A well-balanced diet is recognized globally as a key contributor to overall health, with an emphasis on the importance of consuming vegetables. While vegetables play a pivotal role in providing nutrients and promoting good health, the consumption of meat—particularly red meat—has been linked to chronic health conditions such as cardiovascular disease. Central to this relationship between food and health is the gut microbiome, a complex ecosystem of microorganisms that inhabit our intestines. There is growing awareness about how our dietary choices directly impact the composition of the gut microbiome and its associated health outcomes. But the question arises: What foods in particular are responsible for determining the differences in our gut microbiome?
The gut microbiome is a critical player in maintaining health, affecting numerous aspects from digestion to immune function. Over the years, researchers have begun to appreciate the importance of microbiomes in influencing human well-being. The influence of diet on gut microbes remains a central topic of interest, given its implications for both general health and disease prevention. Most available studies exploring the impact of diet on the microbiome have been limited in scope. However, new groundbreaking research has shed light on this question, exploring how different diets shape the gut microbiome, providing novel insights into the types of microorganisms that are beneficial for overall health.
A team of researchers recently conducted a large-scale analysis involving biological samples from over 21,000 individuals living in the United States, the United Kingdom, and Italy. These participants were grouped based on their dietary habits: vegans, vegetarians, and omnivores. The findings, published in Nature Microbiology, demonstrate the significant impact that diet can have on the composition and diversity of gut microbes. This study represents one of the largest-scale efforts to date examining how diet interacts with the human microbiome, helping to improve our understanding of how specific dietary patterns can promote or inhibit health.
The research was guided by the principle that the gut microbiome plays an essential role in determining health outcomes. Our gut microbiome, which is made up of bacteria, fungi, viruses, and other microorganisms, has been shown to contribute to vital bodily functions, including digestion, nutrient absorption, and immune modulation. It influences various diseases, including obesity, diabetes, inflammatory bowel disease (IBD), and even mental health disorders. Despite this, few studies have sought to clarify the links between specific dietary patterns and the microbiome on such a large scale.
The researchers’ objective was to determine how various dietary patterns, including veganism, vegetarianism, and omnivorism, affect the microbiomes of individuals, particularly in terms of identifying which microorganisms are associated with health-promoting effects. As more people in the Western world adopt vegan or vegetarian diets, there has been growing interest in understanding whether these eating habits lead to healthier microbiomes and how microbiome differences correspond with diet.
One of the key findings of the study is that there are significant microbial signature patterns associated with different dietary habits. Notably, the study indicates that omnivores, vegans, and vegetarians each exhibited unique microbiomes, with differences in microbial composition linked to the foods they consumed.
Vegans, for example, were found to have the most beneficial dietary patterns overall, with their diets characterized by high fiber intake and a lack of animal products. This distinction contributed to a diverse and healthy microbiome. However, what became apparent in the study was the importance of microbial diversity. The researchers discovered that the diversity of the gut microbiome was higher in omnivores than in vegans or vegetarians. While microbial diversity has often been considered a strong indicator of gut health, the study highlighted that microbial diversity alone is not sufficient to determine whether the microbiome is functioning optimally. In fact, diversity needs to be evaluated in conjunction with the quality and functionality of the microorganisms present in the gut.
While a greater diversity of bacteria was observed in omnivores, the microbiomes of these individuals also showed higher levels of bacteria known to be associated with inflammation and certain gastrointestinal diseases. For instance, the presence of certain bacteria such as Ruminococcus torques and Bilophila wadsworthia was found to be significantly higher among omnivores. These bacteria have been linked to inflammatory bowel disease (IBD) and an elevated risk of colon cancer, highlighting that the types of microbes present are just as important as the diversity within the gut microbiome.
On the other hand, vegans were characterized by microbiomes rich in bacteria related to fiber fermentation. Bacteria from the Bacteroides and Firmicutes phyla, which are important for breaking down fiber into short-chain fatty acids such as butyrate, were significantly more prevalent. These short-chain fatty acids play an essential role in maintaining a healthy gut lining and reducing inflammation, contributing to improved overall gut health and metabolic function. A plant-based diet, with its rich content of fruits, vegetables, whole grains, legumes, and nuts, is a substantial driver of the growth of these beneficial microbes.
The study also differentiated vegetarians from vegans, noting that there was a single distinguishing factor—the presence of Streptococcus thermophilus, a bacterium commonly associated with dairy products. This bacterium is used in the production of yogurt and other fermented dairy products. While both vegans and vegetarians consume a plant-heavy diet, vegetarians incorporate dairy into their meals, which may account for this unique microbial trait.
The findings reinforce an essential conclusion: that the quality of one’s diet, not necessarily the food group that is consumed or avoided, is the determining factor influencing the gut microbiome. Individuals on healthier diets, regardless of their classification as omnivores, vegetarians, or vegans, exhibited microbiomes with higher levels of health-promoting bacteria. This suggests that a well-rounded diet, emphasizing whole, minimally processed foods such as fruits, vegetables, whole grains, and legumes, leads to better microbiome health, regardless of the avoidance of specific food groups.
Furthermore, the research emphasized that the bacteria in the gut may not just come from food, but also transfer directly into the gut microbiome as people consume various foods. Vegans, for example, were found to have fewer food-associated bacteria overall, apart from the beneficial bacteria obtained from consuming fruits and vegetables. On the other hand, vegetarians and omnivores exhibited increased levels of bacteria associated with dairy and fermented foods.
From the study’s perspective, the takeaway is clear: while avoiding meat or dairy might not inherently lead to a healthier microbiome, integrating a diverse range of plant-based foods—particularly those rich in fiber—can lead to positive outcomes. A varied and balanced diet, replete with high-quality fruits and vegetables, could be essential for fostering microbial health. This focus on dietary diversity, especially plant-based diversity, holds promise as a straightforward and practical strategy to optimize gut health.
The study also reinforces the growing field of precision nutrition, which tailors dietary recommendations based on the specific microbiome of each individual. By understanding how the microbiome interacts with different food choices, scientists hope to design personalized nutrition strategies that can target and improve health outcomes in a way that is unique to each person.
Reference: 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
