Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications

Cell Host Microbe. 2012 Nov 15;12(5):611-22. doi: 10.1016/j.chom.2012.10.012.


Indigenous microbiota are an essential component in the modern concept of human health, but the composition and functional characteristics of a healthy microbiome remain to be precisely defined. Patterns of microbial colonization associated with disease states have been documented, but the health-associated microbial patterns and their functional characteristics are less clear. A healthy microbiome, considered in the context of body habitat or body site, could be described in terms of ecologic stability (i.e., ability to resist community structure change under stress or to rapidly return to baseline following a stress-related change), by an idealized (presumably health-associated) composition or by a desirable functional profile (including metabolic and trophic provisions to the host). Elucidation of the properties of healthy microbiota would provide a target for dietary interventions and/or microbial modifications aimed at sustaining health in generally healthy populations and improving the health of individuals exhibiting disrupted microbiota and associated diseases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Intestinal Diseases / microbiology*
  • Metagenome*
  • Microbial Consortia
  • Prebiotics
  • Probiotics


  • Anti-Bacterial Agents
  • Prebiotics