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A groundbreaking study published in Nature Microbiology has revealed that dietary choices significantly shape the gut microbiome, which in turn impacts overall health outcomes. Researchers analyzed biological samples from 21,561 individuals across the United States, the United Kingdom, and Italy, focusing on vegans, vegetarians, and omnivores. The findings highlight how distinct diets influence the microbial communities in our intestines, which play a pivotal role in digestion, immune function, and chronic disease prevention.
The gut microbiome consists of trillions of microorganisms that reside in the human digestive system. These microbes help process food, modulate immune responses, and maintain gut health. However, few large-scale studies have explored the intricate relationship between diet and the composition of gut microbiota. This new research, led by Nicola Segata and conducted by a team from Italy’s University of Trento and King’s College London, sheds light on how varying diets lead to different microbial signatures.
The study found that vegans, who follow plant-based diets, have the healthiest dietary patterns on average, followed by vegetarians, and then omnivores. However, a surprising conclusion was that while vegans and vegetarians typically had less microbial diversity than omnivores, diversity alone is not a reliable indicator of gut health. Researchers emphasize that the quality and functionality of bacteria matter more than sheer diversity.
Dr. Gloria Fackelmann, the study’s first author, explained, “As more people adopt vegan and vegetarian diets, we wanted to investigate how their microbiomes differ and identify which microorganisms are responsible for these differences.” The results reveal that diet patterns have a profound influence on both the acquisition of microbes and their roles in digestion.
The microbial differences between the three diet groups are striking. Omnivores, for example, have a higher presence of bacteria that aid in protein fermentation, such as Alistipes putredinis, and are more likely to harbor bacteria linked to inflammatory bowel disease and colon cancer, including Ruminococcus torques and Bilophila wadsworthia. In contrast, vegans exhibit a higher abundance of bacteria involved in fiber fermentation, like species in the Bacteroides and Firmicutes phyla, which produce beneficial short-chain fatty acids such as butyrate. These compounds help reduce inflammation and support metabolic and immune system balance.
Interestingly, vegetarians have a unique microbial signature marked by the presence of Streptococcus thermophilus, a bacterium commonly found in dairy products and used in yogurt production. This sets them apart from vegans, who avoid dairy entirely.
The researchers emphasize that diet quality is more important than adhering strictly to a particular diet. People who eat a balanced, nutrient-dense diet—whether vegan, vegetarian, or omnivorous—tend to have a healthier microbiome. The study underscores the benefits of consuming more plant-based foods, especially those high in fiber, while limiting processed and animal-based products.
One of the most innovative aspects of the study was examining how bacteria from food transfer into the microbiome. The findings show that vegans have fewer food-associated bacteria, aside from those derived from fruits and vegetables. Vegetarians and omnivores, on the other hand, exhibited higher levels of bacteria linked to dairy consumption, particularly fermented products.
Professor Segata stated, “The quantity and diversity of plant-based foods positively impact the microbiome. Avoiding meat or dairy products does not automatically result in a healthier microbiome unless it is replaced with a variety of high-quality, fiber-rich plant-based foods. A diverse diet is key.”
This research forms part of a larger project aimed at understanding how specific diets influence health, particularly in relation to cardiometabolic conditions. The team hopes to build on this work with precision nutrition, offering personalized dietary recommendations based on an individual’s microbiome.
For further details, refer to the study: Gut microbiome signatures of vegan, vegetarian, and omnivore diets and associated health outcomes across 21,561 individuals by Nicola Segata et al., published in Nature Microbiology (2025). DOI: 10.1038/s41564-024-01870-z.
