-1,2-diol                                                         NaN  \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                             NaN  \n",
       "Adenosylcobalamin                                                            NaN  \n",
       "...                                                                          ...  \n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                           NaN  \n",
       "sulfate                                                                -0.000537  \n",
       "tetradecanoate (n-C14:0)                                               -2.242054  \n",
       "uracil                                                                 -3.808581  \n",
       "Glycine                                                                -6.616224  \n",
       "\n",
       "[390 rows x 2 columns]"
      ]
     },
     "execution_count": 91,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_roseburia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "id": "c56cc27e-c6cc-4e81-b876-95b228d33cd2",
   "metadata": {},
   "outputs": [],
   "source": [
    "roseburia_imports_for_both_diets = combined_diet_fluxes_roseburia.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "id": "d605330f-b95b-4deb-bb41-ef3f7f33315d",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_roseburia_imports</th>\n",
       "      <th>high_fiber_roseburia_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-51.907105</td>\n",
       "      <td>-32.508383</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-20.961509</td>\n",
       "      <td>-18.506904</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.001865</td>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Citrate</th>\n",
       "      <td>-0.001837</td>\n",
       "      <td>-0.000550</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Co2+</th>\n",
       "      <td>-0.001834</td>\n",
       "      <td>-0.000494</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.001325</td>\n",
       "      <td>-0.001911</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.001865</td>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.001865</td>\n",
       "      <td>-0.000537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-1.982845</td>\n",
       "      <td>-2.242054</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-2.370423</td>\n",
       "      <td>-3.808581</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>66 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_roseburia_imports  \\\n",
       "name                                                  \n",
       "(R)-lactate                              -51.907105   \n",
       "Ammonium                                 -20.961509   \n",
       "Chloride                                  -0.001865   \n",
       "Citrate                                   -0.001837   \n",
       "Co2+                                      -0.001834   \n",
       "...                                             ...   \n",
       "octadecanoate (n-C18:0)                   -0.001325   \n",
       "potassium                                 -0.001865   \n",
       "sulfate                                   -0.001865   \n",
       "tetradecanoate (n-C14:0)                  -1.982845   \n",
       "uracil                                    -2.370423   \n",
       "\n",
       "                          high_fiber_roseburia_imports  \n",
       "name                                                    \n",
       "(R)-lactate                                 -32.508383  \n",
       "Ammonium                                    -18.506904  \n",
       "Chloride                                     -0.000537  \n",
       "Citrate                                      -0.000550  \n",
       "Co2+                                         -0.000494  \n",
       "...                                                ...  \n",
       "octadecanoate (n-C18:0)                      -0.001911  \n",
       "potassium                                    -0.000537  \n",
       "sulfate                                      -0.000537  \n",
       "tetradecanoate (n-C14:0)                     -2.242054  \n",
       "uracil                                       -3.808581  \n",
       "\n",
       "[66 rows x 2 columns]"
      ]
     },
     "execution_count": 93,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "roseburia_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 94,
   "id": "cd785703-6c85-4787-9b2b-143a4549be38",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "27.39142994145541"
      ]
     },
     "execution_count": 94,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "roseburia_euclidean_distance = ((roseburia_imports_for_both_diets.western_roseburia_imports - roseburia_imports_for_both_diets.high_fiber_roseburia_imports)**2).sum()**(1/2)\n",
    "\n",
    "roseburia_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f4f3090a-0f05-41d0-a541-b37537d3dbaf",
   "metadata": {},
   "source": [
    "# Blautia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "id": "8c421715-000f-420c-afd4-690df869a6a0",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 95,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "id": "877ddb22-019c-4f8d-99de-0ebab63a9caa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000018</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032384</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104814</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104815</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104818</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104819</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032334</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104821</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032384</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5007 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          taxon direction    sample_id   medium  \\\n",
       "15      Blautia    import  SRR15032439  western   \n",
       "20      Blautia    import  SRR15032081  western   \n",
       "28      Blautia    import  SRR15032293  western   \n",
       "43      Blautia    import  SRR15032344  western   \n",
       "49      Blautia    import  SRR15032384  western   \n",
       "...         ...       ...          ...      ...   \n",
       "104814  Blautia    import  SRR15032439  western   \n",
       "104815  Blautia    import  SRR15032323  western   \n",
       "104818  Blautia    import  SRR15032324  western   \n",
       "104819  Blautia    import  SRR15032334  western   \n",
       "104821  Blautia    import  SRR15032384  western   \n",
       "\n",
       "                                       name      flux  \n",
       "15               mucin-type O-glycan No 144 -0.000002  \n",
       "20       released mucin-type O-glycan No 68 -0.000001  \n",
       "28       released mucin-type O-glycan No 68 -0.000018  \n",
       "43       released mucin-type O-glycan No 68 -0.000002  \n",
       "49       released mucin-type O-glycan No 68 -0.000004  \n",
       "...                                     ...       ...  \n",
       "104814  released mucin-type O-glycan No 135 -0.000001  \n",
       "104815                             Nitrogen -0.000001  \n",
       "104818                             Nitrogen -0.000001  \n",
       "104819                             Nitrogen -0.000003  \n",
       "104821                             Nitrogen -0.000001  \n",
       "\n",
       "[5007 rows x 6 columns]"
      ]
     },
     "execution_count": 96,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_blautia_only = western_only.loc[western_only['taxon'] == 'Blautia']\n",
    "western_blautia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "id": "ad6ce962-b727-4d5f-be72-f6804492deaf",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-Pantothenate                                    -0.003154\n",
       "(R)-lactate                                        -53.846407\n",
       "(S)-lactate                                        -52.996872\n",
       "(S)-propane-1,2-diol                               -80.655862\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)    -0.000002\n",
       "                                                      ...    \n",
       "sialyl-T antigen                                    -0.000005\n",
       "sialyl-Tn antigen                                   -0.000005\n",
       "sulfate                                             -1.333703\n",
       "thiosulfate(2-)                                     -0.101832\n",
       "uracil                                              -0.119477\n",
       "Name: flux, Length: 449, dtype: float64"
      ]
     },
     "execution_count": 97,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_blautia = western_blautia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_blautia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "id": "a9d7102b-8d48-46db-9d7c-4b096a186bfc",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 98,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "id": "54579e46-a154-4f9d-9de3-77aff9453cbc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>88</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032089</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-5.551465</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-9.220314</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032083</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-7.777798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102382</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032500</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>2-Dehydro-3-deoxy-D-gluconate</td>\n",
       "      <td>-0.001381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102383</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032505</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>2-Dehydro-3-deoxy-D-gluconate</td>\n",
       "      <td>-0.001331</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102384</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>2-Dehydro-3-deoxy-D-gluconate</td>\n",
       "      <td>-0.001490</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102408</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032104</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.000294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102615</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032373</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.000151</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3612 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          taxon direction    sample_id      medium  \\\n",
       "69      Blautia    import  SRR15032094  high_fiber   \n",
       "77      Blautia    import  SRR15032095  high_fiber   \n",
       "88      Blautia    import  SRR15032089  high_fiber   \n",
       "96      Blautia    import  SRR15032079  high_fiber   \n",
       "104     Blautia    import  SRR15032083  high_fiber   \n",
       "...         ...       ...          ...         ...   \n",
       "102382  Blautia    import  SRR15032500  high_fiber   \n",
       "102383  Blautia    import  SRR15032505  high_fiber   \n",
       "102384  Blautia    import  SRR15032503  high_fiber   \n",
       "102408  Blautia    import  SRR15032104  high_fiber   \n",
       "102615  Blautia    import  SRR15032373  high_fiber   \n",
       "\n",
       "                                 name       flux  \n",
       "69                  hydrogenphosphate -11.983896  \n",
       "77                  hydrogenphosphate -10.552848  \n",
       "88                  hydrogenphosphate  -5.551465  \n",
       "96                  hydrogenphosphate  -9.220314  \n",
       "104                 hydrogenphosphate  -7.777798  \n",
       "...                               ...        ...  \n",
       "102382  2-Dehydro-3-deoxy-D-gluconate  -0.001381  \n",
       "102383  2-Dehydro-3-deoxy-D-gluconate  -0.001331  \n",
       "102384  2-Dehydro-3-deoxy-D-gluconate  -0.001490  \n",
       "102408        octadecanoate (n-C18:0)  -0.000294  \n",
       "102615        octadecanoate (n-C18:0)  -0.000151  \n",
       "\n",
       "[3612 rows x 6 columns]"
      ]
     },
     "execution_count": 99,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_blautia_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Blautia']\n",
    "high_fiber_blautia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "id": "f2012076-60ce-4c8d-95e8-04d3bee47833",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                     -54.519062\n",
       "(S)-lactate                     -52.357205\n",
       "(S)-propane-1,2-diol            -84.472959\n",
       "2-Dehydro-3-deoxy-D-gluconate    -0.001249\n",
       "Ammonium                        -45.831205\n",
       "                                   ...    \n",
       "octadecanoate (n-C18:0)          -0.000223\n",
       "potassium                        -0.000505\n",
       "proton                          -65.154104\n",
       "sulfate                          -0.870799\n",
       "thiosulfate(2-)                  -0.098400\n",
       "Name: flux, Length: 76, dtype: float64"
      ]
     },
     "execution_count": 100,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_blautia = high_fiber_blautia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_blautia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 101,
   "id": "fc5c54db-2ced-41bb-951b-52bd9404f209",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_blautia_imports = pd.DataFrame (mean_import_of_western_blautia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "id": "96f2bc87-466a-4398-9514-2503906eaf27",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_blautia_imports.rename(columns={\"flux\": \"western_flux_blautia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "id": "0ebe2356-8aba-48ff-9937-73c98caee741",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>western_flux_blautia</th>\n",
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       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.003154</td>\n",
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       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-53.846407</td>\n",
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       "      <th>(S)-lactate</th>\n",
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       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-80.655862</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-T antigen</th>\n",
       "      <td>-0.000005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-1.333703</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
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       "    <tr>\n",
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       "</table>\n",
       "<p>449 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                  western_flux_blautia\n",
       "name                                                                  \n",
       "(R)-Pantothenate                                             -0.003154\n",
       "(R)-lactate                                                 -53.846407\n",
       "(S)-lactate                                                 -52.996872\n",
       "(S)-propane-1,2-diol                                        -80.655862\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)             -0.000002\n",
       "...                                                                ...\n",
       "sialyl-T antigen                                             -0.000005\n",
       "sialyl-Tn antigen                                            -0.000005\n",
       "sulfate                                                      -1.333703\n",
       "thiosulfate(2-)                                              -0.101832\n",
       "uracil                                                       -0.119477\n",
       "\n",
       "[449 rows x 1 columns]"
      ]
     },
     "execution_count": 103,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_blautia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "id": "4da6c39c-1cee-4e69-bac4-79b22b03f19e",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_blautia_imports = pd.DataFrame (mean_import_of_high_fiber_blautia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "id": "ebaaac3a-cc60-44ac-b3af-a09ea087f57e",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_blautia_imports.rename(columns={\"flux\": \"high_fiber_flux_blautia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "id": "9188f4ef-74cd-4153-96cf-a5fb2cd54b9f",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "    </tr>\n",
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       "      <th>(R)-lactate</th>\n",
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       "      <td>-52.357205</td>\n",
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       "      <td>-84.472959</td>\n",
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       "    <tr>\n",
       "      <th>2-Dehydro-3-deoxy-D-gluconate</th>\n",
       "      <td>-0.001249</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-45.831205</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.000223</td>\n",
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       "      <th>potassium</th>\n",
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       "      <th>proton</th>\n",
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       "<p>76 rows × 1 columns</p>\n",
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      "text/plain": [
       "                               high_fiber_flux_blautia\n",
       "name                                                  \n",
       "(R)-lactate                                 -54.519062\n",
       "(S)-lactate                                 -52.357205\n",
       "(S)-propane-1,2-diol                        -84.472959\n",
       "2-Dehydro-3-deoxy-D-gluconate                -0.001249\n",
       "Ammonium                                    -45.831205\n",
       "...                                                ...\n",
       "octadecanoate (n-C18:0)                      -0.000223\n",
       "potassium                                    -0.000505\n",
       "proton                                      -65.154104\n",
       "sulfate                                      -0.870799\n",
       "thiosulfate(2-)                              -0.098400\n",
       "\n",
       "[76 rows x 1 columns]"
      ]
     },
     "execution_count": 106,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_blautia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "id": "e1fa2db4-07cc-4b7f-95ee-e3e4e837920d",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_blautia = pd.concat([western_blautia_imports['western_flux_blautia'], high_fiber_blautia_imports['high_fiber_flux_blautia']], axis=1, keys= ['western_blautia_imports', 'high_fiber_blautia_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "id": "e7674e2d-4fa2-47d4-8bb2-2b846b917254",
   "metadata": {},
   "outputs": [
    {
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       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
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       "    <tr>\n",
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       "      <th>sialyl-T antigen</th>\n",
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       "      <th>thiosulfate(2-)</th>\n",
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       "<p>449 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                  western_blautia_imports  \\\n",
       "name                                                                        \n",
       "(R)-Pantothenate                                                -0.003154   \n",
       "(R)-lactate                                                    -53.846407   \n",
       "(S)-lactate                                                    -52.996872   \n",
       "(S)-propane-1,2-diol                                           -80.655862   \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                -0.000002   \n",
       "...                                                                   ...   \n",
       "sialyl-T antigen                                                -0.000005   \n",
       "sialyl-Tn antigen                                               -0.000005   \n",
       "sulfate                                                         -1.333703   \n",
       "thiosulfate(2-)                                                 -0.101832   \n",
       "uracil                                                          -0.119477   \n",
       "\n",
       "                                                  high_fiber_blautia_imports  \n",
       "name                                                                          \n",
       "(R)-Pantothenate                                                         NaN  \n",
       "(R)-lactate                                                       -54.519062  \n",
       "(S)-lactate                                                       -52.357205  \n",
       "(S)-propane-1,2-diol                                              -84.472959  \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                         NaN  \n",
       "...                                                                      ...  \n",
       "sialyl-T antigen                                                         NaN  \n",
       "sialyl-Tn antigen                                                        NaN  \n",
       "sulfate                                                            -0.870799  \n",
       "thiosulfate(2-)                                                    -0.098400  \n",
       "uracil                                                                   NaN  \n",
       "\n",
       "[449 rows x 2 columns]"
      ]
     },
