M2R

M2R integrates gut microbiota metabolic fluxes into human genome-scale metabolic reconstructions (e.g., RECON3D) by modifying exchange reaction bounds within COBRApy-based models to enable simulation of host–microbiome metabolic interactions.

Key Features:

• COBRApy integration: Implements functionality as a Python add-on to the COBRApy framework for working with constraint-based models.
• Integration with human GEMs: Incorporates gut microbiota metabolism into human genome-scale metabolic reconstructions such as RECON3D.
• Exchange reaction modification: Adjusts lower bounds of exchange reactions in the human GEM based on aggregated in- and out-fluxes from selected gut microbes.
• Use of microbial metabolic models: Leverages existing metabolic reconstructions of gut microbes to derive flux contributions for the human model.

Scientific Applications:

• Host–microbiome metabolic interaction modeling: Simulates how microbial metabolites influence human metabolic processes within a GEM framework.
• Physiology and immunity studies: Explores potential impacts of microbial metabolites on human physiology and immune-related metabolic pathways.
• Dysbiosis and disease investigation: Studies metabolic alterations associated with gut microbiome imbalances and their links to disease states.

Methodology:

Aggregates in- and out-fluxes from existing gut microbial metabolic models and integrates them into human GEMs (e.g., RECON3D) by adjusting exchange reaction lower bounds using COBRApy-based model manipulations.