How your diet affects your gut: secrets of vegans, vegetarians and omnivores

The study is published in Nature Microbiology and shows that different dietary habits form unique microbial "signatures" that influence health outcomes.

Source: Nicola Segata et al, "Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals", Nature Microbiology (2025). DOI: 10.1038/s41564-024-01870-z

What is the gut microbiome?
It is the community of billions of bacteria living in our gut. They help us digest food, support our immune system and even influence our metabolism. According to the paper, it's the mix of foods in your diet - not just avoiding animal foods - that largely determines which bacteria will dominate.

Study results
The scientists found that, on average, vegans have the "healthiest" diets: they consume more fruits and vegetables, which means more fibre and nutrients. However, vegans and vegetarians show a slightly lower "diversity" of gut bacteria than meat eaters. But high diversity alone does not guarantee benefit: bacteria associated with an increased risk of colorectal cancer and inflammation (e.g. Ruminococcus torques and Bilophila wadsworthia) have been identified in the microbiome of meat eaters.

Vegans, on the other hand, are dominated by fibre-degrading microbes - they produce short-chain fatty acids such as butyrate, which helps reduce inflammation in the body and keep metabolic processes balanced. Vegetarians are found to have Streptococcus thermophilus, a bacterium commonly found in dairy products and used in the production of yoghurt.

Quality is more important than the name of the diet
Researchers emphasise that a healthier diet is one that contains enough plant fibre and less processed animal products.

We must also consider that microbes come directly from food: vegans have a higher prevalence of bacteria from fruit and vegetables, while those who eat meat or dairy products are much more likely to have bacteria from these sources.