This repository contains data (except raw sequencing and metabolomics data), jupyter notebooks and other source code used in our recent project on microbial release rates. In this project we test the hypothesis that microbial release rates are negatively correlated with metabolites' inherent value. We also ask how important this factor is compared to other factors in explaining metabolite release rates and how microbial release rates change over a 4-6 week long evolution experiment with E. coli kockout mutants.
Detailed description of folder content is given in the README located in each folder.
Matlab and python code used to parse and analyse data.
This folder contains all data (except sequencing data) used for the analyses and plots presented in the associated paper, including experimental data generated in this project and data collected from other sources. The raw sequencing data is available in the NCBI SRA database under the BioProject ID PRJNA1270783. The raw FIA-TOF mass-spectrometry data from the transporter KO experiment is available on MassIVE under the dataset identifier MSV000097105.
This folder contains the data and source code for the interactive web application hosted on keio.unil.ch. This web application can be used to explore the large dataset of untargeted exometabolome data from 66 E. coli knockout mutants, each mutant devoid of a gene associated with metabolite transport across the inner or outer membrane.
This folder contains the original and modified genome-scale metabolic models used in this project. This include the following species:
- B. licheniformis
- C. glutamicum
- E. coli
- P. putida
- S. cerevisiae
All jupyter notebooks used for the analyses and plots presented in the associated paper.
If you use these results, analyses or data, please cite this preprint:
Snorre Sulheim, Gunn Broli, Peter F. Doubleday, Prajwal Padmanabha, Alisson Gillon, Julien S. Luneau, Andrew Quinn, Eric Ulrich, Margaret A. Vogel, Nicola Zamboni, Philipp Engel, and Sara Mitri. "Microbes use transporters to regulate the release of metabolites based on value.", bioRxiv (2025)
See environment.yml