Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease

Bioessays. 2017 Dec;39(12). doi: 10.1002/bies.201700032. Epub 2017 Oct 4.


The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of "functional" classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease.

Keywords: IgA-Seq; evolution; functional genomics; immunology; metagenomics; microbiota.

Publication types

  • Review

MeSH terms

  • Dysbiosis / genetics
  • Dysbiosis / immunology*
  • Dysbiosis / microbiology
  • Gastrointestinal Microbiome / immunology*
  • Gastrointestinal Tract / immunology
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Immunity, Innate*
  • Immunoglobulin A / genetics
  • Metabolome / immunology
  • Metagenome / immunology*
  • Microbial Consortia / immunology
  • Terminology as Topic


  • Immunoglobulin A