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PLoS Comput Biol. 2019 Dec 19;15(12):e1007524. doi: 10.1371/journal.pcbi.1007524. eCollection 2019 Dec.

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

Author information

1
Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
2
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.
3
Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
4
Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America.

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.

Conflict of interest statement

The authors have declared that no competing interests exist.

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