PyCoMo: a python package for community metabolic model creation and analysis

Abstract

Summary: PyCoMo is a python package for quick and easy generation of genome-scale compartmentalized community metabolic models that are compliant with current openCOBRA file formats. The resulting models can be used to predict (i) the maximum growth rate at a given abundance profile, (ii) the feasible community compositions at a given growth rate, and (iii) all exchange metabolites and cross-feeding interactions in a community metabolic model independent of the abundance profile; we demonstrate PyCoMo's capability by analysing methane production in a previously published simplified biogas community metabolic model.

Availability and implementation: PyCoMo is freely available under an MIT licence at http://github.com/univieCUBE/PyCoMo, the Python Package Index, and Zenodo.

Figure 1.

Summary of PyCoMo. (A) Overview of the automated steps in compartmentalized community metabolic model creation and the available analysis. All components of the final model can be traced back to their community member of origin. The community metabolic models can be saved and loaded into SBML format while retaining the original flux bounds, making the models reusable. Mass and charge balance of the entire model is checked, including all external metabolites matched between community members. The community metabolic model structure can be set to fixed growth or fixed abundance. All functionalities are available via a command-line interface. (B) Feasible compositions at different community growth rates in a three species biogas community (Koch et al. 2019). DV, Desulfovibrio vulgaris; MH, Methanospirillum hungatei; MB, Methanosarcina barkeri. The medium is specified to contain ethanol and CO₂, with ethanol being the substrate for Desulfovibrio vulgaris, which produces the substrates for the other community members. (C) Visualization of the community metabolic model and its cross-feeding interactions using ScyNet. The metabolite exchanges were calculated independently of the community composition and growth rate. Arrow colours denote feasible metabolite production (orange), uptake (green) or both (violet) by the communities’ members.