A large-scale study of over 21,500 individuals has identified distinct gut microbiome patterns associated with vegan, vegetarian, and omnivore diets.
In the study, published in Nature Microbiology, investigators analyzed gut microbiome samples, finding that microbial profiles could distinguish between these common diet patterns with high accuracy (mean area under the receiver operating characteristic curve [AUC] = 0.85). After excluding 22 samples as outliers from the alpha diversity analysis, the study provided robust insights into diet-microbiome relationships. The research was conducted across five independent cohorts, including three from the ZOE PREDICT program and two Italian cohorts.
"Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes negatively correlated with host cardiometabolic health markers," the study authors reported. Key microbes associated with omnivore diets included Ruminococcus torques, Bilophila wadsworthia, and Alistipes putredinis.
In contrast, vegan-associated gut microbes showed positive correlations with more favorable cardiometabolic health markers and were found to be enriched in omnivores who consumed more plant-based foods. Signature microbes in vegan gut microbiomes included known butyrate producers like Lachnospiraceae, Butyricicoccus sp., and Roseburia hominis.
The study identified Streptococcus thermophilus, a common dairy starter culture, as having the highest effect size in vegetarian vs vegan gut microbiomes (standardized mean difference = of –0.67) and the second highest effect size in omnivore vs vegan gut microbiomes (SMD = –0.62), highlighting the influence of dairy consumption on gut microbial composition.
Notably, several food-derived microbes showed distinct patterns. Vegans had the highest prevalence of microbes shared with fruits and vegetables, including soil-based organisms like Enterobacter hormaechei and Klebsiella pneumoniae, which are known to promote plant growth.
An analysis of healthy plant-based diet index scores revealed statistically significant differences between diet patterns, with vegans showing higher scores compared with vegetarians, and vegetarians scoring higher compared with omnivores. These dietary factors influenced gut microbiome composition regardless of overall diet pattern, suggesting that omnivores could modulate their gut microbial signatures by incorporating more plant-based foods into their diets.
The study utilized shotgun metagenomic sequencing to analyze the stool samples of 656 vegans, 1,088 vegetarians, and 19,817 omnivores across the multinational cohorts.
These findings suggested potential applications for improving clinical intervention studies and epidemiologic research related to diet patterns. The investigators emphasized that their work "reinforces how humans can shape their own gut microbiomes, and by extension their health, directly through simple dietary choices as well as more indirectly through agricultural and food production practices."
The investigators noted study limitations, including the inability to track when participants may have switched diet patterns, suggesting that some associations might actually be stronger than observed.
This comprehensive analysis, the largest to date on common Western diet patterns and gut microbiome composition, examined associations between dietary habits and microbial communities.
Full disclosures can be found in the study.