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  • Review Article
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The gut microbiome connects nutrition and human health

Nature Reviews Gastroenterology & Hepatology volume 22, pages 534–555 (2025)Cite this article

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Abstract

The gut microbiome has an undeniable role in mediating the health effects of the diet, given its ability to co-digest nutrients and influence nutrient signalling to multiple organ systems. As a suboptimal diet is a major risk factor for and contributor to disease, understanding the multidirectional interactions between the food we eat, the gut microbiome and the different body organ systems is crucial from a public health perspective. Indeed, this research area is leading to the refinement of nutritional concepts and strategies to optimize health through diet. In this Review, we provide an update on how dietary patterns and food intake shape gut microbiome features, the mode of action of diet–microorganism interactions on the immune, nervous and cardiometabolic systems and how this knowledge could explain the heterogeneity of dietary responses, and support food-based dietary guidelines and medical and precision nutrition. Finally, we discuss the knowledge gaps and research efforts needed to progress towards the integration of microbiome science with more precise dietary advice to leverage the role of nutrition in human health.

Key points

  • Exploring the granularity of the diet and multidimensional aspects of foods together with advanced big data-driven analyses offers opportunities to better capture diet–microbiome–health relationships and explain unsolved response patterns and mechanisms in humans.

  • Microbially produced metabolites from dietary sources and microbial cell structural constituents have been demonstrated to regulate immune, endocrine and nervous system functions, supporting their causal role in diverse health domains.

  • Current food-based dietary guidelines are not yet microbiome-oriented but generally provide advice for maintaining diet–microorganism synergies relevant to human health.

  • Further understanding of the contribution of the gut microbiome to the heterogeneity of diet-related responses is vital to optimizing the role of nutrition in public health.

  • The gut microbiome contributes to postprandial responses to meals, suggesting the potential to predict the long-term health consequences of our diet more accurately.

  • The response to the diet and the links to the gut microbiome vary in health and disease contexts and need to be scrutinized for the development of more precise nutritional practices.

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Fig. 1: Dietary orchestration of gut barrier and immunity is linked to the microbiome.
Fig. 2: Diet and gut microbiome interactions orchestrate nervous system function.
Fig. 3: Dietary influence on cardio-metabolism is linked to the gut microbiome.

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Acknowledgements

The work of Y.S. is funded by the Spanish Ministry of Science, Innovation and Universities (grant PID2023-150693OB-I00), and a “Severo Ochoa” grant of the National Agency for Research (AEI)–Spanish Ministry of Science and Innovation (ref. CEX2021-001189-S). The work of P.V. is funded in part by a Metagenopolis grant (ANR-11-DPBS-0001) and the PEPR-SAMS Cohortes-Microbiomes Project (ANR-24-PESA-0005). J.F.C. is supported by Science Foundation Ireland (SFI/12/RC/2273_P2), Saks Kavanaugh Foundation and Swiss National Science Foundation (CRSII5_186346/NMS2068). E.E. is supported by the European Union Thrive and Nutriome Consortiums and is a partner, Novo Nordisk Foundation Microbiome Health Initiative (MHI). R.L. is grateful to the Azrieli Foundation for an Azrieli Fellowship.

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Authors and Affiliations

  1. Microbiome Innovation in Nutrition and Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain

    Yolanda Sanz

  2. APC Microbiome Ireland, University College Cork, Cork, Ireland

    John F. Cryan

  3. Department of Anatomy and Neuroscience, School of Medicine, University College Cork, Cork, Ireland

    John F. Cryan

  4. Université Sorbonne Paris Nord and Université Paris Cité, INSERM, INRAE, CNAM, Center for Research in Epidemiology and Statistics (CRESS), Nutritional Epidemiology Research Team (EREN), Bobigny, France

    Mélanie Deschasaux-Tanguy

  5. Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel

    Eran Elinav & Rebekka Lambrecht

  6. Microbiome & Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Eran Elinav

  7. Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France

    Patrick Veiga

  8. Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, France

    Patrick Veiga

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  1. Yolanda Sanz
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  4. Eran Elinav
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  6. Patrick Veiga
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Contributions

The authors contributed equally to all aspects of the preparing the manuscript.

Corresponding author

Correspondence to Yolanda Sanz.

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Competing interests

Y.S. is a co-author of probiotic patents, serves as a scientific adviser for Arla Foods and has been awarded by IFF. P.V. serves as a scientific consultant and adviser for Arla Foods and Newroad Innovations Ltd. J.F.C. is the co-author of probiotic patents and has received research funding from IFF, Nutricia and Kerry Foods, and has been an invited speaker at meetings organized by Bromotech and Nestlé. The other authors declare no competing interests.

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Sanz, Y., Cryan, J.F., Deschasaux-Tanguy, M. et al. The gut microbiome connects nutrition and human health. Nat Rev Gastroenterol Hepatol 22, 534–555 (2025). https://doi.org/10.1038/s41575-025-01077-5

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