What you eat is one of the most critical factors that keep your gut microbiome in good shape, even outweighing your genes. However, it’s unclear if diet shapes the gut microbiome similarly between people from different countries who eat a variety of types of diets and the extent to which food microorganisms impact the human gut.
After looking at data from 21,561 people from the United States of America, the United Kingdom, and Italy, scientists found the amount of healthy plant-based foods you consume, rather than what type of diet you follow, appears to have a more significant impact on gut microbes that favor heart health.
To find diet-related microbial signatures, the authors leveraged the collective genomes and genes of gut microorganisms of a large microbiome dataset based on stool samples from 21,561 participants who also self-reported their long-term dietary patterns. Analyzing all the microbial DNA in feces (named shotgun metagenomics) through machine learning methods allowed researchers to identify microorganisms down to the strain level and estimate microbial functional potential.
Vegan, vegetarian, and omnivore diets were associated with highly distinguishable gut bacteria profiles that may influence health. A vegan diet was associated with more beneficial gut bacteria, including short-chain fatty acid producers, with potential benefits for heart health.
In contrast, red meat eaters showed higher levels of microbes that aid meat digestion and were associated with an increased risk of colon cancer, inflammatory bowel disease, and cardiovascular diseases. Vegetarians showed an intermediate gut microbial signature that was between that of vegans and omnivores.
That doesn’t mean that people eating a mixed diet with animal foods will have necessarily condemned gut health. Each food group has its unique effect on the gut, and people following an omnivore diet shared some gut bacteria with vegetarians and vegans, especially if they eat similar amounts of fruits, vegetables, whole grains, and pulses on their menus.
But the reality is that individuals who consumed a mixed diet in the study ate notably fewer healthy plant-based foods than vegans or vegetarians, which limits the gut benefits seen in those groups.
Foods also led to the acquisition of microbes from foods, especially from dairy. For example, Streptococcus thermophilus, which is generally used in the production of yogurt, was the species with the greatest ability to differentiate between vegan and vegetarian gut microbiomes. Food-associated microorganisms were higher in omnivores and vegetarians who eat dairy, fruits, and vegetables. In contrast, the fecal microbiome of vegans shared the lowest number of microorganisms with foods. Dairy, fruits, and vegetables were the foods that transferred most of their microorganisms to the participants’ gut microbiome, highlighting that soil and plant cultivation practices may also contribute to the human gut microbiome diversity.
In summary, these new findings in a vast population consuming vegan, vegetarian, and omnivore diets show gut microbial diversity reflecting dietary patterns, with plant-based diets fostering gut health. Omnivores, vegans, and vegetarians share microbes that are driven by the whole diet and overlap with microorganisms inherently present in dairy, fruits, and vegetables.
References:
- Fackelmann G, Manghi P, Carlino N, et al. Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nat Microbiol. 2025; 10(1):41-52. doi: 10.1038/s41564-024-01870-z.
- Wicaksono WA, Cernava T, Wassermann B, et al. The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut. Gut Microbes. 2023; 15(2):2258565. doi: 10.1080/19490976.2023.2258565.