Clinical Review State of the Art Review

The role of the gut microbiome in systemic inflammatory disease

BMJ 2018; 360 doi: (Published 08 January 2018) Cite this as: BMJ 2018;360:j5145
  1. Jose C Clemente, assistant professor1,
  2. Julia Manasson, medical doctor2,
  3. Jose U Scher, assistant professor2
  1. 1Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
  2. 2Department of Medicine, Division of Rheumatology, New York University School of Medicine and Hospital for Joint Diseases, New York, NY 10003, USA
  1. Correspondence to: J U Scher Jose.Scher{at}


The role of the gut microbiome in models of inflammatory and autoimmune disease is now well characterized. Renewed interest in the human microbiome and its metabolites, as well as notable advances in host mucosal immunology, has opened multiple avenues of research to potentially modulate inflammatory responses. The complexity and interdependence of these diet-microbe-metabolite-host interactions are rapidly being unraveled. Importantly, most of the progress in the field comes from new knowledge about the functional properties of these microorganisms in physiology and their effect in mucosal immunity and distal inflammation. This review summarizes the preclinical and clinical evidence on how dietary, probiotic, prebiotic, and microbiome based therapeutics affect our understanding of wellness and disease, particularly in autoimmunity.


  • Series explanation: State of the Art Reviews are commissioned on the basis of their relevance to academics and specialists in the US and internationally. For this reason they are written predominantly by US authors

  • Contributors: All three authors were involved the conception, writing, and editing of the manuscript. All are guarantors.

  • Funding: Supported by grant No K23AR064318 and 1R03AR072182 from NIH/NIAMS to JUS, SUCCESS grant to JCC, Crohn’s and Colitis Foundation of America #362048 to JCC, the Judith and Stewart NYU Colton Center for Autoimmunity, and the Riley Family Foundation.

  • Competing interests: We have read and understood the BMJ policy on declaration of interests and declare the following interests: none.

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

  • Patient involvement: No patients were involved in the creation of this article.

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