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Leveraging diet to engineer the gut microbiome

Abstract

Autoimmune diseases, including inflammatory bowel disease, multiple sclerosis and rheumatoid arthritis, have distinct clinical presentations but share underlying patterns of gut microbiome perturbation and intestinal barrier dysfunction. Their potentially common microbial drivers advocate for treatment strategies aimed at restoring appropriate microbiome function, but individual variation in host factors makes a uniform approach unlikely. In this Perspective, we consolidate knowledge on diet–microbiome interactions in local inflammation, gut microbiota imbalance and host immune dysregulation. By understanding and incorporating the effects of individual dietary components on microbial metabolic output and host physiology, we examine the potential for diet-based therapies for autoimmune disease prevention and treatment. We also discuss tools targeting the gut microbiome, such as faecal microbiota transplantation, probiotics and orthogonal niche engineering, which could be optimized using custom dietary interventions. These approaches highlight paths towards leveraging diet for precise engineering of the gut microbiome at a time of increasing autoimmune disease.

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Fig. 1: Temporal trends in human host, the gut microbiome and diet.
Fig. 2: Diet–gut microbiome–host axis in autoimmune diseases and homeostasis.
Fig. 3: Approaches for personalized application of gut microbiome engineering tools.

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Acknowledgements

This work was supported by the following grants in the laboratory of M.S.D.: Luxembourg National Research Fund (FNR) CORE grants (C15/BM/10318186 and C18/BM/12585940) to M.S.D.; M.B. was supported by a European Commission Horizon 2020 Marie Skłodowska-Curie Actions individual fellowship (897408); M.W. was supported by a Fulbright grant for Visiting Scholars from the Commission for Educational Exchange between the United States of America, Belgium and Luxembourg; E.T.G. was supported by the Luxembourg National Research Fund PRIDE (17/11823097) and the Fondation du Pélican de Mie et Pierre Hippert-Faber, under the aegis of the Fondation de Luxembourg. G.V.P. was supported by a fellowship from the W. Garfield Weston Foundation and E.C.M. acknowledges the financial support from National Institutes of Health (DK118024).

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Wolter, M., Grant, E.T., Boudaud, M. et al. Leveraging diet to engineer the gut microbiome. Nat Rev Gastroenterol Hepatol 18, 885–902 (2021). https://doi.org/10.1038/s41575-021-00512-7

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