Bridging Intestinal Immunity and Gut Microbiota by Metabolites

Cell Mol Life Sci. 2019 Oct;76(20):3917-3937. doi: 10.1007/s00018-019-03190-6. Epub 2019 Jun 27.


The gastrointestinal tract is the site of nutrient digestion and absorption and is also colonized by diverse, highly mutualistic microbes. The intestinal microbiota has diverse effects on the development and function of the gut-specific immune system, and provides some protection from infectious pathogens. However, interactions between intestinal immunity and microorganisms are very complex, and recent studies have revealed that this intimate crosstalk may depend on the production and sensing abilities of multiple bioactive small molecule metabolites originating from direct produced by the gut microbiota or by the metabolism of dietary components. Here, we review the interplay between the host immune system and the microbiota, how commensal bacteria regulate the production of metabolites, and how these microbiota-derived products influence the function of several major innate and adaptive immune cells involved in modulating host immune homeostasis.

Keywords: Fecal microbiota transplantation; Germ-free animals; Innate and adaptive immune cells.

Publication types

  • Review

MeSH terms

  • Adaptive Immunity*
  • Amino Acids / immunology
  • Amino Acids / metabolism
  • Animals
  • Bile Acids and Salts / immunology
  • Bile Acids and Salts / metabolism
  • Dysbiosis / immunology
  • Dysbiosis / metabolism*
  • Dysbiosis / microbiology
  • Dysbiosis / therapy
  • Fatty Acids / immunology
  • Fatty Acids / metabolism
  • Fecal Microbiota Transplantation
  • Gastrointestinal Microbiome / immunology*
  • Germ-Free Life / immunology
  • Homeostasis / immunology
  • Humans
  • Immunity, Innate*
  • Intestinal Mucosa / immunology
  • Intestinal Mucosa / metabolism*
  • Intestinal Mucosa / microbiology
  • Lymphocytes / immunology
  • Lymphocytes / metabolism
  • Lymphocytes / microbiology
  • Metabolome / immunology*
  • Myeloid Cells / immunology
  • Myeloid Cells / metabolism
  • Myeloid Cells / microbiology
  • Symbiosis / immunology


  • Amino Acids
  • Bile Acids and Salts
  • Fatty Acids