Evidence for a multi-level trophic organization of the human gut microbiome

The human gut microbiome is a complex ecosystem, in which hundreds of microbial
species and metabolites coexist, in part due to an extensive network of cross-feeding
interactions. However, both the large-scale trophic organization of this ecosystem and
its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified
model, we provide quantitative support for a multi-level trophic organization of the
human gut microbiome, where microbes consume and secrete metabolites in multiple
iterative steps. Using a manually-curated set of metabolic interactions between
microbes, our model suggests about four trophic levels, each characterized by a high
level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical
metabolic environment of the gut (fecal metabolome) in approximate agreement with
the real data. To understand the consequences of this trophic organization, we quantify
the metabolic flow and biomass distribution and explore patterns of microbial and
metabolic diversity at different levels. The hierarchical trophic organization suggested
by our model can help mechanistically establish causal links between the abundances
of microbes and metabolites in the human gut.