     "execution_count": 108,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_blautia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 109,
   "id": "c53cc9e8-4046-4772-917c-65192fe9579c",
   "metadata": {},
   "outputs": [],
   "source": [
    "blautia_imports_for_both_diets = combined_diet_fluxes_blautia.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 110,
   "id": "69ae3883-bb9d-4845-b61b-f75ae73827ea",
   "metadata": {},
   "outputs": [
    {
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       "      <th>2-Dehydro-3-deoxy-D-gluconate</th>\n",
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       "      <th>octadecanoate (n-C18:0)</th>\n",
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       "    <tr>\n",
       "      <th>potassium</th>\n",
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       "      <td>-0.000505</td>\n",
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       "    <tr>\n",
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       "      <td>-65.154104</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-1.333703</td>\n",
       "      <td>-0.870799</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.101832</td>\n",
       "      <td>-0.098400</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>76 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                               western_blautia_imports  \\\n",
       "name                                                     \n",
       "(R)-lactate                                 -53.846407   \n",
       "(S)-lactate                                 -52.996872   \n",
       "(S)-propane-1,2-diol                        -80.655862   \n",
       "2-Dehydro-3-deoxy-D-gluconate                -0.514621   \n",
       "Ammonium                                    -39.819990   \n",
       "...                                                ...   \n",
       "octadecanoate (n-C18:0)                      -0.007047   \n",
       "potassium                                    -0.002052   \n",
       "proton                                      -66.185996   \n",
       "sulfate                                      -1.333703   \n",
       "thiosulfate(2-)                              -0.101832   \n",
       "\n",
       "                               high_fiber_blautia_imports  \n",
       "name                                                       \n",
       "(R)-lactate                                    -54.519062  \n",
       "(S)-lactate                                    -52.357205  \n",
       "(S)-propane-1,2-diol                           -84.472959  \n",
       "2-Dehydro-3-deoxy-D-gluconate                   -0.001249  \n",
       "Ammonium                                       -45.831205  \n",
       "...                                                   ...  \n",
       "octadecanoate (n-C18:0)                         -0.000223  \n",
       "potassium                                       -0.000505  \n",
       "proton                                         -65.154104  \n",
       "sulfate                                         -0.870799  \n",
       "thiosulfate(2-)                                 -0.098400  \n",
       "\n",
       "[76 rows x 2 columns]"
      ]
     },
     "execution_count": 110,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "blautia_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "id": "c6b10ba3-7b17-4427-9d14-2055c03ed3c7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "28.36475275549472"
      ]
     },
     "execution_count": 111,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "blautia_euclidean_distance = ((blautia_imports_for_both_diets.western_blautia_imports - blautia_imports_for_both_diets.high_fiber_blautia_imports)**2).sum()**(1/2)\n",
    "\n",
    "blautia_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "691611b4-4644-4b75-9d36-d0ce6888a616",
   "metadata": {},
   "source": [
    "# Alistipes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "id": "07c15f96-5e01-46ea-8453-c95fb57ba76d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 112,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "id": "2d5b22cd-0efb-4ef5-b0dc-0c098db756f7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032384</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>589</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-1.749855</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104767</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032323</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 149</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104773</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 149</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104781</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104787</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 145</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104812</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4720 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            taxon direction    sample_id   medium  \\\n",
       "8       Alistipes    import  SRR15032323  western   \n",
       "19      Alistipes    import  SRR15032081  western   \n",
       "47      Alistipes    import  SRR15032384  western   \n",
       "53      Alistipes    import  SRR15032392  western   \n",
       "589     Alistipes    import  SRR15032344  western   \n",
       "...           ...       ...          ...      ...   \n",
       "104767  Alistipes    import  SRR15032323  western   \n",
       "104773  Alistipes    import  SRR15032439  western   \n",
       "104781  Alistipes    import  SRR15032324  western   \n",
       "104787  Alistipes    import  SRR15032510  western   \n",
       "104812  Alistipes    import  SRR15032344  western   \n",
       "\n",
       "                                       name      flux  \n",
       "8                mucin-type O-glycan No 144 -0.000001  \n",
       "19       released mucin-type O-glycan No 68 -0.000001  \n",
       "47       released mucin-type O-glycan No 68 -0.000007  \n",
       "53       released mucin-type O-glycan No 68 -0.000001  \n",
       "589                       hydrogenphosphate -1.749855  \n",
       "...                                     ...       ...  \n",
       "104767  released mucin-type O-glycan No 149 -0.000003  \n",
       "104773  released mucin-type O-glycan No 149 -0.000003  \n",
       "104781  released mucin-type O-glycan No 145 -0.000003  \n",
       "104787  released mucin-type O-glycan No 145 -0.000003  \n",
       "104812  released mucin-type O-glycan No 135 -0.000002  \n",
       "\n",
       "[4720 rows x 6 columns]"
      ]
     },
     "execution_count": 113,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_alistipes_only = western_only.loc[western_only['taxon'] == 'Alistipes']\n",
    "western_alistipes_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "id": "f903a5e9-eb1b-4c9d-8c83-c72c2a127f40",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-Pantothenate            -0.001493\n",
       "(R)-lactate                -68.704137\n",
       "2-Demethylmenaquinone 8     -0.000002\n",
       "2-Oxoglutarate             -15.910667\n",
       "2-deoxyadenosine           -18.267387\n",
       "                              ...    \n",
       "sialyl-T antigen            -0.000005\n",
       "sialyl-Tn antigen           -0.000005\n",
       "sulfate                     -0.000873\n",
       "tetradecanoate (n-C14:0)    -2.258106\n",
       "uracil                     -55.178674\n",
       "Name: flux, Length: 431, dtype: float64"
      ]
     },
     "execution_count": 114,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_alistipes = western_alistipes_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_alistipes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 115,
   "id": "4a8ac9f0-9404-4e6e-b6e9-8eb316eb692c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 115,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 116,
   "id": "a9cf4246-8357-4df0-9f8d-fc02374bde07",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>167</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032121</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-21.642279</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1967</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-45.311422</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1975</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032089</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-39.776000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1988</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032083</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-58.982622</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1992</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-53.620560</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102608</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032372</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.010824</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102612</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032373</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.002547</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102657</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032423</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.004230</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102660</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032428</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.009166</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102728</th>\n",
       "      <td>Alistipes</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032494</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.009082</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>4184 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            taxon direction    sample_id      medium                     name  \\\n",
       "167     Alistipes    import  SRR15032121  high_fiber        hydrogenphosphate   \n",
       "1967    Alistipes    import  SRR15032095  high_fiber                  Glycine   \n",
       "1975    Alistipes    import  SRR15032089  high_fiber                  Glycine   \n",
       "1988    Alistipes    import  SRR15032083  high_fiber                  Glycine   \n",
       "1992    Alistipes    import  SRR15032082  high_fiber                  Glycine   \n",
       "...           ...       ...          ...         ...                      ...   \n",
       "102608  Alistipes    import  SRR15032372  high_fiber  octadecanoate (n-C18:0)   \n",
       "102612  Alistipes    import  SRR15032373  high_fiber  octadecanoate (n-C18:0)   \n",
       "102657  Alistipes    import  SRR15032423  high_fiber  octadecanoate (n-C18:0)   \n",
       "102660  Alistipes    import  SRR15032428  high_fiber  octadecanoate (n-C18:0)   \n",
       "102728  Alistipes    import  SRR15032494  high_fiber  octadecanoate (n-C18:0)   \n",
       "\n",
       "             flux  \n",
       "167    -21.642279  \n",
       "1967   -45.311422  \n",
       "1975   -39.776000  \n",
       "1988   -58.982622  \n",
       "1992   -53.620560  \n",
       "...           ...  \n",
       "102608  -0.010824  \n",
       "102612  -0.002547  \n",
       "102657  -0.004230  \n",
       "102660  -0.009166  \n",
       "102728  -0.009082  \n",
       "\n",
       "[4184 rows x 6 columns]"
      ]
     },
     "execution_count": 116,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_alistipes_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Alistipes']\n",
    "high_fiber_alistipes_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 117,
   "id": "2b990512-b146-4544-8b83-00defa3fe7f1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                -66.738824\n",
       "2-Oxoglutarate             -11.511520\n",
       "2-deoxyadenosine           -23.056857\n",
       "4-hydroxybenzoate          -55.916727\n",
       "Adenine                    -25.609691\n",
       "                              ...    \n",
       "potassium                   -0.001044\n",
       "proton                     -73.993715\n",
       "sulfate                     -0.001044\n",
       "tetradecanoate (n-C14:0)    -2.592348\n",
       "uracil                     -55.865618\n",
       "Name: flux, Length: 84, dtype: float64"
      ]
     },
     "execution_count": 117,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_alistipes = high_fiber_alistipes_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_alistipes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 118,
   "id": "62cde357-5f28-4cb4-8e18-75c0166b2ef6",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_alistipes_imports = pd.DataFrame (mean_import_of_western_alistipes, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 119,
   "id": "6f028891-d106-4b94-a259-3be7a36f96ca",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_alistipes_imports.rename(columns={\"flux\": \"western_flux_alistipes\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 120,
   "id": "f683dac1-7d0a-49af-94a5-4483eba6c870",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_alistipes</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.001493</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-68.704137</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Demethylmenaquinone 8</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-15.910667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-18.267387</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-T antigen</th>\n",
       "      <td>-0.000005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000005</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000873</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.258106</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-55.178674</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>431 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_flux_alistipes\n",
       "name                                            \n",
       "(R)-Pantothenate                       -0.001493\n",
       "(R)-lactate                           -68.704137\n",
       "2-Demethylmenaquinone 8                -0.000002\n",
       "2-Oxoglutarate                        -15.910667\n",
       "2-deoxyadenosine                      -18.267387\n",
       "...                                          ...\n",
       "sialyl-T antigen                       -0.000005\n",
       "sialyl-Tn antigen                      -0.000005\n",
       "sulfate                                -0.000873\n",
       "tetradecanoate (n-C14:0)               -2.258106\n",
       "uracil                                -55.178674\n",
       "\n",
       "[431 rows x 1 columns]"
      ]
     },
     "execution_count": 120,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_alistipes_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 121,
   "id": "c13146c1-77e1-4574-a723-616bc27fa943",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_alistipes_imports = pd.DataFrame (mean_import_of_high_fiber_alistipes, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "id": "35961b42-29f0-448f-8281-308624fa872f",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_alistipes_imports.rename(columns={\"flux\": \"high_fiber_flux_alistipes\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 123,
   "id": "7bc0e0a5-b9c8-4c56-87bb-894dc412d9ef",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-11.511520</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-23.056857</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-55.916727</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenine</th>\n",
       "      <td>-25.609691</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.001044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-73.993715</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.001044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.592348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-55.865618</td>\n",
       "    </tr>\n",
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       "</table>\n",
       "<p>84 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_alistipes\n",
       "name                                               \n",
       "(R)-lactate                              -66.738824\n",
       "2-Oxoglutarate                           -11.511520\n",
       "2-deoxyadenosine                         -23.056857\n",
       "4-hydroxybenzoate                        -55.916727\n",
       "Adenine                                  -25.609691\n",
       "...                                             ...\n",
       "potassium                                 -0.001044\n",
       "proton                                   -73.993715\n",
       "sulfate                                   -0.001044\n",
       "tetradecanoate (n-C14:0)                  -2.592348\n",
       "uracil                                   -55.865618\n",
       "\n",
       "[84 rows x 1 columns]"
      ]
     },
     "execution_count": 123,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_alistipes_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 124,
   "id": "f3189b22-6065-4e4a-96c2-fe7bb48832a5",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_alistipes = pd.concat([western_alistipes_imports['western_flux_alistipes'], high_fiber_alistipes_imports['high_fiber_flux_alistipes']], axis=1, keys= ['western_alistipes_imports', 'high_fiber_alistipes_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 125,
   "id": "d2fd37ce-badd-40a0-ba23-8a15ca4f7f45",
   "metadata": {},
   "outputs": [
    {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_alistipes_imports</th>\n",
       "      <th>high_fiber_alistipes_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-Pantothenate</th>\n",
       "      <td>-0.001493</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-68.704137</td>\n",
       "      <td>-66.738824</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Demethylmenaquinone 8</th>\n",
       "      <td>-0.000002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-15.910667</td>\n",
       "      <td>-11.511520</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-18.267387</td>\n",
       "      <td>-23.056857</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000005</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000873</td>\n",
       "      <td>-0.001044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.258106</td>\n",
       "      <td>-2.592348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-55.178674</td>\n",
       "      <td>-55.865618</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Urea</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.147937</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>432 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_alistipes_imports  \\\n",
       "name                                                  \n",
       "(R)-Pantothenate                          -0.001493   \n",
       "(R)-lactate                              -68.704137   \n",
       "2-Demethylmenaquinone 8                   -0.000002   \n",
       "2-Oxoglutarate                           -15.910667   \n",
       "2-deoxyadenosine                         -18.267387   \n",
       "...                                             ...   \n",
       "sialyl-Tn antigen                         -0.000005   \n",
       "sulfate                                   -0.000873   \n",
       "tetradecanoate (n-C14:0)                  -2.258106   \n",
       "uracil                                   -55.178674   \n",
       "Urea                                            NaN   \n",
       "\n",
       "                          high_fiber_alistipes_imports  \n",
       "name                                                    \n",
       "(R)-Pantothenate                                   NaN  \n",
       "(R)-lactate                                 -66.738824  \n",
       "2-Demethylmenaquinone 8                            NaN  \n",
       "2-Oxoglutarate                              -11.511520  \n",
       "2-deoxyadenosine                            -23.056857  \n",
       "...                                                ...  \n",
       "sialyl-Tn antigen                                  NaN  \n",
       "sulfate                                      -0.001044  \n",
       "tetradecanoate (n-C14:0)                     -2.592348  \n",
       "uracil                                      -55.865618  \n",
       "Urea                                         -0.147937  \n",
       "\n",
       "[432 rows x 2 columns]"
      ]
     },
     "execution_count": 125,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_alistipes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 126,
   "id": "cae79488-7ee8-42b9-9b2b-390ca3216e7a",
   "metadata": {},
   "outputs": [],
   "source": [
    "alistipes_imports_for_both_diets = combined_diet_fluxes_alistipes.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 127,
   "id": "ebd992e4-bb89-4f11-8a55-183684a7c39c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_alistipes_imports</th>\n",
       "      <th>high_fiber_alistipes_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-68.704137</td>\n",
       "      <td>-66.738824</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxoglutarate</th>\n",
       "      <td>-15.910667</td>\n",
       "      <td>-11.511520</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-18.267387</td>\n",
       "      <td>-23.056857</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-58.842055</td>\n",
       "      <td>-55.916727</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenine</th>\n",
       "      <td>-24.370497</td>\n",
       "      <td>-25.609691</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000873</td>\n",
       "      <td>-0.001044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-75.996451</td>\n",
