Intended for healthcare professionals

Clinical Review State of the Art Review

The role of the microbiome in human health and disease: an introduction for clinicians

BMJ 2017; 356 doi: (Published 15 March 2017) Cite this as: BMJ 2017;356:j831
  1. Vincent B Young, professor1
  1. 1Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI 48109-5666, USA
  1. Correspondence to: V B Young youngvi{at}


Research into the microbiome—the indigenous microbial communities (microbiota) and the host environment that they inhabit—has changed clinicians’ ideas about microbes in human health and disease. Perhaps the most radical change is the realization that most of the microbes that inhabit our body supply crucial ecosystem services that benefit the entire host-microbe system. These services include the production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. Thus disease can result from a loss of beneficial functions or the introduction of maladaptive functions by invading microbes. This review will show how an understanding of the dynamics and function of the indigenous microbiota has altered our view of microbes in maintaining homeostasis and causing disease. It will discuss how disruption of the beneficial functions of the microbiota can lead to disease. Methods for studying the microbiota will be introduced as part of a conceptual framework for using these methods to delineate novel roles for microbes in health. Key associations between specific changes in the microbiome and disease will be discussed. This will lead to an explanation of how the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful functions, may lead to novel methods to prevent or treat a variety of diseases. With the explosion of studies relating the microbiome to health and disease, this review aims to provide a foundation for clinicians to follow this developing area of biomedical research.


  • Competing interests: I have read and understood BMJ policy on declaration of interests and declare that I have received money for consultancy work from Merck, Sharp & Dohme, Vedanta Biosciences, and MedImmune and have received a research grant from MedImmune.

  • Provenance and peer review: Commissioned; externally peer reviewed.

  • Patient involvement was not sought.

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