Figure 4

Incorporating metabolic and taxonomic structure. (a) Three-tiered secretion model used for simulating human and marine microbiomes. M = 300 resource types are grouped into T = 6 classes of equal size, labeled A through F. These groups represent different kinds of metabolites, e.g. lipids, sugars, amino acids, etc. Group F is the “waste” class, containing common byproducts generated by many metabolic pathways, e.g., carboxylic acids. A fraction f_s of the byproduct flux from metabolism of a given resource is partitioned among resources of the same class. A fraction f_w of the flux is partitioned among “waste” resources (class F). The rest of the flux is nonspecifically partitioned among all the other classes. In all simulations shown here, f_s = f_w = 0.45. (b) Heatmap of a metabolic matrix D_αβ encoding the three-tiered secretion model. (c) Taxonomic structure used for human and marine microbiome simulations. Microbial species are grouped into “families,” with each family specializing in a different resource class. Specialist families allocate a fraction q of their consumption capacity to their favored resource class. In all the simulations shown here, q = 0.9. There is also a generalist family whose preferences are uniformly sampled across all resource types.