       "      <td>-73.993715</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000873</td>\n",
       "      <td>-0.001044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-2.258106</td>\n",
       "      <td>-2.592348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-55.178674</td>\n",
       "      <td>-55.865618</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_alistipes_imports  \\\n",
       "name                                                  \n",
       "(R)-lactate                              -68.704137   \n",
       "2-Oxoglutarate                           -15.910667   \n",
       "2-deoxyadenosine                         -18.267387   \n",
       "4-hydroxybenzoate                        -58.842055   \n",
       "Adenine                                  -24.370497   \n",
       "...                                             ...   \n",
       "potassium                                 -0.000873   \n",
       "proton                                   -75.996451   \n",
       "sulfate                                   -0.000873   \n",
       "tetradecanoate (n-C14:0)                  -2.258106   \n",
       "uracil                                   -55.178674   \n",
       "\n",
       "                          high_fiber_alistipes_imports  \n",
       "name                                                    \n",
       "(R)-lactate                                 -66.738824  \n",
       "2-Oxoglutarate                              -11.511520  \n",
       "2-deoxyadenosine                            -23.056857  \n",
       "4-hydroxybenzoate                           -55.916727  \n",
       "Adenine                                     -25.609691  \n",
       "...                                                ...  \n",
       "potassium                                    -0.001044  \n",
       "proton                                      -73.993715  \n",
       "sulfate                                      -0.001044  \n",
       "tetradecanoate (n-C14:0)                     -2.592348  \n",
       "uracil                                      -55.865618  \n",
       "\n",
       "[83 rows x 2 columns]"
      ]
     },
     "execution_count": 127,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alistipes_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 128,
   "id": "d28f878e-9bf9-41c7-b432-3d8e3be20440",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "51.161930368231786"
      ]
     },
     "execution_count": 128,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alistipes_euclidean_distance = ((alistipes_imports_for_both_diets.western_alistipes_imports - alistipes_imports_for_both_diets.high_fiber_alistipes_imports)**2).sum()**(1/2)\n",
    "\n",
    "alistipes_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0aa2968c-3998-4f8f-ad8f-48b9917c2bb9",
   "metadata": {},
   "source": [
    "# Ruminococcus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 129,
   "id": "cbdb3a2d-744d-495b-9beb-a83d2eb7fefa",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 129,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 130,
   "id": "d4734ab4-2b3a-4e99-9104-b5b27222eb30",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
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       "      <th>direction</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000028</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104794</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104798</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl...</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104799</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032293</td>\n",
       "      <td>western</td>\n",
       "      <td>Biotin</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104802</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>Biotin</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104825</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>Nitrogen</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3578 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               taxon direction    sample_id   medium  \\\n",
       "7       Ruminococcus    import  SRR15032293  western   \n",
       "17      Ruminococcus    import  SRR15032439  western   \n",
       "27      Ruminococcus    import  SRR15032099  western   \n",
       "32      Ruminococcus    import  SRR15032293  western   \n",
       "60      Ruminococcus    import  SRR15032439  western   \n",
       "...              ...       ...          ...      ...   \n",
       "104794  Ruminococcus    import  SRR15032392  western   \n",
       "104798  Ruminococcus    import  SRR15032439  western   \n",
       "104799  Ruminococcus    import  SRR15032293  western   \n",
       "104802  Ruminococcus    import  SRR15032439  western   \n",
       "104825  Ruminococcus    import  SRR15032392  western   \n",
       "\n",
       "                                                     name      flux  \n",
       "7                              mucin-type O-glycan No 144 -0.000001  \n",
       "17                             mucin-type O-glycan No 144 -0.000001  \n",
       "27                     released mucin-type O-glycan No 68 -0.000003  \n",
       "32                     released mucin-type O-glycan No 68 -0.000028  \n",
       "60                     released mucin-type O-glycan No 68 -0.000009  \n",
       "...                                                   ...       ...  \n",
       "104794  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000003  \n",
       "104798  starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Gl... -0.000002  \n",
       "104799                                             Biotin -0.000001  \n",
       "104802                                             Biotin -0.000001  \n",
       "104825                                           Nitrogen -0.000001  \n",
       "\n",
       "[3578 rows x 6 columns]"
      ]
     },
     "execution_count": 130,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_ruminococcus_only = western_only.loc[western_only['taxon'] == 'Ruminococcus']\n",
    "western_ruminococcus_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 131,
   "id": "e0aaeaf7-877d-44b8-9a1c-a6cd26a2a281",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                                          -79.871701\n",
       "(S)-lactate                                          -78.742605\n",
       "(S)-propane-1,2-diol                                 -34.347199\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)      -0.000001\n",
       "12-Dehydrocholate                                    -55.534588\n",
       "                                                        ...    \n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})    -0.000002\n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})     -0.000007\n",
       "sulfate                                               -0.426998\n",
       "thiosulfate(2-)                                       -0.166330\n",
       "uracil                                               -20.704723\n",
       "Name: flux, Length: 388, dtype: float64"
      ]
     },
     "execution_count": 131,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_ruminococcus = western_ruminococcus_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_ruminococcus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 132,
   "id": "4525b195-bbcc-479b-8842-bfd5b7af2e83",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 132,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 133,
   "id": "d0588ee7-984d-4c04-a930-f797dccc4575",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1961</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-55.253978</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1969</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-67.451611</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1991</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032083</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-58.896965</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1995</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-53.589062</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2000</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032096</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Glycine</td>\n",
       "      <td>-59.462865</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102238</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032379</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.002267</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102241</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032385</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.021512</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102269</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032453</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.002831</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102278</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032455</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.003689</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102282</th>\n",
       "      <td>Ruminococcus</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032474</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>thiosulfate(2-)</td>\n",
       "      <td>-0.144373</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2669 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               taxon direction    sample_id      medium             name  \\\n",
       "1961    Ruminococcus    import  SRR15032094  high_fiber          Glycine   \n",
       "1969    Ruminococcus    import  SRR15032095  high_fiber          Glycine   \n",
       "1991    Ruminococcus    import  SRR15032083  high_fiber          Glycine   \n",
       "1995    Ruminococcus    import  SRR15032082  high_fiber          Glycine   \n",
       "2000    Ruminococcus    import  SRR15032096  high_fiber          Glycine   \n",
       "...              ...       ...          ...         ...              ...   \n",
       "102238  Ruminococcus    import  SRR15032379  high_fiber  thiosulfate(2-)   \n",
       "102241  Ruminococcus    import  SRR15032385  high_fiber  thiosulfate(2-)   \n",
       "102269  Ruminococcus    import  SRR15032453  high_fiber  thiosulfate(2-)   \n",
       "102278  Ruminococcus    import  SRR15032455  high_fiber  thiosulfate(2-)   \n",
       "102282  Ruminococcus    import  SRR15032474  high_fiber  thiosulfate(2-)   \n",
       "\n",
       "             flux  \n",
       "1961   -55.253978  \n",
       "1969   -67.451611  \n",
       "1991   -58.896965  \n",
       "1995   -53.589062  \n",
       "2000   -59.462865  \n",
       "...           ...  \n",
       "102238  -0.002267  \n",
       "102241  -0.021512  \n",
       "102269  -0.002831  \n",
       "102278  -0.003689  \n",
       "102282  -0.144373  \n",
       "\n",
       "[2669 rows x 6 columns]"
      ]
     },
     "execution_count": 133,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_ruminococcus_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Ruminococcus']\n",
    "high_fiber_ruminococcus_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 134,
   "id": "4c15a95a-ff96-40c8-9fec-953f16d6b5e2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(R)-lactate                                                                                                          -75.849324\n",
       "(S)-lactate                                                                                                          -74.240000\n",
       "(S)-propane-1,2-diol                                                                                                 -53.671188\n",
       "12-Dehydrocholate                                                                                                    -59.554308\n",
       "2-Oxobutanoate                                                                                                       -14.214149\n",
       "                                                                                                                        ...    \n",
       "potassium                                                                                                             -0.000419\n",
       "proton                                                                                                               -57.603115\n",
       "starch n=1200 repeat units (300 repeat units amylose, 900 repeat units amylopectin, corresponds to potatoe starch)    -0.007225\n",
       "sulfate                                                                                                               -0.181014\n",
       "thiosulfate(2-)                                                                                                       -0.037623\n",
       "Name: flux, Length: 87, dtype: float64"
      ]
     },
     "execution_count": 134,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_ruminococcus = high_fiber_ruminococcus_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_ruminococcus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 135,
   "id": "52fea0d6-1a1e-492d-8728-465871656fd2",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_ruminococcus_imports = pd.DataFrame (mean_import_of_western_ruminococcus, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 136,
   "id": "112c3f11-d517-4ed3-8c53-dd47f6b83f61",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_ruminococcus_imports.rename(columns={\"flux\": \"western_flux_ruminococcus\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 137,
   "id": "a619ca1a-7764-4764-8cd7-93e9cf5cc6e4",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_ruminococcus</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
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       "      <th>(R)-lactate</th>\n",
       "      <td>-79.871701</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-78.742605</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-34.347199</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-55.534588</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})</th>\n",
       "      <td>-0.000007</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.426998</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.166330</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-20.704723</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>388 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_flux_ruminococcus\n",
       "name                                                                         \n",
       "(R)-lactate                                                        -79.871701\n",
       "(S)-lactate                                                        -78.742605\n",
       "(S)-propane-1,2-diol                                               -34.347199\n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                    -0.000001\n",
       "12-Dehydrocholate                                                  -55.534588\n",
       "...                                                                       ...\n",
       "starch, structure 1 (1,6-{7[1,4-Glc], 4[1,4-Glc]})                  -0.000002\n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})                   -0.000007\n",
       "sulfate                                                             -0.426998\n",
       "thiosulfate(2-)                                                     -0.166330\n",
       "uracil                                                             -20.704723\n",
       "\n",
       "[388 rows x 1 columns]"
      ]
     },
     "execution_count": 137,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_ruminococcus_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 138,
   "id": "7544b2a6-a7a8-4c20-abcc-8cb8e432edf1",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_ruminococcus_imports = pd.DataFrame (mean_import_of_high_fiber_ruminococcus, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 139,
   "id": "c4eb2d54-5ae7-4b3a-bd19-009b687b3faf",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_ruminococcus_imports.rename(columns={\"flux\": \"high_fiber_flux_ruminococcus\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 140,
   "id": "1b1eea52-4d29-41b4-bc11-03994e964968",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>high_fiber_flux_ruminococcus</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-75.849324</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-74.240000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-53.671188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-59.554308</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-14.214149</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000419</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-57.603115</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch n=1200 repeat units (300 repeat units amylose, 900 repeat units amylopectin, corresponds to potatoe starch)</th>\n",
       "      <td>-0.007225</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.181014</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.037623</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>87 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    high_fiber_flux_ruminococcus\n",
       "name                                                                            \n",
       "(R)-lactate                                                           -75.849324\n",
       "(S)-lactate                                                           -74.240000\n",
       "(S)-propane-1,2-diol                                                  -53.671188\n",
       "12-Dehydrocholate                                                     -59.554308\n",
       "2-Oxobutanoate                                                        -14.214149\n",
       "...                                                                          ...\n",
       "potassium                                                              -0.000419\n",
       "proton                                                                -57.603115\n",
       "starch n=1200 repeat units (300 repeat units am...                     -0.007225\n",
       "sulfate                                                                -0.181014\n",
       "thiosulfate(2-)                                                        -0.037623\n",
       "\n",
       "[87 rows x 1 columns]"
      ]
     },
     "execution_count": 140,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_ruminococcus_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 141,
   "id": "c145f77a-4611-4680-9a5b-9a548c6393d3",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_ruminococcus = pd.concat([western_ruminococcus_imports['western_flux_ruminococcus'], high_fiber_ruminococcus_imports['high_fiber_flux_ruminococcus']], axis=1, keys= ['western_ruminococcus_imports', 'high_fiber_ruminococcus_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 142,
   "id": "78a35d98-11b9-4bc2-b45e-0a085e475409",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>western_ruminococcus_imports</th>\n",
       "      <th>high_fiber_ruminococcus_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-79.871701</td>\n",
       "      <td>-75.849324</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-78.742605</td>\n",
       "      <td>-74.240000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-34.347199</td>\n",
       "      <td>-53.671188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)</th>\n",
       "      <td>-0.000001</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-55.534588</td>\n",
       "      <td>-59.554308</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})</th>\n",
       "      <td>-0.000007</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.426998</td>\n",
       "      <td>-0.181014</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.166330</td>\n",
       "      <td>-0.037623</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-20.704723</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Glycerol</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-34.510348</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>389 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                   western_ruminococcus_imports  \\\n",
       "name                                                                              \n",
       "(R)-lactate                                                          -79.871701   \n",
       "(S)-lactate                                                          -78.742605   \n",
       "(S)-propane-1,2-diol                                                 -34.347199   \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                      -0.000001   \n",
       "12-Dehydrocholate                                                    -55.534588   \n",
       "...                                                                         ...   \n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})                     -0.000007   \n",
       "sulfate                                                               -0.426998   \n",
       "thiosulfate(2-)                                                       -0.166330   \n",
       "uracil                                                               -20.704723   \n",
       "Glycerol                                                                    NaN   \n",
       "\n",
       "                                                   high_fiber_ruminococcus_imports  \n",
       "name                                                                                \n",
       "(R)-lactate                                                             -75.849324  \n",
       "(S)-lactate                                                             -74.240000  \n",
