Microbiome research has often been criticized for overhype, but it has become increasingly clear that interactions between diet and the microbial communities that inhabit our gut can have profound effects on host health. Indeed, the theme of this year’s World Microbiome Day, celebrated on 27 June, is “Feed your microbes — How diet shapes your gut microbiome”. We now know much more about how diet impacts gut microbiome function, how gut microbes process dietary components, how this interlinks with host health and disease, and how this knowledge can be harnessed for therapeutic interventions1,2. Yet, there is still so much unknown. New microbial metabolisms are being uncovered, as well as the associated ecological mechanisms, underlying chemistry, immunological consequences and implications for host physiology. Understanding the complexity of the host, microbiome and diet interactions is necessary to replace hype with actionable research outcomes.

A quick PubMed search in June 2024 using the keywords ‘gut microbiota’ and ‘nutrition’ demonstrates the recent expansion of research in this space: there were more than 11,000 hits between 2020 and 2024 but fewer than 9,000 in the preceding 10 years. Public interest has also soared in recent years. Buzzwords such as ‘gut health’, ‘high fibre’ and ‘microbiome-friendly’ are used to entice consumers to buy a range of food products, while an increasing number of microbiome scientists, nutritionists and clinicians have produced books, podcasts and even a couple of TV shows. This is an exciting time for the microbiome field. However, as with all science, our understanding is constantly evolving. In particular, the gut microbiota is variable across individuals, thus findings in animal models may not readily translate due to context-dependent processes. We therefore all have the responsibility to ensure accurate dissemination of information to the public, including the limitations.

For example, several studies have uncovered a beneficial role for the gut bacterium Akkermansia muciniphila in metabolic disease, which holds promise as a next-generation probiotic. On the other hand, recent work has shown it can also exacerbate food allergy in mice3. More work must be done to understand these opposing effects, the context for each and the factors driving them. Until recently, A. muciniphila was genetically intractable and so the functions and genetics of this intriguing bacterium had been unexplored. Lauren Davey, assistant professor at the University of Victoria, Canada, shares her experience of working with A. muciniphila and how she transformed it into a genetically tractable microbe in this month’s Microbe Matters. Methodological developments such as these are key for the progression of the microbiome field and will help to build understanding of how A. muciniphila and other potentially beneficial microbes could be harnessed for clinical applications.

Another approach that can help disentangle the complexities of microbiome–diet interactions is genome-scale metabolic modelling. This is increasingly being used to predict the metabolic potential of microbiomes in response to different variables using genomic data. In an Article in this issue of Nature Microbiology, Sean Gibbons and colleagues report they applied microbial community-scale metabolic modelling in the context of the human gut microbiota and different dietary interventions to predict short-chain fatty acid (SCFA) production. SCFAs are well-known microbiota-derived metabolites associated with fibre intake and health, but concentrations are highly variable across individuals. The authors confirm this variability, show that SCFA predictions are associated with health readouts, including cardiometabolic and immunological markers, and harness their models to design personalized dietary interventions to optimize SCFA production in the gut. Although these are encouraging results, further work is needed to validate this approach in cohorts and demonstrate its use for personalized dietary interventions.

While preclinical research in this space is promising, the leap from animal models to humans and consequent clinical implementation is challenging4. This is discussed in a Perspective by Wendy Garrett and colleagues in the context of colorectal cancer. Numerous metabolites resulting from microbiota–diet interactions have been shown to protect against, or exacerbate, carcinogenesis or impact host response to immunotherapy in mouse models. Multiple clinical trials have tested different dietary interventions to treat and prevent various cancer types, but outcomes have been variable. Garrett and colleagues provide a pragmatic conclusion: there is currently insufficient evidence to pursue dietary interventions for cancer outside of clinical studies, but there are promising experimental study results that could hold potential.

There is certainly much to celebrate when it comes to World Microbiome Day. The end of June also marks the closing date for our call for papers on microbiome and nutrition, in collaboration with Nature Communications, but we remain committed to highlighting research in this growing area beyond the collection. We look forward to working with researchers to communicate their work effectively and accurately to reduce the hype rhetoric surrounding the microbiome.