Fig. 1

Approaches for genome-scale metabolic modeling of communities. Metabolic modeling of microbial communities is largely performed by selecting metabolic models of the human gut microbiome from AGORA, generating community models using A Compartmentalized model: a single stoichiometric matrix representing the two models joined by a lumen compartment wherein metabolites can be freely exchanged; B Lumped model: a single stoichiometric matrix representing the union of each individual model’s reactions, thereby ignoring all separation between cells; and C Costless secretion: individual stoichiometric networks for each model, whose exchange reactions are constrained to reflect the shared extracellular media