       "(S)-propane-1,2-diol                                                    -53.671188  \n",
       "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)                               NaN  \n",
       "12-Dehydrocholate                                                       -59.554308  \n",
       "...                                                                            ...  \n",
       "starch, structure 2 (1,6-{2[1,4-Glc], [1,4-Glc]})                              NaN  \n",
       "sulfate                                                                  -0.181014  \n",
       "thiosulfate(2-)                                                          -0.037623  \n",
       "uracil                                                                         NaN  \n",
       "Glycerol                                                                -34.510348  \n",
       "\n",
       "[389 rows x 2 columns]"
      ]
     },
     "execution_count": 142,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_ruminococcus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 143,
   "id": "f94a42b1-655f-4b22-961d-63e946bdf3c6",
   "metadata": {},
   "outputs": [],
   "source": [
    "ruminococcus_imports_for_both_diets = combined_diet_fluxes_ruminococcus.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 144,
   "id": "c6c279af-d1a1-4dad-a592-8cc4b6fcaabc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_ruminococcus_imports</th>\n",
       "      <th>high_fiber_ruminococcus_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(R)-lactate</th>\n",
       "      <td>-79.871701</td>\n",
       "      <td>-75.849324</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-lactate</th>\n",
       "      <td>-78.742605</td>\n",
       "      <td>-74.240000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-34.347199</td>\n",
       "      <td>-53.671188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12-Dehydrocholate</th>\n",
       "      <td>-55.534588</td>\n",
       "      <td>-59.554308</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2-Oxobutanoate</th>\n",
       "      <td>-14.247240</td>\n",
       "      <td>-14.214149</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.001709</td>\n",
       "      <td>-0.000419</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-66.528615</td>\n",
       "      <td>-57.603115</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>starch n=1200 repeat units (300 repeat units amylose, 900 repeat units amylopectin, corresponds to potatoe starch)</th>\n",
       "      <td>-0.000128</td>\n",
       "      <td>-0.007225</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.426998</td>\n",
       "      <td>-0.181014</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>thiosulfate(2-)</th>\n",
       "      <td>-0.166330</td>\n",
       "      <td>-0.037623</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>86 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_ruminococcus_imports  \\\n",
       "name                                                                               \n",
       "(R)-lactate                                                           -79.871701   \n",
       "(S)-lactate                                                           -78.742605   \n",
       "(S)-propane-1,2-diol                                                  -34.347199   \n",
       "12-Dehydrocholate                                                     -55.534588   \n",
       "2-Oxobutanoate                                                        -14.247240   \n",
       "...                                                                          ...   \n",
       "potassium                                                              -0.001709   \n",
       "proton                                                                -66.528615   \n",
       "starch n=1200 repeat units (300 repeat units am...                     -0.000128   \n",
       "sulfate                                                                -0.426998   \n",
       "thiosulfate(2-)                                                        -0.166330   \n",
       "\n",
       "                                                    high_fiber_ruminococcus_imports  \n",
       "name                                                                                 \n",
       "(R)-lactate                                                              -75.849324  \n",
       "(S)-lactate                                                              -74.240000  \n",
       "(S)-propane-1,2-diol                                                     -53.671188  \n",
       "12-Dehydrocholate                                                        -59.554308  \n",
       "2-Oxobutanoate                                                           -14.214149  \n",
       "...                                                                             ...  \n",
       "potassium                                                                 -0.000419  \n",
       "proton                                                                   -57.603115  \n",
       "starch n=1200 repeat units (300 repeat units am...                        -0.007225  \n",
       "sulfate                                                                   -0.181014  \n",
       "thiosulfate(2-)                                                           -0.037623  \n",
       "\n",
       "[86 rows x 2 columns]"
      ]
     },
     "execution_count": 144,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ruminococcus_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 145,
   "id": "ccce3a8a-437c-4c6c-8513-50b4b30bf122",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "46.76183246583985"
      ]
     },
     "execution_count": 145,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ruminococcus_euclidean_distance = ((ruminococcus_imports_for_both_diets.western_ruminococcus_imports - ruminococcus_imports_for_both_diets.high_fiber_ruminococcus_imports)**2).sum()**(1/2)\n",
    "\n",
    "ruminococcus_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4f6139e0-d44e-4ea4-9f21-49dcf8cacf65",
   "metadata": {},
   "source": [
    "# Akkermansia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 146,
   "id": "926e418b-bcd7-4de4-b011-0bb6d491861f",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 146,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 147,
   "id": "73d4f5f0-a77a-4f79-be25-0660eb74fbf9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 68</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>62</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.137294</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.309431</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104679</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 32</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104729</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 138</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104750</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032324</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 173</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104759</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>released mucin-type O-glycan No 173</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1574 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              taxon direction    sample_id   medium  \\\n",
       "0       Akkermansia    import  SRR15032081  western   \n",
       "18      Akkermansia    import  SRR15032081  western   \n",
       "41      Akkermansia    import  SRR15032344  western   \n",
       "62      Akkermansia    import  SRR15032081  western   \n",
       "119     Akkermansia    import  SRR15032099  western   \n",
       "...             ...       ...          ...      ...   \n",
       "104679  Akkermansia    import  SRR15032324  western   \n",
       "104729  Akkermansia    import  SRR15032439  western   \n",
       "104750  Akkermansia    import  SRR15032324  western   \n",
       "104759  Akkermansia    import  SRR15032439  western   \n",
       "104835  Akkermansia    import  SRR15032439  western   \n",
       "\n",
       "                                       name      flux  \n",
       "0                mucin-type O-glycan No 144 -0.000001  \n",
       "18       released mucin-type O-glycan No 68 -0.000001  \n",
       "41       released mucin-type O-glycan No 68 -0.000001  \n",
       "62                        hydrogenphosphate -0.137294  \n",
       "119                       hydrogenphosphate -0.309431  \n",
       "...                                     ...       ...  \n",
       "104679   released mucin-type O-glycan No 32 -0.000003  \n",
       "104729           mucin-type O-glycan No 138 -0.000001  \n",
       "104750  released mucin-type O-glycan No 173 -0.000003  \n",
       "104759  released mucin-type O-glycan No 173 -0.000001  \n",
       "104835           mucin-type O-glycan No 135 -0.000001  \n",
       "\n",
       "[1574 rows x 6 columns]"
      ]
     },
     "execution_count": 147,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_akkermansia_only = western_only.loc[western_only['taxon'] == 'Akkermansia']\n",
    "western_akkermansia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 148,
   "id": "0ea758c1-480b-455f-9480-911e83d0643d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(S)-propane-1,2-diol                                  -72.412195\n",
       "Adenosine                                              -0.000004\n",
       "Alpha-1,3-Galactose-N-acetylgalactosamine              -0.000001\n",
       "Alpha-2,6-N-acetylneuraminate-N-acetylgalactosamine    -0.000003\n",
       "Ammonium                                              -27.286958\n",
       "                                                         ...    \n",
       "released sialyl-Tn antigen                             -0.000003\n",
       "sialyl-T antigen                                       -0.000002\n",
       "sialyl-Tn antigen                                      -0.000002\n",
       "sulfate                                                -0.196022\n",
       "uracil                                                 -0.013216\n",
       "Name: flux, Length: 247, dtype: float64"
      ]
     },
     "execution_count": 148,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_akkermansia = western_akkermansia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_akkermansia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 149,
   "id": "32c62a41-41c6-4215-a435-de54389e38b2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 149,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 150,
   "id": "709748c9-9d22-47a2-bab0-ce3c8dbddb31",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
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       "      <th>221</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032130</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.459514</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>233</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032141</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.407931</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032161</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.497020</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>340</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032288</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.257341</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>385</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032290</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.219296</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99293</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032353</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>O2</td>\n",
       "      <td>-1.545350</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102477</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032288</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.006533</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102491</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032290</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.005710</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102656</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032423</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.005796</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102659</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032428</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.013069</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>667 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              taxon direction    sample_id      medium  \\\n",
       "221     Akkermansia    import  SRR15032130  high_fiber   \n",
       "233     Akkermansia    import  SRR15032141  high_fiber   \n",
       "283     Akkermansia    import  SRR15032161  high_fiber   \n",
       "340     Akkermansia    import  SRR15032288  high_fiber   \n",
       "385     Akkermansia    import  SRR15032290  high_fiber   \n",
       "...             ...       ...          ...         ...   \n",
       "99293   Akkermansia    import  SRR15032353  high_fiber   \n",
       "102477  Akkermansia    import  SRR15032288  high_fiber   \n",
       "102491  Akkermansia    import  SRR15032290  high_fiber   \n",
       "102656  Akkermansia    import  SRR15032423  high_fiber   \n",
       "102659  Akkermansia    import  SRR15032428  high_fiber   \n",
       "\n",
       "                           name      flux  \n",
       "221           hydrogenphosphate -0.459514  \n",
       "233           hydrogenphosphate -0.407931  \n",
       "283           hydrogenphosphate -0.497020  \n",
       "340           hydrogenphosphate -0.257341  \n",
       "385           hydrogenphosphate -0.219296  \n",
       "...                         ...       ...  \n",
       "99293                        O2 -1.545350  \n",
       "102477  octadecanoate (n-C18:0) -0.006533  \n",
       "102491  octadecanoate (n-C18:0) -0.005710  \n",
       "102656  octadecanoate (n-C18:0) -0.005796  \n",
       "102659  octadecanoate (n-C18:0) -0.013069  \n",
       "\n",
       "[667 rows x 6 columns]"
      ]
     },
     "execution_count": 150,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_akkermansia_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Akkermansia']\n",
    "high_fiber_akkermansia_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 151,
   "id": "5e8991ba-f6c1-4efd-bc60-bdf9d3d3d3b9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(S)-propane-1,2-diol            -70.948112\n",
       "Adenosine                        -0.000001\n",
       "Ammonium                        -15.552513\n",
       "Chloride                         -0.000826\n",
       "Co2+                             -0.000826\n",
       "Cu2+                             -0.000826\n",
       "Cytidine                         -0.031032\n",
       "D-Fructose                       -5.239300\n",
       "D-Glucosamine                    -4.209554\n",
       "D-glucose                        -0.096235\n",
       "Fe2+                             -0.000826\n",
       "Fe3+                             -0.000826\n",
       "Glycine                         -38.101644\n",
       "Hexadecanoate (n-C16:0)          -0.312693\n",
       "Hydrogen                         -7.145183\n",
       "Hydrogen sulfide                -10.106159\n",
       "Indole                           -0.012591\n",
       "L-asparagine                     -0.053570\n",
       "L-aspartate(1-)                 -90.277755\n",
       "L-cysteinylglycine               -0.002508\n",
       "L-fucose                         -8.830317\n",
       "L-glutamate(1-)                  -5.171648\n",
       "L-histidine                      -0.021143\n",
       "L-leucine                        -0.100133\n",
       "L-phenylalanine                  -0.027876\n",
       "L-proline                       -31.902013\n",
       "L-serine                         -3.323203\n",
       "L-threonine                     -75.710833\n",
       "L-tyrosine                       -0.064381\n",
       "Menaquinone 8                    -0.000826\n",
       "Mn2+                             -0.000826\n",
       "N-acetyl-D-galactosamine         -0.000432\n",
       "N-acetyl-D-glucosamine           -5.016333\n",
       "N-acetylneuraminate              -3.360959\n",
       "O2                               -0.752554\n",
       "Protoheme                        -0.000826\n",
       "Spermidine                       -0.000826\n",
       "Succinate                       -13.802546\n",
       "Thiamin                          -0.000825\n",
       "Ubiquinone-8                     -0.000826\n",
       "Water                           -20.619941\n",
       "Zinc                             -0.000826\n",
       "acetaldehyde                    -60.724300\n",
       "acetate                         -16.612541\n",
       "calcium(2+)                      -0.000826\n",
       "carbon dioxide                  -84.643348\n",
       "ethanol                         -83.974809\n",
       "hydrogenphosphate                -0.441473\n",
       "laurate                          -8.938050\n",
       "magnesium                        -0.000826\n",
       "meso-2,6-Diaminoheptanedioate    -1.013601\n",
       "octadecanoate (n-C18:0)          -0.007777\n",
       "potassium                        -0.000826\n",
       "sulfate                          -0.624982\n",
       "uracil                           -0.009109\n",
       "Name: flux, dtype: float64"
      ]
     },
     "execution_count": 151,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_akkermansia = high_fiber_akkermansia_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_akkermansia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 152,
   "id": "beba6528-4980-418f-bb03-aaa92cb590f2",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_akkermansia_imports = pd.DataFrame (mean_import_of_western_akkermansia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 153,
   "id": "8b4a8617-2237-4452-ae60-7f2df9a63aac",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_akkermansia_imports.rename(columns={\"flux\": \"western_flux_akkermansia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 154,
   "id": "6999f3d3-c8f6-4ee3-91c5-62e27deb3a88",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_akkermansia</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-72.412195</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Alpha-1,3-Galactose-N-acetylgalactosamine</th>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Alpha-2,6-N-acetylneuraminate-N-acetylgalactosamine</th>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-27.286958</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released sialyl-Tn antigen</th>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-T antigen</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.196022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-0.013216</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>247 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_flux_akkermansia\n",
       "name                                                                        \n",
       "(S)-propane-1,2-diol                                              -72.412195\n",
       "Adenosine                                                          -0.000004\n",
       "Alpha-1,3-Galactose-N-acetylgalactosamine                          -0.000001\n",
       "Alpha-2,6-N-acetylneuraminate-N-acetylgalactosa...                 -0.000003\n",
       "Ammonium                                                          -27.286958\n",
       "...                                                                      ...\n",
       "released sialyl-Tn antigen                                         -0.000003\n",
       "sialyl-T antigen                                                   -0.000002\n",
       "sialyl-Tn antigen                                                  -0.000002\n",
       "sulfate                                                            -0.196022\n",
       "uracil                                                             -0.013216\n",
       "\n",
       "[247 rows x 1 columns]"
      ]
     },
     "execution_count": 154,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_akkermansia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 155,
   "id": "f7c47824-a088-47f2-916f-3fc8148820ad",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_akkermansia_imports = pd.DataFrame (mean_import_of_high_fiber_akkermansia, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 156,
   "id": "7d321030-3683-40bd-923c-554798d5d23b",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_akkermansia_imports.rename(columns={\"flux\": \"high_fiber_flux_akkermansia\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 157,
   "id": "1a4bdb6e-0029-4985-86f2-98fcb5be8958",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>high_fiber_flux_akkermansia</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-70.948112</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-15.552513</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Co2+</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cu2+</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cytidine</th>\n",
       "      <td>-0.031032</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-Fructose</th>\n",
       "      <td>-5.239300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-Glucosamine</th>\n",
       "      <td>-4.209554</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-glucose</th>\n",
       "      <td>-0.096235</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe2+</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe3+</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Glycine</th>\n",
