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Translating the gut microbiome: ready for the clinic?


Research into the gut microbiota and its role in health and disease has expanded rapidly in the past two decades. However, much of the early focus has been on cataloguing the microorganisms present, identifying correlations between microbial species and disease and using preclinical animal models to understand phenotypes. Now efforts are under way to provide functional insights into the gut microbiota and its mechanisms of action, improve understanding of the role of the microbiota beyond the gut and advance the development of microbiota-based therapeutics so that the microbiome can be harnessed in the clinic. In this Viewpoint article, we asked a selection of scientists and clinicians working in the gut microbiome field for their opinions on the major advances in and the challenges and solutions for translating gut microbiome research to the clinic, and where they expect progress to be made in the future.

The contributors

Susan V. Lynch is a professor in the Department of Medicine at the University of California, San Francisco and Director of the Benioff Center for Microbiome Medicine, United States. Her research focuses on the gut microbiome and chronic inflammatory disease, with specific emphasis on childhood allergy and asthma, and adult inflammatory bowel disease.

Siew C. Ng is a professor in the Department of Medicine and Therapeutics, Associate Director of the Centre for Gut Microbiota Research, Director of the Microbiota Innovation Centre (MagIC) and Assistant Dean for Development at the Chinese University of Hong Kong, Hong Kong. She is an Associate Editor of Gut. Her interest focuses on studies of the human gut microbiota in health and diseases, such as inflammatory bowel disease, cancer and obesity, and the increasing role of the virome and fungi in faecal microbiota transplantation.

Fergus Shanahan is Emeritus Professor of Medicine at University College Cork, National University of Ireland, and Foundation Director of APC Microbiome Ireland, a research centre funded by Science Foundation Ireland since 2003, which investigates host–microorganism interactions in the gut. His interests include most things that affect the experience of illness.

Herbert Tilg is Head of the Department of Gastroenterology, Hepatology, Endocrinology and Metabolism at Medical University Innsbruck, Austria. His main research interest is inflammation, innate immunity and interaction with the gut microbiome in gastrointestinal and liver disorders. He is an Associate Editor of Gut and Chairman of the Scientific Committee, United European Gastroenterology.

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S.V.L. is funded by awards from the US National Institutes of Health (P0515267, AI113916, AI133765, DH082147, DA040532), the Crohn’s and Colitis Foundation of America (598710) and the Rainin Foundation. S.C.N. acknowledges Z. Tao and W. Tang for their scientific input. F.S. is funded in part by Science Foundation Ireland (centre grant APC SFI/12RC/2273).

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Corresponding authors

Correspondence to Susan V. Lynch or Siew C. Ng or Fergus Shanahan or Herbert Tilg.

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Competing interests

S.V.L. cofounded Siolta Therapeutics and is a board member and consultant for this company. She also served on the scientific advisory board of Bloom Science. F.S. is a cofounder and shareholder of Alimentary Health, Tucana Health and Atlantia Food Clinical Trials. These facts neither influenced nor constrained the contents of his responses here. S.C.N. and H.T. declare no competing interests.

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Lynch, S.V., Ng, S.C., Shanahan, F. et al. Translating the gut microbiome: ready for the clinic?. Nat Rev Gastroenterol Hepatol 16, 656–661 (2019).

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