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
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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.
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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.
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Current food-based dietary guidelines are not yet microbiome-oriented but generally provide advice for maintaining diet–microorganism synergies relevant to human health.
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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.
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The gut microbiome contributes to postprandial responses to meals, suggesting the potential to predict the long-term health consequences of our diet more accurately.
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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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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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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 (2025). https://doi.org/10.1038/s41575-025-01077-5
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Accepted: 02 May 2025
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Published: 04 June 2025
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DOI: https://doi.org/10.1038/s41575-025-01077-5