       "      <td>-38.101644</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hexadecanoate (n-C16:0)</th>\n",
       "      <td>-0.312693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hydrogen</th>\n",
       "      <td>-7.145183</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hydrogen sulfide</th>\n",
       "      <td>-10.106159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Indole</th>\n",
       "      <td>-0.012591</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-asparagine</th>\n",
       "      <td>-0.053570</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-aspartate(1-)</th>\n",
       "      <td>-90.277755</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-cysteinylglycine</th>\n",
       "      <td>-0.002508</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-fucose</th>\n",
       "      <td>-8.830317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-glutamate(1-)</th>\n",
       "      <td>-5.171648</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-histidine</th>\n",
       "      <td>-0.021143</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-leucine</th>\n",
       "      <td>-0.100133</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-phenylalanine</th>\n",
       "      <td>-0.027876</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-proline</th>\n",
       "      <td>-31.902013</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-serine</th>\n",
       "      <td>-3.323203</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-threonine</th>\n",
       "      <td>-75.710833</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-tyrosine</th>\n",
       "      <td>-0.064381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Menaquinone 8</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Mn2+</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetyl-D-galactosamine</th>\n",
       "      <td>-0.000432</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetyl-D-glucosamine</th>\n",
       "      <td>-5.016333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetylneuraminate</th>\n",
       "      <td>-3.360959</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>O2</th>\n",
       "      <td>-0.752554</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Protoheme</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Spermidine</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Succinate</th>\n",
       "      <td>-13.802546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thiamin</th>\n",
       "      <td>-0.000825</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ubiquinone-8</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Water</th>\n",
       "      <td>-20.619941</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zinc</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetaldehyde</th>\n",
       "      <td>-60.724300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetate</th>\n",
       "      <td>-16.612541</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>calcium(2+)</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>carbon dioxide</th>\n",
       "      <td>-84.643348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ethanol</th>\n",
       "      <td>-83.974809</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hydrogenphosphate</th>\n",
       "      <td>-0.441473</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>laurate</th>\n",
       "      <td>-8.938050</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>magnesium</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>meso-2,6-Diaminoheptanedioate</th>\n",
       "      <td>-1.013601</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.007777</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.624982</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-0.009109</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                               high_fiber_flux_akkermansia\n",
       "name                                                      \n",
       "(S)-propane-1,2-diol                            -70.948112\n",
       "Adenosine                                        -0.000001\n",
       "Ammonium                                        -15.552513\n",
       "Chloride                                         -0.000826\n",
       "Co2+                                             -0.000826\n",
       "Cu2+                                             -0.000826\n",
       "Cytidine                                         -0.031032\n",
       "D-Fructose                                       -5.239300\n",
       "D-Glucosamine                                    -4.209554\n",
       "D-glucose                                        -0.096235\n",
       "Fe2+                                             -0.000826\n",
       "Fe3+                                             -0.000826\n",
       "Glycine                                         -38.101644\n",
       "Hexadecanoate (n-C16:0)                          -0.312693\n",
       "Hydrogen                                         -7.145183\n",
       "Hydrogen sulfide                                -10.106159\n",
       "Indole                                           -0.012591\n",
       "L-asparagine                                     -0.053570\n",
       "L-aspartate(1-)                                 -90.277755\n",
       "L-cysteinylglycine                               -0.002508\n",
       "L-fucose                                         -8.830317\n",
       "L-glutamate(1-)                                  -5.171648\n",
       "L-histidine                                      -0.021143\n",
       "L-leucine                                        -0.100133\n",
       "L-phenylalanine                                  -0.027876\n",
       "L-proline                                       -31.902013\n",
       "L-serine                                         -3.323203\n",
       "L-threonine                                     -75.710833\n",
       "L-tyrosine                                       -0.064381\n",
       "Menaquinone 8                                    -0.000826\n",
       "Mn2+                                             -0.000826\n",
       "N-acetyl-D-galactosamine                         -0.000432\n",
       "N-acetyl-D-glucosamine                           -5.016333\n",
       "N-acetylneuraminate                              -3.360959\n",
       "O2                                               -0.752554\n",
       "Protoheme                                        -0.000826\n",
       "Spermidine                                       -0.000826\n",
       "Succinate                                       -13.802546\n",
       "Thiamin                                          -0.000825\n",
       "Ubiquinone-8                                     -0.000826\n",
       "Water                                           -20.619941\n",
       "Zinc                                             -0.000826\n",
       "acetaldehyde                                    -60.724300\n",
       "acetate                                         -16.612541\n",
       "calcium(2+)                                      -0.000826\n",
       "carbon dioxide                                  -84.643348\n",
       "ethanol                                         -83.974809\n",
       "hydrogenphosphate                                -0.441473\n",
       "laurate                                          -8.938050\n",
       "magnesium                                        -0.000826\n",
       "meso-2,6-Diaminoheptanedioate                    -1.013601\n",
       "octadecanoate (n-C18:0)                          -0.007777\n",
       "potassium                                        -0.000826\n",
       "sulfate                                          -0.624982\n",
       "uracil                                           -0.009109"
      ]
     },
     "execution_count": 157,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_akkermansia_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 158,
   "id": "8b147da2-1abf-4b83-99fb-84f4071cd22c",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_akkermansia = pd.concat([western_akkermansia_imports['western_flux_akkermansia'], high_fiber_akkermansia_imports['high_fiber_flux_akkermansia']], axis=1, keys= ['western_akkermansia_imports', 'high_fiber_akkermansia_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 159,
   "id": "696bba9f-d6af-48cb-a24f-51fc92fb857e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_akkermansia_imports</th>\n",
       "      <th>high_fiber_akkermansia_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-72.412195</td>\n",
       "      <td>-70.948112</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-0.000004</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Alpha-1,3-Galactose-N-acetylgalactosamine</th>\n",
       "      <td>-0.000001</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Alpha-2,6-N-acetylneuraminate-N-acetylgalactosamine</th>\n",
       "      <td>-0.000003</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-27.286958</td>\n",
       "      <td>-15.552513</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released sialyl-Tn antigen</th>\n",
       "      <td>-0.000003</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-T antigen</th>\n",
       "      <td>-0.000002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sialyl-Tn antigen</th>\n",
       "      <td>-0.000002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.196022</td>\n",
       "      <td>-0.624982</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-0.013216</td>\n",
       "      <td>-0.009109</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>247 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    western_akkermansia_imports  \\\n",
       "name                                                                              \n",
       "(S)-propane-1,2-diol                                                 -72.412195   \n",
       "Adenosine                                                             -0.000004   \n",
       "Alpha-1,3-Galactose-N-acetylgalactosamine                             -0.000001   \n",
       "Alpha-2,6-N-acetylneuraminate-N-acetylgalactosa...                    -0.000003   \n",
       "Ammonium                                                             -27.286958   \n",
       "...                                                                         ...   \n",
       "released sialyl-Tn antigen                                            -0.000003   \n",
       "sialyl-T antigen                                                      -0.000002   \n",
       "sialyl-Tn antigen                                                     -0.000002   \n",
       "sulfate                                                               -0.196022   \n",
       "uracil                                                                -0.013216   \n",
       "\n",
       "                                                    high_fiber_akkermansia_imports  \n",
       "name                                                                                \n",
       "(S)-propane-1,2-diol                                                    -70.948112  \n",
       "Adenosine                                                                -0.000001  \n",
       "Alpha-1,3-Galactose-N-acetylgalactosamine                                      NaN  \n",
       "Alpha-2,6-N-acetylneuraminate-N-acetylgalactosa...                             NaN  \n",
       "Ammonium                                                                -15.552513  \n",
       "...                                                                            ...  \n",
       "released sialyl-Tn antigen                                                     NaN  \n",
       "sialyl-T antigen                                                               NaN  \n",
       "sialyl-Tn antigen                                                              NaN  \n",
       "sulfate                                                                  -0.624982  \n",
       "uracil                                                                   -0.009109  \n",
       "\n",
       "[247 rows x 2 columns]"
      ]
     },
     "execution_count": 159,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_akkermansia"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 160,
   "id": "f167be59-23cb-491c-942e-5db3052acebc",
   "metadata": {},
   "outputs": [],
   "source": [
    "akkermansia_imports_for_both_diets = combined_diet_fluxes_akkermansia.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 161,
   "id": "1287c9ff-6daa-49f5-ade1-2937d6ef363b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_akkermansia_imports</th>\n",
       "      <th>high_fiber_akkermansia_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>(S)-propane-1,2-diol</th>\n",
       "      <td>-72.412195</td>\n",
       "      <td>-70.948112</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-0.000004</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-27.286958</td>\n",
       "      <td>-15.552513</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Co2+</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cu2+</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cytidine</th>\n",
       "      <td>-0.046708</td>\n",
       "      <td>-0.031032</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-Fructose</th>\n",
       "      <td>-6.403369</td>\n",
       "      <td>-5.239300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-Glucosamine</th>\n",
       "      <td>-5.039943</td>\n",
       "      <td>-4.209554</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-glucose</th>\n",
       "      <td>-0.134181</td>\n",
       "      <td>-0.096235</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe2+</th>\n",
       "      <td>-0.000452</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe3+</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Glycine</th>\n",
       "      <td>-50.362016</td>\n",
       "      <td>-38.101644</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hexadecanoate (n-C16:0)</th>\n",
       "      <td>-0.102622</td>\n",
       "      <td>-0.312693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hydrogen</th>\n",
       "      <td>-7.932640</td>\n",
       "      <td>-7.145183</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Hydrogen sulfide</th>\n",
       "      <td>-12.109352</td>\n",
       "      <td>-10.106159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Indole</th>\n",
       "      <td>-0.006882</td>\n",
       "      <td>-0.012591</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-asparagine</th>\n",
       "      <td>-0.029279</td>\n",
       "      <td>-0.053570</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-aspartate(1-)</th>\n",
       "      <td>-89.864216</td>\n",
       "      <td>-90.277755</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-cysteinylglycine</th>\n",
       "      <td>-0.078959</td>\n",
       "      <td>-0.002508</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-fucose</th>\n",
       "      <td>-3.687175</td>\n",
       "      <td>-8.830317</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-glutamate(1-)</th>\n",
       "      <td>-4.383999</td>\n",
       "      <td>-5.171648</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-histidine</th>\n",
       "      <td>-0.011556</td>\n",
       "      <td>-0.021143</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-leucine</th>\n",
       "      <td>-0.040049</td>\n",
       "      <td>-0.100133</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-phenylalanine</th>\n",
       "      <td>-0.019912</td>\n",
       "      <td>-0.027876</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-proline</th>\n",
       "      <td>-27.045172</td>\n",
       "      <td>-31.902013</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-serine</th>\n",
       "      <td>-8.280051</td>\n",
       "      <td>-3.323203</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-threonine</th>\n",
       "      <td>-80.530178</td>\n",
       "      <td>-75.710833</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-tyrosine</th>\n",
       "      <td>-0.030141</td>\n",
       "      <td>-0.064381</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Menaquinone 8</th>\n",
       "      <td>-0.000452</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Mn2+</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetyl-D-galactosamine</th>\n",
       "      <td>-0.000069</td>\n",
       "      <td>-0.000432</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetyl-D-glucosamine</th>\n",
       "      <td>-6.047826</td>\n",
       "      <td>-5.016333</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>N-acetylneuraminate</th>\n",
       "      <td>-4.143576</td>\n",
       "      <td>-3.360959</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>O2</th>\n",
       "      <td>-0.739859</td>\n",
       "      <td>-0.752554</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Protoheme</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Spermidine</th>\n",
       "      <td>-0.000453</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Succinate</th>\n",
       "      <td>-19.209017</td>\n",
       "      <td>-13.802546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thiamin</th>\n",
       "      <td>-0.000456</td>\n",
       "      <td>-0.000825</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ubiquinone-8</th>\n",
       "      <td>-0.000452</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Water</th>\n",
       "      <td>-20.455297</td>\n",
       "      <td>-20.619941</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zinc</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetaldehyde</th>\n",
       "      <td>-62.422946</td>\n",
       "      <td>-60.724300</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetate</th>\n",
       "      <td>-23.401726</td>\n",
       "      <td>-16.612541</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>calcium(2+)</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>carbon dioxide</th>\n",
       "      <td>-82.652359</td>\n",
       "      <td>-84.643348</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ethanol</th>\n",
       "      <td>-84.779249</td>\n",
       "      <td>-83.974809</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hydrogenphosphate</th>\n",
       "      <td>-0.242483</td>\n",
       "      <td>-0.441473</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>laurate</th>\n",
       "      <td>-10.572231</td>\n",
       "      <td>-8.938050</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>magnesium</th>\n",
       "      <td>-0.000452</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>meso-2,6-Diaminoheptanedioate</th>\n",
       "      <td>-0.646182</td>\n",
       "      <td>-1.013601</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.005321</td>\n",
       "      <td>-0.007777</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000451</td>\n",
       "      <td>-0.000826</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.196022</td>\n",
       "      <td>-0.624982</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-0.013216</td>\n",
       "      <td>-0.009109</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                               western_akkermansia_imports  \\\n",
       "name                                                         \n",
       "(S)-propane-1,2-diol                            -72.412195   \n",
       "Adenosine                                        -0.000004   \n",
       "Ammonium                                        -27.286958   \n",
       "Chloride                                         -0.000451   \n",
       "Co2+                                             -0.000451   \n",
       "Cu2+                                             -0.000451   \n",
       "Cytidine                                         -0.046708   \n",
       "D-Fructose                                       -6.403369   \n",
       "D-Glucosamine                                    -5.039943   \n",
       "D-glucose                                        -0.134181   \n",
       "Fe2+                                             -0.000452   \n",
       "Fe3+                                             -0.000451   \n",
       "Glycine                                         -50.362016   \n",
       "Hexadecanoate (n-C16:0)                          -0.102622   \n",
       "Hydrogen                                         -7.932640   \n",
       "Hydrogen sulfide                                -12.109352   \n",
       "Indole                                           -0.006882   \n",
       "L-asparagine                                     -0.029279   \n",
       "L-aspartate(1-)                                 -89.864216   \n",
       "L-cysteinylglycine                               -0.078959   \n",
       "L-fucose                                         -3.687175   \n",
       "L-glutamate(1-)                                  -4.383999   \n",
       "L-histidine                                      -0.011556   \n",
       "L-leucine                                        -0.040049   \n",
       "L-phenylalanine                                  -0.019912   \n",
       "L-proline                                       -27.045172   \n",
       "L-serine                                         -8.280051   \n",
       "L-threonine                                     -80.530178   \n",
       "L-tyrosine                                       -0.030141   \n",
       "Menaquinone 8                                    -0.000452   \n",
       "Mn2+                                             -0.000451   \n",
       "N-acetyl-D-galactosamine                         -0.000069   \n",
       "N-acetyl-D-glucosamine                           -6.047826   \n",
