Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration

Dig Dis Sci. 2020 Mar;65(3):695-705. doi: 10.1007/s10620-020-06118-4.


The human gastrointestinal (GI) tract contains communities of microbes (bacteria, fungi, viruses) that vary by anatomic location and impact human health. Microbial communities differ in composition based on age, diet, and location in the gastrointestinal tract. Differences in microbial composition have been associated with chronic disease states. In terms of function, microbial metabolites provide key signals that help maintain healthy human physiology. Alterations of the healthy gastrointestinal microbiome have been linked to the development of various disease states including inflammatory bowel disease, diabetes, and colorectal cancer. While the definition of a healthy GI microbiome cannot be precisely identified, features of a healthy gut microbiome include relatively greater biodiversity and relative abundances of specific phyla and genera. Microbes with desirable functional profiles for the human host have been identified, in addition to specific metabolic features of the microbiome. This article reviews the composition and function of the healthy human GI microbiome, including the relative abundances of different bacterial taxa and the specific metabolic pathways and classes of microbial metabolites contributing to human health and disease prevention.

Keywords: Healthy; Human; Metabolites; Microbiome.

Publication types

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

MeSH terms

  • Biomedical Research / methods
  • Biomedical Research / trends*
  • Gastrointestinal Microbiome / physiology*
  • Gastrointestinal Tract / microbiology*
  • Gastrointestinal Tract / physiology*
  • Health Status*
  • Humans
  • Microbiota / physiology