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

Abstract

Abstract Summary PyCoMo is a python package for quick and easy generation of genome-scale compartmentalised 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 (Koch et al., 2019). Availability and Implementation PyCoMo is freely available under an MIT licence at http://github.com/univieCUBE/PyCoMo, the Python Package Index and Zenodo (https://doi.org/10.5281/zenodo.10431322). Supplementary information Explanation of bound-free model structure, community metabolic model structure for a linear optimisation problem, and runtime measurements.