       "N-acetylneuraminate                              -4.143576   \n",
       "O2                                               -0.739859   \n",
       "Protoheme                                        -0.000451   \n",
       "Spermidine                                       -0.000453   \n",
       "Succinate                                       -19.209017   \n",
       "Thiamin                                          -0.000456   \n",
       "Ubiquinone-8                                     -0.000452   \n",
       "Water                                           -20.455297   \n",
       "Zinc                                             -0.000451   \n",
       "acetaldehyde                                    -62.422946   \n",
       "acetate                                         -23.401726   \n",
       "calcium(2+)                                      -0.000451   \n",
       "carbon dioxide                                  -82.652359   \n",
       "ethanol                                         -84.779249   \n",
       "hydrogenphosphate                                -0.242483   \n",
       "laurate                                         -10.572231   \n",
       "magnesium                                        -0.000452   \n",
       "meso-2,6-Diaminoheptanedioate                    -0.646182   \n",
       "octadecanoate (n-C18:0)                          -0.005321   \n",
       "potassium                                        -0.000451   \n",
       "sulfate                                          -0.196022   \n",
       "uracil                                           -0.013216   \n",
       "\n",
       "                               high_fiber_akkermansia_imports  \n",
       "name                                                           \n",
       "(S)-propane-1,2-diol                               -70.948112  \n",
       "Adenosine                                           -0.000001  \n",
       "Ammonium                                           -15.552513  \n",
       "Chloride                                            -0.000826  \n",
       "Co2+                                                -0.000826  \n",
       "Cu2+                                                -0.000826  \n",
       "Cytidine                                            -0.031032  \n",
       "D-Fructose                                          -5.239300  \n",
       "D-Glucosamine                                       -4.209554  \n",
       "D-glucose                                           -0.096235  \n",
       "Fe2+                                                -0.000826  \n",
       "Fe3+                                                -0.000826  \n",
       "Glycine                                            -38.101644  \n",
       "Hexadecanoate (n-C16:0)                             -0.312693  \n",
       "Hydrogen                                            -7.145183  \n",
       "Hydrogen sulfide                                   -10.106159  \n",
       "Indole                                              -0.012591  \n",
       "L-asparagine                                        -0.053570  \n",
       "L-aspartate(1-)                                    -90.277755  \n",
       "L-cysteinylglycine                                  -0.002508  \n",
       "L-fucose                                            -8.830317  \n",
       "L-glutamate(1-)                                     -5.171648  \n",
       "L-histidine                                         -0.021143  \n",
       "L-leucine                                           -0.100133  \n",
       "L-phenylalanine                                     -0.027876  \n",
       "L-proline                                          -31.902013  \n",
       "L-serine                                            -3.323203  \n",
       "L-threonine                                        -75.710833  \n",
       "L-tyrosine                                          -0.064381  \n",
       "Menaquinone 8                                       -0.000826  \n",
       "Mn2+                                                -0.000826  \n",
       "N-acetyl-D-galactosamine                            -0.000432  \n",
       "N-acetyl-D-glucosamine                              -5.016333  \n",
       "N-acetylneuraminate                                 -3.360959  \n",
       "O2                                                  -0.752554  \n",
       "Protoheme                                           -0.000826  \n",
       "Spermidine                                          -0.000826  \n",
       "Succinate                                          -13.802546  \n",
       "Thiamin                                             -0.000825  \n",
       "Ubiquinone-8                                        -0.000826  \n",
       "Water                                              -20.619941  \n",
       "Zinc                                                -0.000826  \n",
       "acetaldehyde                                       -60.724300  \n",
       "acetate                                            -16.612541  \n",
       "calcium(2+)                                         -0.000826  \n",
       "carbon dioxide                                     -84.643348  \n",
       "ethanol                                            -83.974809  \n",
       "hydrogenphosphate                                   -0.441473  \n",
       "laurate                                             -8.938050  \n",
       "magnesium                                           -0.000826  \n",
       "meso-2,6-Diaminoheptanedioate                       -1.013601  \n",
       "octadecanoate (n-C18:0)                             -0.007777  \n",
       "potassium                                           -0.000826  \n",
       "sulfate                                             -0.624982  \n",
       "uracil                                              -0.009109  "
      ]
     },
     "execution_count": 161,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "akkermansia_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 162,
   "id": "e6391a87-b332-4c75-bdad-f89d2c3a5c37",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "21.97892630802339"
      ]
     },
     "execution_count": 162,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "akkermansia_euclidean_distance = ((akkermansia_imports_for_both_diets.western_akkermansia_imports - akkermansia_imports_for_both_diets.high_fiber_akkermansia_imports)**2).sum()**(1/2)\n",
    "\n",
    "akkermansia_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a8a6734c-6dc9-4c24-b95a-a59b7687e6e6",
   "metadata": {},
   "source": [
    "# Paraprevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 163,
   "id": "67340800-6d12-413e-a960-76d0204630a5",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 163,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 164,
   "id": "d9a0ec99-6da7-4e27-b895-646b92c47a19",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>358</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032287</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.015989</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>527</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032308</td>\n",
       "      <td>western</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.128883</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2899</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032195</td>\n",
       "      <td>western</td>\n",
       "      <td>D-Galactose</td>\n",
       "      <td>-0.048843</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2959</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032314</td>\n",
       "      <td>western</td>\n",
       "      <td>D-Galactose</td>\n",
       "      <td>-0.057318</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2983</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032331</td>\n",
       "      <td>western</td>\n",
       "      <td>D-Galactose</td>\n",
       "      <td>-0.022026</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104373</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032313</td>\n",
       "      <td>western</td>\n",
       "      <td>4-Aminobenzoate</td>\n",
       "      <td>-0.000894</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104374</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032314</td>\n",
       "      <td>western</td>\n",
       "      <td>4-Aminobenzoate</td>\n",
       "      <td>-0.000935</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104375</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032308</td>\n",
       "      <td>western</td>\n",
       "      <td>4-Aminobenzoate</td>\n",
       "      <td>-0.001208</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104376</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032331</td>\n",
       "      <td>western</td>\n",
       "      <td>4-Aminobenzoate</td>\n",
       "      <td>-0.001220</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104377</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032330</td>\n",
       "      <td>western</td>\n",
       "      <td>4-Aminobenzoate</td>\n",
       "      <td>-0.001089</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>476 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 taxon direction    sample_id   medium               name  \\\n",
       "358     Paraprevotella    import  SRR15032287  western  hydrogenphosphate   \n",
       "527     Paraprevotella    import  SRR15032308  western  hydrogenphosphate   \n",
       "2899    Paraprevotella    import  SRR15032195  western        D-Galactose   \n",
       "2959    Paraprevotella    import  SRR15032314  western        D-Galactose   \n",
       "2983    Paraprevotella    import  SRR15032331  western        D-Galactose   \n",
       "...                ...       ...          ...      ...                ...   \n",
       "104373  Paraprevotella    import  SRR15032313  western    4-Aminobenzoate   \n",
       "104374  Paraprevotella    import  SRR15032314  western    4-Aminobenzoate   \n",
       "104375  Paraprevotella    import  SRR15032308  western    4-Aminobenzoate   \n",
       "104376  Paraprevotella    import  SRR15032331  western    4-Aminobenzoate   \n",
       "104377  Paraprevotella    import  SRR15032330  western    4-Aminobenzoate   \n",
       "\n",
       "            flux  \n",
       "358    -0.015989  \n",
       "527    -0.128883  \n",
       "2899   -0.048843  \n",
       "2959   -0.057318  \n",
       "2983   -0.022026  \n",
       "...          ...  \n",
       "104373 -0.000894  \n",
       "104374 -0.000935  \n",
       "104375 -0.001208  \n",
       "104376 -0.001220  \n",
       "104377 -0.001089  \n",
       "\n",
       "[476 rows x 6 columns]"
      ]
     },
     "execution_count": 164,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_paraprevotella_only = western_only.loc[western_only['taxon'] == 'Paraprevotella']\n",
    "western_paraprevotella_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 165,
   "id": "ac9f787a-0169-4088-a9be-51b3a535f598",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "2-deoxyadenosine                     -15.940884\n",
       "4-Aminobenzoate                       -0.000866\n",
       "4-hydroxybenzoate                     -0.000468\n",
       "AMP                                   -0.203012\n",
       "Adenosine                            -29.210891\n",
       "                                        ...    \n",
       "released mucin-type O-glycan No 22    -0.000006\n",
       "released mucin-type O-glycan No 3     -0.000001\n",
       "sulfate                               -0.000450\n",
       "tetradecanoate (n-C14:0)              -0.021832\n",
       "uracil                               -54.776683\n",
       "Name: flux, Length: 66, dtype: float64"
      ]
     },
     "execution_count": 165,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_paraprevotella = western_paraprevotella_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_paraprevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 166,
   "id": "a44fb832-4a7c-42c3-9880-fa35670c9c4c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "    }\n",
       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 166,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 167,
   "id": "9e20ddaa-f971-4290-af4f-18d4a94bf04a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>150</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032110</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.244693</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>160</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032119</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.042179</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>172</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032117</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.334265</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>461</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032312</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.030583</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>484</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032321</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.229457</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102563</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032329</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.056107</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102611</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032372</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.002830</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102703</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032456</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.008641</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102705</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032455</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.015942</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102730</th>\n",
       "      <td>Paraprevotella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032494</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>octadecanoate (n-C18:0)</td>\n",
       "      <td>-0.007518</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>566 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 taxon direction    sample_id      medium  \\\n",
       "150     Paraprevotella    import  SRR15032110  high_fiber   \n",
       "160     Paraprevotella    import  SRR15032119  high_fiber   \n",
       "172     Paraprevotella    import  SRR15032117  high_fiber   \n",
       "461     Paraprevotella    import  SRR15032312  high_fiber   \n",
       "484     Paraprevotella    import  SRR15032321  high_fiber   \n",
       "...                ...       ...          ...         ...   \n",
       "102563  Paraprevotella    import  SRR15032329  high_fiber   \n",
       "102611  Paraprevotella    import  SRR15032372  high_fiber   \n",
       "102703  Paraprevotella    import  SRR15032456  high_fiber   \n",
       "102705  Paraprevotella    import  SRR15032455  high_fiber   \n",
       "102730  Paraprevotella    import  SRR15032494  high_fiber   \n",
       "\n",
       "                           name      flux  \n",
       "150           hydrogenphosphate -0.244693  \n",
       "160           hydrogenphosphate -0.042179  \n",
       "172           hydrogenphosphate -0.334265  \n",
       "461           hydrogenphosphate -0.030583  \n",
       "484           hydrogenphosphate -0.229457  \n",
       "...                         ...       ...  \n",
       "102563  octadecanoate (n-C18:0) -0.056107  \n",
       "102611  octadecanoate (n-C18:0) -0.002830  \n",
       "102703  octadecanoate (n-C18:0) -0.008641  \n",
       "102705  octadecanoate (n-C18:0) -0.015942  \n",
       "102730  octadecanoate (n-C18:0) -0.007518  \n",
       "\n",
       "[566 rows x 6 columns]"
      ]
     },
     "execution_count": 167,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_paraprevotella_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Paraprevotella']\n",
    "high_fiber_paraprevotella_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 168,
   "id": "b4f1a241-d422-44cf-92d3-20ac11ae6c16",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "2-deoxyadenosine           -23.035010\n",
       "4-hydroxybenzoate           -0.000804\n",
       "Adenine                     -7.558186\n",
       "Adenosine                  -23.061214\n",
       "Ammonium                   -11.335716\n",
       "                              ...    \n",
       "potassium                   -0.000804\n",
       "proton                     -81.691022\n",
       "sulfate                     -0.000804\n",
       "tetradecanoate (n-C14:0)    -0.038975\n",
       "uracil                     -58.973646\n",
       "Name: flux, Length: 62, dtype: float64"
      ]
     },
     "execution_count": 168,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_paraprevotella = high_fiber_paraprevotella_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_paraprevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 169,
   "id": "ba0ab844-bbf9-429e-be72-3d37d2d1c14d",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_paraprevotella_imports = pd.DataFrame (mean_import_of_western_paraprevotella, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 170,
   "id": "e653c941-7d9f-4254-8036-f9e3fe2e365e",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_paraprevotella_imports.rename(columns={\"flux\": \"western_flux_paraprevotella\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 171,
   "id": "a2dc7351-55e6-4f9d-b061-8fec61d07023",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_flux_paraprevotella</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-15.940884</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-Aminobenzoate</th>\n",
       "      <td>-0.000866</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-0.000468</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AMP</th>\n",
       "      <td>-0.203012</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-29.210891</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released mucin-type O-glycan No 22</th>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>released mucin-type O-glycan No 3</th>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000450</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.021832</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-54.776683</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>66 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                    western_flux_paraprevotella\n",
       "name                                                           \n",
       "2-deoxyadenosine                                     -15.940884\n",
       "4-Aminobenzoate                                       -0.000866\n",
       "4-hydroxybenzoate                                     -0.000468\n",
       "AMP                                                   -0.203012\n",
       "Adenosine                                            -29.210891\n",
       "...                                                         ...\n",
       "released mucin-type O-glycan No 22                    -0.000006\n",
       "released mucin-type O-glycan No 3                     -0.000001\n",
       "sulfate                                               -0.000450\n",
       "tetradecanoate (n-C14:0)                              -0.021832\n",
       "uracil                                               -54.776683\n",
       "\n",
       "[66 rows x 1 columns]"
      ]
     },
     "execution_count": 171,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_paraprevotella_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "id": "3b6aee1f-6204-4dce-85ed-cec8e1396453",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_paraprevotella_imports = pd.DataFrame (mean_import_of_high_fiber_paraprevotella, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 173,
   "id": "52656954-06de-40d7-9acb-314428c05c27",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_paraprevotella_imports.rename(columns={\"flux\": \"high_fiber_flux_paraprevotella\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 174,
   "id": "15a6cc8b-6695-417f-9a04-9a497df8e8ba",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>high_fiber_flux_paraprevotella</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-23.035010</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenine</th>\n",
       "      <td>-7.558186</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-23.061214</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-11.335716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
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       "      <th>proton</th>\n",
       "      <td>-81.691022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.038975</td>\n",
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       "    <tr>\n",
       "      <th>uracil</th>\n",
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       "<p>62 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_paraprevotella\n",
       "name                                                    \n",
       "2-deoxyadenosine                              -23.035010\n",
       "4-hydroxybenzoate                              -0.000804\n",
       "Adenine                                        -7.558186\n",
       "Adenosine                                     -23.061214\n",
       "Ammonium                                      -11.335716\n",
       "...                                                  ...\n",
       "potassium                                      -0.000804\n",
       "proton                                        -81.691022\n",
       "sulfate                                        -0.000804\n",
