Study finds vegans have less diverse gut bacteria than meat eaters, even though they consume more fiber and have several healthier metabolic markers.
It is widely accepted that plant-based diets promote a healthy gut, in part because fiber feeds beneficial bacteria.
Scientists therefore expected that vegans would have a greater variety of gut microbes than people who eat meat. But a study in Denmark of 150 healthy adults found otherwise.
Vegans had less diverse gut bacteria, even though several other measures of their gut and metabolic health appeared more favorable.
The study was led by Oluf Borbye Pedersen, a professor at the Center for Basic Metabolic Research at the Novo Nordisk Foundation at the University of Copenhagen.
“That was a major surprise,” Pedersen said.
“Because vegans eat only plant-based foods and therefore consume high amounts of dietary fiber and other health-promoting plant compounds that boost the gut microbiome, we expected the vegan group to have greater bacterial diversity than omnivores.
“But that wasn’t the case.”
Four days of meals
The volunteers lived in an urban area in Denmark and joined the project through advertisements in newspapers and on social media. They ranged in age from 18 to 65 and each group had an average age of 31, with 40 women and 35 men.
Every vegan had been eating this way for at least a year, with an average of about six and a half years.
The researchers excluded people with bowel diseases, pregnant or breastfeeding women, and anyone who had taken antibiotics or probiotics in the previous three months.
For four days, each person weighed everything they ate on a precision scale, covering two work days and two weekend days. They also gave stool, blood and urine samples.
Scientists at Paris-Saclay University in France read DNA from stools to identify microbes.
Researchers at Imperial College London measured more than 200 small molecules in stool, blood and urine.
Protein May Be Important
Both groups consumed approximately the same number of calories. But protein provided 12% of vegans’ calories, compared to 17% for meat eaters.
Vegans consumed almost 70% more fiber, but their gut bacteria was less varied by most measures. Scientists often use bacterial variety as a sign of good metabolic health.
Among vegans, those who ate more protein tended to have more types of gut bacteria, while fiber showed no such link. People who had been vegan for longer also tended to carry more species.
Protein intake, diet duration and age together explain about a third of the differences in species numbers among vegans.
Pedersen thinks lower protein intake may help explain the lower variety, making protein a factor worth studying more closely.
What bacteria appeared
The team found 109 bacterial species whose quantities differed between groups: 82 were more common in meat eaters and 27 in vegans. Many of these symptoms, more common in vegans, were linked to higher fiber intake.
Two species more common among meat eaters, Streptococcus thermophilus And Lactococcus lactisare also present in dairy products.
To evaluate the bacteria, the researchers used a ranking published in Nature in 2025, based on their links to the heart and metabolic health of American and British populations.
Of the 16 species ranked most common among vegans, 13 were on the healthy side, compared to 28 of the 66 species more common among meat eaters.
Vegans in the top third in terms of protein intake carried more of the healthy species usually found in meat eaters, while those in the bottom third carried less.
“Besides the reduced diversity of gut bacteria, we found that vegans had a health-promoting gut microbiome,” Pedersen said.
What the blood tests showed
Vegans had lower blood sugar levels on two standard tests. They also had lower total cholesterol and LDL cholesterol levels.
Their blood contained fewer white blood cells and less C-reactive protein, a marker of inflammation. Blood pressure was the same in both groups and body size was almost identical.
Meat eaters had more of two compounds that gut bacteria help make in their urine, including TMAO. Previous studies have linked the two compounds to chronic heart and kidney disease.
Here, neither compound clearly tracked cholesterol levels or other health measures after the researchers took into account age, gender, and height.
The team also did not adjust the dilution of the urine samples, which could explain part of the difference.
Other intestinal findings
Despite the different mix of bacteria, both groups carried bacterial genes for almost the same tasks.
Only four of the 320 sets of genes differed, including one involved in the degradation of a building block of a protein and another involved in antibiotic resistance.
Bacteria have their own viruses, and these also differ. Vegans carry fewer types of viruses that kill the bacteria they infect.
Viruses that can live inside bacteria without killing them were about equally common in both groups.
The authors suggest that fewer destructive viruses could mean a more stable gut community, with fewer bacteria killed and replaced.
Another resident of the intestine
A single-celled organism called Blastocyst appeared in 27 of 75 vegans, compared to 14 of 75 meat eaters.
Vegans who wore it had lower systolic blood pressure, the highest number in a reading, after researchers took into account age, gender and height.
Among meat eaters, blood pressure was similar whether people wore meat or not.
The authors think Blastocyst can signal a healthy gut. A 2024 study of nearly 57,000 people in 32 countries linked it to a healthier diet and better heart and metabolic health.
But this team identified it solely through stool DNA, without a second laboratory test to confirm it. Too few people wore each type for researchers to determine which type, if any, might explain the link with blood pressure.
Limitations of the study
The researchers measured each person once and looked at the diets the people were already following. This can reveal links, but it cannot show that diet is causing the differences.
No one changed the vegans’ meals or checked what happened to their gut bacteria.
Eating more protein could affect the bacterial variety, or something else in the people who ate more protein could explain this pattern.
The study included just 150 healthy adults in Denmark, most of whom were of normal weight, so the results may not apply to broader populations.
Rethinking a healthy gut
Pedersen said the findings cannot serve as diet recommendations, although they argue that attention to nutrition should be paid no matter what people eat.
“Vegans in particular should consider whether they are getting enough protein in their diet, since they don’t get it from meat, eggs or dairy,” he added.
“Good vegan sources of protein include beans, lentils, hemp seeds, chia seeds, quinoa, almonds and walnuts. »
The findings challenge the idea that a more diverse gut microbiome is always healthier.
Although protein intake may help explain some differences, researchers need more study to understand how vegan diets shape gut bacteria and what these changes mean for long-term health.
The study is published in the journal Microbiota.
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