PyCoMo

PyCoMo constructs compartmentalized microbial community metabolic models from genomic data and simulates community growth dynamics, feasible compositions, and metabolite exchange and cross-feeding interactions.

Key Features:

• openCOBRA compliance: Generates models compatible with openCOBRA file formats for interoperability.
• Maximum growth rate prediction: Predicts community maximum growth rate from a specified abundance profile.
• Feasible composition inference: Identifies feasible community compositions at specified growth rates.
• Metabolite exchange and cross-feeding: Predicts exchanged metabolites and cross-feeding interactions independent of abundance profiles.
• Methane production analysis: Analyzes methane production in a simplified biogas community metabolic model.

Scientific Applications:

• Biogas production: Analyzes methane production and metabolic interactions in biogas community models.
• Environmental microbiology: Studies community-level metabolism, nutrient cycling, and ecosystem functioning via metabolite exchange and growth simulations.
• Synthetic biology: Evaluates community metabolic interactions and growth behavior under defined conditions.

Methodology:

Integrates genomic data with metabolic modeling to build compartmentalized community models and simulate growth dynamics, feasible community compositions, and metabolite exchange/cross-feeding under specified conditions.