bmc_bioinf_2016_erbilgin

Predicting Resource Depletion of Mixed Bacterial Cultures

A workflow to use exometabolomics data collected over the growth curve of a bacterial species to predict how a co-culture of bacteria will deplete resources in a medium or environment

Authors: Onur Erbilgin and Ben Bowen, Lawrence Berkeley National Laboratory

This workflow is described in the publication:

Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. (2017) Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau, Trent R. Northen. (2017) BMC Bioinformatics 18:57 DOI: 10.1186/s12859-017-1478-2

Required Packages:

• Python 2.7
• Pandas
• NumPy
• SciPy
• MatPlotLib

Input Data:

• Compound concentrations for each species, replicate, and timepoint
  • Example file: Data/20151130_OAM1_QuantResults_v2C.csv
• Biomass measurements for each species, replicate, and timepoint
  • Example file: Data/20151014_3B10_9B05_L13_timecourse.csv
• Growth rate (average and error) of each species on individual carbon sources
  • Example file: Data/singleresource_data.xlsx
• Starting molarity of each compound in the growth medium
  • Example file: Data/molarity.txt
• Percent amino acid composition of the translated genome of each species
  • Example file: Data/percent_AA_composition_genome.xlsx
• Experimental observations of metabolite usage of the co-culture, to compare predictions
  • Example file: averaged: ./data/20160328_Enigma_coculture_avg_v2.csv
  • Example file: standard error: ./data/20160328_Enigma_coculture_stderr_v2.csv

Description of Notebooks

./notebooks/ch1_load_data.ipynb

1. Reads in metabolomics data and organizes it into a dictionary

./notebooks/ch2_fit_data.ipynb

1. Fits the metabolomics data to a published model of resource depletion
2. Calculates "T-half" (time of half depletion)
3. Calculates "Usage Window" (time of resource usage)
4. Calculates maximum resource depletion rate relative to biomass
5. Plots average T-half and Usage Window on the average growth curve of each species

./notebooks/ch3_correlate_data.ipynb

1. Plots T-half, growth rate on a single resource, maximum uptake rate, starting molarity of compound, and percent amino acid composition against each other
2. Calculates correlation coefficients and p-values of the comparisons

./notebooks/ch4_predict_depletion.ipynb

1. Using metabolomics data collected on single-species growth (Notebooks 1 and 2), predict how a co-culture of the different species would deplete resources in the same medium

License Information

• See LICENSE.txt and COPYRIGHT.txt