A varied diet rich in vegetables is known to be healthy for one's well-being. Excessive consumption of meat, especially red meat, can lead to chronic and cardiovascular diseases. That is also because what we eat shapes the gut microbiome. At the same time, excluding certain foods, such as dairy or animal products, is not necessarily a general solution to achieve microbial balance. But can we find out which food products determine differences in the gut microbiome?

Starting from this question, a group of researchers has analyzed biological samples from 21,561 individuals (vegans, vegetarians and omnivores) living in the United States, the United Kingdom and Italy, and found that the dietary pattern has a strong influence on the gut microbiome and on specific gut microbes that are associated with better health. The data is published in Nature Microbiology.

The gut microbiome, the set of microorganisms that inhabit our intestine, plays a crucial role in determining a person's health, as it influences many aspects, from digestion to the immune response. So far, only a few large-scale studies have examined how different diets impact the composition of gut bacteria.

This study focused in particular on the differences and consequences of different diets on the microbiome. The results show that diet patterns shape the gut microbiome, as they not only determine the microbes necessary for digestion, but also the acquisition of microbes directly from the food itself.

Based on the results of the analyses,  on average vegans have the healthiest diets, followed by vegetarians and omnivores. However, the most interesting data emerged from the study of the diversity of the gut microbiome; that is, by measuring the variety of bacteria that inhabit our intestines.

Overall, there was less diversity in vegetarians and vegans than in omnivores, but scientists point out that diversity alone is not a reliable means to determine the health of the microbiome, as it does not take into account the quality and functionality of bacteria.

The microbial signatures of vegan, vegetarian and omnivorous diets:
A key aspect of the study was to examine the differences between gut microbiomes. The researchers were able to see how each dietary pattern leads to a unique microbial signature. The microbiomes of omnivores have an increased presence of bacteria associated with meat digestion, such as Alistipes putredinis, involved in protein fermentation. Omnivores also have more bacteria associated with inflammatory bowel disease and an increased risk of colon cancer, such as Ruminococcus torques and Bilophila wadsworthia.
The microbiomes of vegans differ in the number of bacteria involved in fiber fermentation, such as several species in the Bacteroides and Firmicutes phyla, which help produce short-chain fatty acids, such as butyrate. These compounds have beneficial effects on gut health, as they reduce inflammation and maintain a better homeostatic balance with our metabolism and immune system.

Finally, the main single difference between vegetarians and vegans is the presence of Streptococcus thermophilus in the microbiome of vegetarians, a bacterium found mainly in dairy products and used in the production of yogurt.
Healthy diet and healthy microbiome
The study highlighted that it is the quality of the diet—rather than the dietary pattern itself—that influences the composition of the microbiome. People with healthier dietary patterns, whether vegan, vegetarian or omnivorous, showed a more favorable microbiome composition. This suggests that regardless of the type of diet, eating more plant-based foods and fewer animal-based foods, especially if highly processed, can be good for gut health.
Another innovative aspect of the research was the study of how bacteria transfer from food to the microbiome. The scientists found that vegans had the fewest food-associated bacteria in the microbiome, except for those derived from fruits and vegetables, which were most present. Vegetarians and omnivores, on the other hand, showed a greater number of bacteria linked to dairy products, especially fermented ones.
The researchers observed that the quantity and diversity of plant-based foods have a very positive impact on the microbiome. Avoiding meat or dairy products does not necessarily have a positive effect if it does not come with a variety of quality plant-based products. From the point of view of the microbiome, what we can generally recommend is that it is important to eat many plant-based foods, especially those rich in fiber. And that food diversity is important.

Nicola Segata, 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