Microbial Contribution to the Human Metabolome: Implications for Health and Disease

Annu Rev Pathol. 2020 Jan 24;15:345-369. doi: 10.1146/annurev-pathol-020117-043559. Epub 2019 Oct 17.


The human gastrointestinal tract is home to an incredibly dense population of microbes. These microbes employ unique strategies to capture energy in this largely anaerobic environment. In the process of breaking down dietary- and host-derived substrates, the gut microbiota produce a broad range of metabolic products that accumulate to high levels in the gut. Increasingly, studies are revealing that these chemicals impact host biology, either by acting on cells within the gastrointestinal tract or entering circulation and exerting their effects at distal sites within the body. Given the high level of functional diversity in the gut microbiome and the varied diets that we consume, the repertoire of microbiota-derived molecules within our bodies varies dramatically across individuals. Thus, the microbes in our gut and the metabolic end products they produce represent a phenotypic lever that we can potentially control to develop new therapeutics for personalized medicine. Here, we review current understanding of how microbes in the gastrointestinal tract contribute to the molecules within our gut and those that circulate within our bodies. We also highlight examples of how these molecules affect host physiology and discuss potential strategies for controlling their production to promote human health and to treat disease.

Keywords: human metabolome; human microbiome; metabolomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Diet
  • Gastrointestinal Microbiome / physiology*
  • Gastrointestinal Tract / metabolism
  • Gastrointestinal Tract / microbiology
  • Health*
  • Humans
  • Metabolic Diseases / etiology
  • Metabolic Diseases / microbiology*
  • Metabolome / physiology*