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Minimal Supplying Community Search (misosoup) is a command line tool designed to search for minimal microbial communities, wherein every member is essential for the community’s persistence within a given medium. Its primary functions include:

• Identifying minimal communities within a specified medium.
• Identifying minimal “supplying” communities within a medium, where each member is necessary for the growth of a focal strain or species of interest.

To utilize misosoup, users provide a set of genome-scale metabolic models, each representing a potential member of the community. The program then employs constraint-based optimizations to determine minimal communities. These optimizations assume a metabolic steady-state, akin to Flux Balance Analysis.

Once computations are complete, misosoup outputs information about community members, their respective growth rates, as well as their metabolic consumptions and secretions, presented in a format both readable by humans and parseable by software.

Details

To find minimal microbial communities misosoup solves a repeated sequence of optimization problems using MILP formulations:

1. Minimize the number of community member (see Zelezniak, et al. PNAS doi:10.1073/pnas.1421834112).
2. Fix the active community members and check the feasibility of the entire community.
3. Optionally: Maximize community biomass (sum of individual growth rates).
4. Optionally: Perform an optimization to reflect parsimonious enzyme usage (see Lewis, et al. Mol Syst Bio doi:10.1038/msb.2010.47).

Citation

If you use misosoup, please cite our paper.

Development

Any contributions are welcome.