       "tetradecanoate (n-C14:0)                       -0.038975\n",
       "uracil                                        -58.973646\n",
       "\n",
       "[62 rows x 1 columns]"
      ]
     },
     "execution_count": 174,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_paraprevotella_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 175,
   "id": "5f3d7b08-01a4-4563-a10f-c47ed5123fa1",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_paraprevotella = pd.concat([western_paraprevotella_imports['western_flux_paraprevotella'], high_fiber_paraprevotella_imports['high_fiber_flux_paraprevotella']], axis=1, keys= ['western_paraprevotella_imports', 'high_fiber_paraprevotella_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 176,
   "id": "ce66abce-6112-449d-9e0a-d69754c7c866",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_paraprevotella_imports</th>\n",
       "      <th>high_fiber_paraprevotella_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-15.940884</td>\n",
       "      <td>-23.035010</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-Aminobenzoate</th>\n",
       "      <td>-0.000866</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-0.000468</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AMP</th>\n",
       "      <td>-0.203012</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-29.210891</td>\n",
       "      <td>-23.061214</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-valine</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.043497</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>O2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.000113</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Riboflavin</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.001263</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thymidine</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.002537</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>chorismate</th>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.083587</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>74 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   western_paraprevotella_imports  \\\n",
       "name                                                \n",
       "2-deoxyadenosine                       -15.940884   \n",
       "4-Aminobenzoate                         -0.000866   \n",
       "4-hydroxybenzoate                       -0.000468   \n",
       "AMP                                     -0.203012   \n",
       "Adenosine                              -29.210891   \n",
       "...                                           ...   \n",
       "L-valine                                      NaN   \n",
       "O2                                            NaN   \n",
       "Riboflavin                                    NaN   \n",
       "Thymidine                                     NaN   \n",
       "chorismate                                    NaN   \n",
       "\n",
       "                   high_fiber_paraprevotella_imports  \n",
       "name                                                  \n",
       "2-deoxyadenosine                          -23.035010  \n",
       "4-Aminobenzoate                                  NaN  \n",
       "4-hydroxybenzoate                          -0.000804  \n",
       "AMP                                              NaN  \n",
       "Adenosine                                 -23.061214  \n",
       "...                                              ...  \n",
       "L-valine                                   -0.043497  \n",
       "O2                                         -0.000113  \n",
       "Riboflavin                                 -0.001263  \n",
       "Thymidine                                  -0.002537  \n",
       "chorismate                                 -0.083587  \n",
       "\n",
       "[74 rows x 2 columns]"
      ]
     },
     "execution_count": 176,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_paraprevotella"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 177,
   "id": "d28b6817-6244-4792-957b-9a7a30b1b328",
   "metadata": {},
   "outputs": [],
   "source": [
    "paraprevotella_imports_for_both_diets = combined_diet_fluxes_paraprevotella.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 178,
   "id": "24fae448-a7c1-4b07-a1be-161a8201fd77",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_paraprevotella_imports</th>\n",
       "      <th>high_fiber_paraprevotella_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-15.940884</td>\n",
       "      <td>-23.035010</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4-hydroxybenzoate</th>\n",
       "      <td>-0.000468</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Adenosine</th>\n",
       "      <td>-29.210891</td>\n",
       "      <td>-23.061214</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ammonium</th>\n",
       "      <td>-10.140805</td>\n",
       "      <td>-11.335716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chloride</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Citrate</th>\n",
       "      <td>-45.074534</td>\n",
       "      <td>-38.879291</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Co2+</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cu2+</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cytidine</th>\n",
       "      <td>-45.174282</td>\n",
       "      <td>-6.229609</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-glucose</th>\n",
       "      <td>-0.019727</td>\n",
       "      <td>-0.024099</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>D-glucuronate</th>\n",
       "      <td>-0.000873</td>\n",
       "      <td>-0.001509</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Deoxyguanosine</th>\n",
       "      <td>-16.731900</td>\n",
       "      <td>-14.956636</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe2+</th>\n",
       "      <td>-0.000571</td>\n",
       "      <td>-0.001149</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Fe3+</th>\n",
       "      <td>-0.000413</td>\n",
       "      <td>-0.001380</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Glycerol</th>\n",
       "      <td>-17.593920</td>\n",
       "      <td>-18.411577</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Guanine</th>\n",
       "      <td>-33.021703</td>\n",
       "      <td>-27.561451</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Inosine</th>\n",
       "      <td>-13.975398</td>\n",
       "      <td>-15.561849</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-alanine</th>\n",
       "      <td>-0.073172</td>\n",
       "      <td>-0.130629</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-asparagine</th>\n",
       "      <td>-20.142935</td>\n",
       "      <td>-23.514413</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-aspartate(1-)</th>\n",
       "      <td>-79.536685</td>\n",
       "      <td>-81.696503</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-cysteinylglycine</th>\n",
       "      <td>-0.006522</td>\n",
       "      <td>-0.010229</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-fucose</th>\n",
       "      <td>-12.075688</td>\n",
       "      <td>-16.434108</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-glutamate(1-)</th>\n",
       "      <td>-29.142703</td>\n",
       "      <td>-23.332489</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-glutamine</th>\n",
       "      <td>-13.758310</td>\n",
       "      <td>-14.901524</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-methionine</th>\n",
       "      <td>-0.024502</td>\n",
       "      <td>-0.050263</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-phenylalanine</th>\n",
       "      <td>-0.017200</td>\n",
       "      <td>-0.038370</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>L-threonine</th>\n",
       "      <td>-42.584992</td>\n",
       "      <td>-36.481785</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Maltose</th>\n",
       "      <td>-0.002756</td>\n",
       "      <td>-0.031642</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Menaquinone 8</th>\n",
       "      <td>-0.000221</td>\n",
       "      <td>-0.000876</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Mn2+</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Nicotinamide</th>\n",
       "      <td>-3.211402</td>\n",
       "      <td>-1.240513</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Nicotinate</th>\n",
       "      <td>-2.200344</td>\n",
       "      <td>-2.694991</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Protoheme</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Reduced glutathione</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Siroheme</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Spermidine</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Thiamin</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Urea</th>\n",
       "      <td>-8.113605</td>\n",
       "      <td>-7.047532</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Uridine</th>\n",
       "      <td>-30.554630</td>\n",
       "      <td>-28.759788</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Water</th>\n",
       "      <td>-24.116119</td>\n",
       "      <td>-27.303574</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Xanthine</th>\n",
       "      <td>-6.712875</td>\n",
       "      <td>-10.806284</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zinc</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetaldehyde</th>\n",
       "      <td>-24.762451</td>\n",
       "      <td>-39.846483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>acetate</th>\n",
       "      <td>-2.085388</td>\n",
       "      <td>-14.355037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>calcium(2+)</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hydrogenphosphate</th>\n",
       "      <td>-0.072436</td>\n",
       "      <td>-0.210836</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>magnesium</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>meso-2,6-Diaminoheptanedioate</th>\n",
       "      <td>-1.228526</td>\n",
       "      <td>-1.188592</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>octadecanoate (n-C18:0)</th>\n",
       "      <td>-0.012387</td>\n",
       "      <td>-0.022124</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>proton</th>\n",
       "      <td>-77.750909</td>\n",
       "      <td>-81.691022</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000450</td>\n",
       "      <td>-0.000804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.021832</td>\n",
       "      <td>-0.038975</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>uracil</th>\n",
       "      <td>-54.776683</td>\n",
       "      <td>-58.973646</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                               western_paraprevotella_imports  \\\n",
       "name                                                            \n",
       "2-deoxyadenosine                                   -15.940884   \n",
       "4-hydroxybenzoate                                   -0.000468   \n",
       "Adenosine                                          -29.210891   \n",
       "Ammonium                                           -10.140805   \n",
       "Chloride                                            -0.000450   \n",
       "Citrate                                            -45.074534   \n",
       "Co2+                                                -0.000450   \n",
       "Cu2+                                                -0.000450   \n",
       "Cytidine                                           -45.174282   \n",
       "D-glucose                                           -0.019727   \n",
       "D-glucuronate                                       -0.000873   \n",
       "Deoxyguanosine                                     -16.731900   \n",
       "Fe2+                                                -0.000571   \n",
       "Fe3+                                                -0.000413   \n",
       "Glycerol                                           -17.593920   \n",
       "Guanine                                            -33.021703   \n",
       "Inosine                                            -13.975398   \n",
       "L-alanine                                           -0.073172   \n",
       "L-asparagine                                       -20.142935   \n",
       "L-aspartate(1-)                                    -79.536685   \n",
       "L-cysteinylglycine                                  -0.006522   \n",
       "L-fucose                                           -12.075688   \n",
       "L-glutamate(1-)                                    -29.142703   \n",
       "L-glutamine                                        -13.758310   \n",
       "L-methionine                                        -0.024502   \n",
       "L-phenylalanine                                     -0.017200   \n",
       "L-threonine                                        -42.584992   \n",
       "Maltose                                             -0.002756   \n",
       "Menaquinone 8                                       -0.000221   \n",
       "Mn2+                                                -0.000450   \n",
       "Nicotinamide                                        -3.211402   \n",
       "Nicotinate                                          -2.200344   \n",
       "Protoheme                                           -0.000450   \n",
       "Reduced glutathione                                 -0.000450   \n",
       "Siroheme                                            -0.000450   \n",
       "Spermidine                                          -0.000450   \n",
       "Thiamin                                             -0.000450   \n",
       "Urea                                                -8.113605   \n",
       "Uridine                                            -30.554630   \n",
       "Water                                              -24.116119   \n",
       "Xanthine                                            -6.712875   \n",
       "Zinc                                                -0.000450   \n",
       "acetaldehyde                                       -24.762451   \n",
       "acetate                                             -2.085388   \n",
       "calcium(2+)                                         -0.000450   \n",
       "hydrogenphosphate                                   -0.072436   \n",
       "magnesium                                           -0.000450   \n",
       "meso-2,6-Diaminoheptanedioate                       -1.228526   \n",
       "octadecanoate (n-C18:0)                             -0.012387   \n",
       "potassium                                           -0.000450   \n",
       "proton                                             -77.750909   \n",
       "sulfate                                             -0.000450   \n",
       "tetradecanoate (n-C14:0)                            -0.021832   \n",
       "uracil                                             -54.776683   \n",
       "\n",
       "                               high_fiber_paraprevotella_imports  \n",
       "name                                                              \n",
       "2-deoxyadenosine                                      -23.035010  \n",
       "4-hydroxybenzoate                                      -0.000804  \n",
       "Adenosine                                             -23.061214  \n",
       "Ammonium                                              -11.335716  \n",
       "Chloride                                               -0.000804  \n",
       "Citrate                                               -38.879291  \n",
       "Co2+                                                   -0.000804  \n",
       "Cu2+                                                   -0.000804  \n",
       "Cytidine                                               -6.229609  \n",
       "D-glucose                                              -0.024099  \n",
       "D-glucuronate                                          -0.001509  \n",
       "Deoxyguanosine                                        -14.956636  \n",
       "Fe2+                                                   -0.001149  \n",
       "Fe3+                                                   -0.001380  \n",
       "Glycerol                                              -18.411577  \n",
       "Guanine                                               -27.561451  \n",
       "Inosine                                               -15.561849  \n",
       "L-alanine                                              -0.130629  \n",
       "L-asparagine                                          -23.514413  \n",
       "L-aspartate(1-)                                       -81.696503  \n",
       "L-cysteinylglycine                                     -0.010229  \n",
       "L-fucose                                              -16.434108  \n",
       "L-glutamate(1-)                                       -23.332489  \n",
       "L-glutamine                                           -14.901524  \n",
       "L-methionine                                           -0.050263  \n",
       "L-phenylalanine                                        -0.038370  \n",
       "L-threonine                                           -36.481785  \n",
       "Maltose                                                -0.031642  \n",
       "Menaquinone 8                                          -0.000876  \n",
       "Mn2+                                                   -0.000804  \n",
       "Nicotinamide                                           -1.240513  \n",
       "Nicotinate                                             -2.694991  \n",
       "Protoheme                                              -0.000804  \n",
       "Reduced glutathione                                    -0.000804  \n",
       "Siroheme                                               -0.000804  \n",
       "Spermidine                                             -0.000804  \n",
       "Thiamin                                                -0.000804  \n",
       "Urea                                                   -7.047532  \n",
       "Uridine                                               -28.759788  \n",
       "Water                                                 -27.303574  \n",
       "Xanthine                                              -10.806284  \n",
       "Zinc                                                   -0.000804  \n",
       "acetaldehyde                                          -39.846483  \n",
       "acetate                                               -14.355037  \n",
       "calcium(2+)                                            -0.000804  \n",
       "hydrogenphosphate                                      -0.210836  \n",
       "magnesium                                              -0.000804  \n",
       "meso-2,6-Diaminoheptanedioate                          -1.188592  \n",
       "octadecanoate (n-C18:0)                                -0.022124  \n",
       "potassium                                              -0.000804  \n",
       "proton                                                -81.691022  \n",
       "sulfate                                                -0.000804  \n",
       "tetradecanoate (n-C14:0)                               -0.038975  \n",
       "uracil                                                -58.973646  "
      ]
     },
     "execution_count": 178,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "paraprevotella_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "id": "69ddeb8e-c33e-4c12-9b64-eb762aaa46cf",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "47.27341328355365"
      ]
     },
     "execution_count": 179,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "paraprevotella_euclidean_distance = ((paraprevotella_imports_for_both_diets.western_paraprevotella_imports - paraprevotella_imports_for_both_diets.high_fiber_paraprevotella_imports)**2).sum()**(1/2)\n",
    "\n",
    "paraprevotella_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f42d0bec-975b-4fac-862c-e194bb50f7fc",
   "metadata": {},
   "source": [
    "# Megamonas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 180,
   "id": "2ad11dc3-e51e-4f18-b689-8d0bd21c75db",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Eubacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Faecalibacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032099</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032282</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 144</td>\n",
       "      <td>-0.000004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104834</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032344</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104835</th>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104836</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>mucin-type O-glycan No 135</td>\n",
       "      <td>-0.000008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104838</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032392</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000049</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104839</th>\n",
       "      <td>Parabacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032439</td>\n",
       "      <td>western</td>\n",
       "      <td>laminarin (n=30 repeat units, beta -1,3 glc)</td>\n",
       "      <td>-0.000006</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>42780 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   taxon direction    sample_id   medium  \\\n",
       "0            Akkermansia    import  SRR15032081  western   \n",
       "1            Eubacterium    import  SRR15032081  western   \n",
       "2       Faecalibacterium    import  SRR15032081  western   \n",
