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

TL;DR

This study provides evidence for a multi-level trophic structure in the human gut microbiome, revealing how microbes interact through metabolic exchanges across several iterative levels, influencing microbial diversity and metabolite profiles.

Contribution

The paper introduces a simplified model demonstrating a four-level trophic organization in the gut microbiome, linking microbial interactions with metabolic flow and diversity patterns.

Findings

Approximately four trophic levels identified.

Model predicts gut metabolome consistent with real data.

Hierarchical organization explains microbial and metabolic diversity.

Abstract

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 in 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.