The gut microbiome & dietary patterns
The gut microbiome is a dynamic community of trillions of microorganisms living in our digestive tract—plays a vital role in keeping us healthy. It helps regulate immunity, support digestion, and affects how our bodies process and use energy. In fact, our diet can influence everything from how well we absorb nutrients like calcium to how our brain functions. [1,2] Research shows that what we eat has a powerful impact on the balance and function of these microbes—often more than factors like age, genetics, or where we live. [3]
Despite this, many dietary guidelines have been created without fully considering the microbiome’s role. This may partly explain why there’s often confusion and debate around nutrition science—especially when it comes to topics like vegetarian vs omnivorous dietary patterns.
To investigate the effects of different dietary patterns on microbiome health, a recent, large-scale metagenomic analysis, including 21,561 multi-national subjects, compared the impact of omnivore, vegetarian, and vegan eating patterns on microbial signatures, revealing the following nuanced outcomes:
- Omnivores showed the greatest microbial diversity, likely due to a broader range of substrates. However, they also had elevated levels of certain protein-fermenting species linked to adverse cardiovascular markers.
- Vegetarians shared health-promoting dairy-associated species with omnivores, suggesting dairy’s role in shaping microbial composition.
- Vegans exhibited a dominance of beneficial SCFA-producing microbes, that had favourable outcomes on cardiovascular health. [4]
While each dietary pattern was linked to unique microbial signatures, omnivores showed the greatest microbial diversity, however these patterns had the potential to be linked to both positive and negative health outcomes. Overall data showed that the main determinant of health-promoting factors was not the diet pattern itself, but rather the abundance of plant food consumption. Therefore, researchers concluded that incorporating additional plant foods into an omnivorous dietary pattern could help match the signatures promoted by vegan and vegetarian diets, optimising the quality of diet and thus supporting better gut health. [4]
Conclusion
This study reinforces the notion that humans can play a key role in shaping their microbiome health through simple dietary choices that can be adjusted to suit individual taste, cultural and/or ethical food preferences.
References:
- Barone M, D’amico F, Brigidi P, Turroni S. Gut microbiome–micronutrient interaction: The key to controlling the bioavailability of minerals and vitamins?. Biofactors. 2022 Mar;48(2):307-14.
- Singh RK, Chang HW, Yan DI, Lee KM, Ucmak D, Wong K, Abrouk M, Farahnik B, Nakamura M, Zhu TH, Bhutani T. Influence of diet on the gut microbiome and implications for human health. Journal of translational medicine. 2017 Dec;15:1-7.
- Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555(7695):210–215.
- Fackelmann, G., Paolo Manghi, Carlino, N., et al. (2025). Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nature Microbiology, 10(1), 41–52.