       "3        Bifidobacterium    import  SRR15032099  western   \n",
       "4            Bacteroides    import  SRR15032282  western   \n",
       "...                  ...       ...          ...      ...   \n",
       "104834       Bacteroides    import  SRR15032344  western   \n",
       "104835       Akkermansia    import  SRR15032439  western   \n",
       "104836       Bacteroides    import  SRR15032439  western   \n",
       "104838       Bacteroides    import  SRR15032392  western   \n",
       "104839   Parabacteroides    import  SRR15032439  western   \n",
       "\n",
       "                                                name      flux  \n",
       "0                         mucin-type O-glycan No 144 -0.000001  \n",
       "1                         mucin-type O-glycan No 144 -0.000003  \n",
       "2                         mucin-type O-glycan No 144 -0.000001  \n",
       "3                         mucin-type O-glycan No 144 -0.000002  \n",
       "4                         mucin-type O-glycan No 144 -0.000004  \n",
       "...                                              ...       ...  \n",
       "104834                    mucin-type O-glycan No 135 -0.000001  \n",
       "104835                    mucin-type O-glycan No 135 -0.000001  \n",
       "104836                    mucin-type O-glycan No 135 -0.000008  \n",
       "104838  laminarin (n=30 repeat units, beta -1,3 glc) -0.000049  \n",
       "104839  laminarin (n=30 repeat units, beta -1,3 glc) -0.000006  \n",
       "\n",
       "[42780 rows x 6 columns]"
      ]
     },
     "execution_count": 180,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'western']\n",
    "western_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 181,
   "id": "59d6ce0e-6c20-4b5f-bccf-31ee23259467",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [taxon, direction, sample_id, medium, name, flux]\n",
       "Index: []"
      ]
     },
     "execution_count": 181,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "western_megamonas_only = western_only.loc[western_only['taxon'] == 'Megamonas']\n",
    "western_megamonas_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 182,
   "id": "a40216bf-3bf8-4646-b25b-21640cb76e33",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Series([], Name: flux, dtype: float64)"
      ]
     },
     "execution_count": 182,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_western_megamonas = western_megamonas_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_western_megamonas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 183,
   "id": "33dbc20a-c370-4a5f-b447-543a4f560f95",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-27.456853</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-11.983896</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>76</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-2.522117</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>77</th>\n",
       "      <td>Blautia</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032095</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-10.552848</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104355</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032479</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.422812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104357</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032489</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.165069</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104363</th>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032503</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>3-Dehydrochenodeoxycholate</td>\n",
       "      <td>-0.202800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104391</th>\n",
       "      <td>Sutterella</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032310</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-9.052821</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>104396</th>\n",
       "      <td>Desulfovibrio</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>trimethylamine</td>\n",
       "      <td>-3.537798</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>31824 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                taxon direction    sample_id      medium  \\\n",
       "68        Bacteroides    import  SRR15032094  high_fiber   \n",
       "69            Blautia    import  SRR15032094  high_fiber   \n",
       "70          Megamonas    import  SRR15032094  high_fiber   \n",
       "76        Bacteroides    import  SRR15032095  high_fiber   \n",
       "77            Blautia    import  SRR15032095  high_fiber   \n",
       "...               ...       ...          ...         ...   \n",
       "104355    Bacteroides    import  SRR15032479  high_fiber   \n",
       "104357    Bacteroides    import  SRR15032489  high_fiber   \n",
       "104363    Bacteroides    import  SRR15032503  high_fiber   \n",
       "104391     Sutterella    import  SRR15032310  high_fiber   \n",
       "104396  Desulfovibrio    import  SRR15032511  high_fiber   \n",
       "\n",
       "                              name       flux  \n",
       "68               hydrogenphosphate -27.456853  \n",
       "69               hydrogenphosphate -11.983896  \n",
       "70               hydrogenphosphate  -0.066602  \n",
       "76               hydrogenphosphate  -2.522117  \n",
       "77               hydrogenphosphate -10.552848  \n",
       "...                            ...        ...  \n",
       "104355  3-Dehydrochenodeoxycholate  -0.422812  \n",
       "104357  3-Dehydrochenodeoxycholate  -0.165069  \n",
       "104363  3-Dehydrochenodeoxycholate  -0.202800  \n",
       "104391              trimethylamine  -9.052821  \n",
       "104396              trimethylamine  -3.537798  \n",
       "\n",
       "[31824 rows x 6 columns]"
      ]
     },
     "execution_count": 183,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_only = taxon_imports_table.loc[taxon_imports_table['medium'] == 'high_fiber']\n",
    "high_fiber_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 184,
   "id": "f52225d1-b91c-4659-ac06-0f06fd8d1cb4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>taxon</th>\n",
       "      <th>direction</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>flux</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032094</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.066602</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.096595</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>117</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032103</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.042782</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>729</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032404</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.073747</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>973</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032487</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>hydrogenphosphate</td>\n",
       "      <td>-0.050973</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101108</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>(S)-malate(2-)</td>\n",
       "      <td>-71.033700</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101109</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032103</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>(S)-malate(2-)</td>\n",
       "      <td>-62.980349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101166</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032404</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>(S)-malate(2-)</td>\n",
       "      <td>-65.774984</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101181</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032487</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>(S)-malate(2-)</td>\n",
       "      <td>-63.751716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>101203</th>\n",
       "      <td>Megamonas</td>\n",
       "      <td>import</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>Thymidine</td>\n",
       "      <td>-0.000620</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>277 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            taxon direction    sample_id      medium               name  \\\n",
       "70      Megamonas    import  SRR15032094  high_fiber  hydrogenphosphate   \n",
       "98      Megamonas    import  SRR15032079  high_fiber  hydrogenphosphate   \n",
       "117     Megamonas    import  SRR15032103  high_fiber  hydrogenphosphate   \n",
       "729     Megamonas    import  SRR15032404  high_fiber  hydrogenphosphate   \n",
       "973     Megamonas    import  SRR15032487  high_fiber  hydrogenphosphate   \n",
       "...           ...       ...          ...         ...                ...   \n",
       "101108  Megamonas    import  SRR15032079  high_fiber     (S)-malate(2-)   \n",
       "101109  Megamonas    import  SRR15032103  high_fiber     (S)-malate(2-)   \n",
       "101166  Megamonas    import  SRR15032404  high_fiber     (S)-malate(2-)   \n",
       "101181  Megamonas    import  SRR15032487  high_fiber     (S)-malate(2-)   \n",
       "101203  Megamonas    import  SRR15032079  high_fiber          Thymidine   \n",
       "\n",
       "             flux  \n",
       "70      -0.066602  \n",
       "98      -0.096595  \n",
       "117     -0.042782  \n",
       "729     -0.073747  \n",
       "973     -0.050973  \n",
       "...           ...  \n",
       "101108 -71.033700  \n",
       "101109 -62.980349  \n",
       "101166 -65.774984  \n",
       "101181 -63.751716  \n",
       "101203  -0.000620  \n",
       "\n",
       "[277 rows x 6 columns]"
      ]
     },
     "execution_count": 184,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_megamonas_only = high_fiber_only.loc[high_fiber_only['taxon'] == 'Megamonas']\n",
    "high_fiber_megamonas_only"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 185,
   "id": "c1142b74-6f81-4d95-802a-f3a2663ceca9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "name\n",
       "(S)-lactate                -14.270235\n",
       "(S)-malate(2-)             -65.332070\n",
       "2-Demethylmenaquinone 8     -0.000103\n",
       "2-deoxyadenosine           -13.444643\n",
       "Adenine                    -35.077348\n",
       "                              ...    \n",
       "potassium                   -0.000363\n",
       "proton                      -9.075639\n",
       "sulfate                     -0.000363\n",
       "tetradecanoate (n-C14:0)    -0.000915\n",
       "uracil                     -23.836852\n",
       "Name: flux, Length: 63, dtype: float64"
      ]
     },
     "execution_count": 185,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mean_import_of_high_fiber_megamonas = high_fiber_megamonas_only.groupby('name')[\"flux\"].mean()\n",
    "mean_import_of_high_fiber_megamonas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 186,
   "id": "c41c2802-3c59-4ea8-acb4-5e1cdea88ab3",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_megamonas_imports = pd.DataFrame (mean_import_of_western_megamonas, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 187,
   "id": "00840695-1ed8-4ce1-9cfd-93b86e25d58f",
   "metadata": {},
   "outputs": [],
   "source": [
    "western_megamonas_imports.rename(columns={\"flux\": \"western_flux_megamonas\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 188,
   "id": "405c7db0-4696-40f4-b9f2-f10782f3b9cf",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "Empty DataFrame\n",
       "Columns: [western_flux_megamonas]\n",
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     "execution_count": 188,
     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "western_megamonas_imports"
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  {
   "cell_type": "code",
   "execution_count": 189,
   "id": "f7d6cf41-7e32-4a54-b04d-a214008fb065",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_megamonas_imports = pd.DataFrame (mean_import_of_high_fiber_megamonas, columns = ['flux'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 190,
   "id": "5220d196-3f88-4aaf-b178-39391a37aee5",
   "metadata": {},
   "outputs": [],
   "source": [
    "high_fiber_megamonas_imports.rename(columns={\"flux\": \"high_fiber_flux_megamonas\"}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 191,
   "id": "48f3625a-698e-4415-b481-f47e133b8a7d",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
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       "  <tbody>\n",
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       "      <th>(S)-malate(2-)</th>\n",
       "      <td>-65.332070</td>\n",
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       "      <th>2-Demethylmenaquinone 8</th>\n",
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       "      <th>2-deoxyadenosine</th>\n",
       "      <td>-13.444643</td>\n",
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       "      <th>Adenine</th>\n",
       "      <td>-35.077348</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>potassium</th>\n",
       "      <td>-0.000363</td>\n",
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       "      <th>proton</th>\n",
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       "    <tr>\n",
       "      <th>sulfate</th>\n",
       "      <td>-0.000363</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tetradecanoate (n-C14:0)</th>\n",
       "      <td>-0.000915</td>\n",
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       "      <th>uracil</th>\n",
       "      <td>-23.836852</td>\n",
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       "<p>63 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          high_fiber_flux_megamonas\n",
       "name                                               \n",
       "(S)-lactate                              -14.270235\n",
       "(S)-malate(2-)                           -65.332070\n",
       "2-Demethylmenaquinone 8                   -0.000103\n",
       "2-deoxyadenosine                         -13.444643\n",
       "Adenine                                  -35.077348\n",
       "...                                             ...\n",
       "potassium                                 -0.000363\n",
       "proton                                    -9.075639\n",
       "sulfate                                   -0.000363\n",
       "tetradecanoate (n-C14:0)                  -0.000915\n",
       "uracil                                   -23.836852\n",
       "\n",
       "[63 rows x 1 columns]"
      ]
     },
     "execution_count": 191,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "high_fiber_megamonas_imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 192,
   "id": "ce487aa9-e1d0-46ec-b593-3d38ac269c37",
   "metadata": {},
   "outputs": [],
   "source": [
    "combined_diet_fluxes_megamonas = pd.concat([western_megamonas_imports['western_flux_megamonas'], high_fiber_megamonas_imports['high_fiber_flux_megamonas']], axis=1, keys= ['western_megamonas_imports', 'high_fiber_megamonas_imports'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 193,
   "id": "b976a9d7-e9f5-44a6-aa12-fed5d1dc8498",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>tetradecanoate (n-C14:0)</th>\n",
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       "      <td>-0.000915</td>\n",
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       "    <tr>\n",
       "      <th>uracil</th>\n",
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       "      <td>-23.836852</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>63 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                          western_megamonas_imports  \\\n",
       "name                                                  \n",
       "(S)-lactate                                     NaN   \n",
       "(S)-malate(2-)                                  NaN   \n",
       "2-Demethylmenaquinone 8                         NaN   \n",
       "2-deoxyadenosine                                NaN   \n",
       "Adenine                                         NaN   \n",
       "...                                             ...   \n",
       "potassium                                       NaN   \n",
       "proton                                          NaN   \n",
       "sulfate                                         NaN   \n",
       "tetradecanoate (n-C14:0)                        NaN   \n",
       "uracil                                          NaN   \n",
       "\n",
       "                          high_fiber_megamonas_imports  \n",
       "name                                                    \n",
       "(S)-lactate                                 -14.270235  \n",
       "(S)-malate(2-)                              -65.332070  \n",
       "2-Demethylmenaquinone 8                      -0.000103  \n",
       "2-deoxyadenosine                            -13.444643  \n",
       "Adenine                                     -35.077348  \n",
       "...                                                ...  \n",
       "potassium                                    -0.000363  \n",
       "proton                                       -9.075639  \n",
       "sulfate                                      -0.000363  \n",
       "tetradecanoate (n-C14:0)                     -0.000915  \n",
       "uracil                                      -23.836852  \n",
       "\n",
       "[63 rows x 2 columns]"
      ]
     },
     "execution_count": 193,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_diet_fluxes_megamonas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 194,
   "id": "6356450b-0009-4121-99dc-232ad03229a0",
   "metadata": {},
   "outputs": [],
   "source": [
    "megamonas_imports_for_both_diets = combined_diet_fluxes_megamonas.dropna()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 195,
   "id": "95b68c4c-dcf4-435e-ba7a-b4430369bfbf",
   "metadata": {},
   "outputs": [
    {
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>western_megamonas_imports</th>\n",
       "      <th>high_fiber_megamonas_imports</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>name</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [western_megamonas_imports, high_fiber_megamonas_imports]\n",
       "Index: []"
      ]
     },
     "execution_count": 195,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "megamonas_imports_for_both_diets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 197,
   "id": "487cfce4-415a-4f3a-94ec-f5a6c89ca720",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.0"
      ]
     },
     "execution_count": 197,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "megamonas_euclidean_distance = ((megamonas_imports_for_both_diets.western_megamonas_imports - megamonas_imports_for_both_diets.high_fiber_megamonas_imports)**2).sum()**(1/2)\n",
    "\n",
    "megamonas_euclidean_distance"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3c575ce2-b294-4fa1-b78a-1765c8829840",
   "metadata": {},
   "source": [
    "# all the euclidean distances"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 198,
   "id": "ec661977-4606-468b-9b7e-fcce0aedfe9b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "63.35243012853294"
      ]
     },
     "execution_count": 198,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bacteroides_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 199,
   "id": "7d0f08f6-ec53-4432-ba66-2d662bb6a21e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "64.56405495878849"
      ]
     },
     "execution_count": 199,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prevotella_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 200,
   "id": "b6e99c48-28a0-4f31-81fc-9190f295bce9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "48.68283693595469"
      ]
     },
     "execution_count": 200,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "faecalibacterium_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 201,
   "id": "d241e2be-9d3b-4c6a-99dc-8463d0cf7924",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "27.39142994145541"
      ]
     },
     "execution_count": 201,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "roseburia_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 202,
   "id": "94e6ff5f-22b3-403b-91d7-725f9435c9f7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "28.36475275549472"
      ]
     },
     "execution_count": 202,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "blautia_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 203,
   "id": "ab7f2f49-ecaf-450d-9b41-39ec5f801e90",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "51.161930368231786"
      ]
     },
     "execution_count": 203,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alistipes_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 204,
   "id": "e723cf06-8d3e-4a46-af3b-5c65b370ba97",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "46.76183246583985"
      ]
     },
     "execution_count": 204,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ruminococcus_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 205,
   "id": "74b086f0-e558-4f3d-bbe1-8c4895132c98",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "21.97892630802339"
      ]
     },
     "execution_count": 205,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "akkermansia_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 207,
   "id": "aaaf6692-558d-437d-9265-9dd318279587",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "47.27341328355365"
      ]
     },
     "execution_count": 207,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "paraprevotella_euclidean_distance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1e452804-1e17-409f-932d-737a6d08f104",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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