Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome

Cell Metab. 2014 Nov 4;20(5):742-752. doi: 10.1016/j.cmet.2014.07.021. Epub 2014 Aug 28.


The human gut microbiome is a major contributor to human metabolism and health, yet the metabolic processes that are carried out by various community members, the way these members interact with each other and with the host, and the impact of such interactions on the overall metabolic machinery of the microbiome have not yet been mapped. Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. We will specifically highlight two interrelated lines of work, the first aiming to deconvolve the microbiome and to characterize the metabolic capacity of various microbiome species and the second aiming to utilize computational modeling to infer and study metabolic interactions between these species.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Bacteria / genetics
  • Bacteria / metabolism
  • Computer Simulation
  • Fungi / genetics
  • Fungi / metabolism
  • Humans
  • Metabolic Networks and Pathways
  • Metabolome
  • Metabolomics* / methods
  • Metagenome
  • Metagenomics* / methods
  • Microbial Interactions
  • Microbiota*
  • Models, Biological