This repository contains data, code, and analysis notebooks for a study of robust coexistence in simple microbial communities. The work examines how four bacteria assemble and coexist across varying carbon source environments, and uses a consumer-resource model (CRM) to explore the mechanistic basis of coexistence.
| Abbreviation | Species |
|---|---|
| At | Agrobacterium tumefaciens |
| Ct | Comamonas testosteroni |
| Ml | Microbacterium liquefaciens |
| Oa | Ochrobactrum anthropi |
data/ Experimental data, organized by experiment
notebooks/ Jupyter notebooks for analysis and figure generation
python/ Python scripts for consumer-resource model (CRM) simulations
simulation_results/ Output files from CRM parameter sweeps and dFBA simulations
The numbered folders in data/, notebooks/, and Figures/ follow the same ordering:
- Growth phenotyping of monocultures
- First community assembly experiment
- Second community assembly experiment
- Chemostat coexistence experiments
- Pairwise interaction measurements
- Consumer-resource model (CRM) parameterization and simulation
Run notebooks in order within each section. CRM parameter sweeps (section 6) are run via scripts in python/6_CRM/ and results are saved to simulation_results/.
- Python 3.x
numpy,scipy,pandas,matplotlib,seabornjoblib(for parallel CRM sweeps)- Jupyter for notebooks
Snorre Sulheim, Miguel Teixeira, Eric Ulrich, Alisson Gillon, Samuel Testa, Prajwal Padmanabha, Daniel Machado & Sara Mitri (2026). Cross-feeding enables robust coexistence between four bacterial species. bioRxiv 2026年04月20日.719729