Vegan or not, plant-based foods boost gut microbes for better health

By Priyanjana Pramanik, MSc.Reviewed by Danielle Ellis, B.Sc.Jan 7 2025

Analysis of microbiome data from over 21,000 individuals suggests that diet diversity and quality, rather than strict veganism, drive gut microbes linked to better health

In a recent article in Nature Microbiology, researchers explored how dietary patterns impact the gut microbiome across diverse populations.

Their findings indicate that gut microbial profiles are reliable indicators of diet type. They identified specific microbes linked to poorer cardiometabolic health, particularly in omnivores consuming red meat, highlighting the benefits of plant-based diets.

Background

Diet plays a crucial role in human health, with poor diets high in processed and animal-based foods contributing to major diseases like type 2 diabetes, heart disease, and cancer. These diets also have significant environmental impacts, including climate change and biodiversity loss. As a result, there is growing interest in plant-based diets, which can improve health and reduce environmental harm.

The gut microbiome, which is influenced by diet, is key to maintaining health. Plant-based foods support gut health by promoting beneficial bacteria that produce short-chain fatty acids (SCFAs), strengthen the gut barrier, and reduce inflammation. In contrast, animal-based diets can lead to harmful protein fermentation, causing gut inflammation and increased risk of diseases like cardiovascular issues and colorectal cancer.

However, current research on the diet-microbiome relationship lacks large-scale, diverse studies. This limits understanding of how specific foods affect individual gut microbes across different populations.

About the study

The study included data from five cohort studies. Participants provided dietary information and stool samples for metagenomic sequencing. The cohorts consisted of 656 vegans, 1,088 vegetarians, and 19,817 omnivores, and informed consent was obtained from all participants.

Participants' diets were classified using Food Frequency Questionnaires (FFQs) and the Metagenomic Estimation of Dietary Intake (MEDI) tool. MEDI's classification was compared to FFQs, showing that while MEDI can identify dietary patterns, it is less accurate than FFQs. FFQs were used to calculate the healthy Plant-based Diet Index (hPDI). Stool samples were also processed and sequenced for genetic analysis, and relative abundances of microbes were calculated.

Machine learning, specifically random forest models, was used to link diet patterns to microbiome profiles. The models were validated through cross-validation and leave-one-dataset-out approaches.

Differential abundance of microbes was assessed using linear models, and meta-analysis was performed to pool results. Correlations between diet and microbiome features were analyzed using Spearman's correlation, adjusted for confounders like age and body mass index (BMI).

Findings

The study found that gut microbial diversity and composition differ significantly across diet patterns, with vegans and vegetarians having lower microbial richness than omnivores. This suggests that omnivores, with their more varied diets, support a broader range of gut microbes. The gut microbiomes of different diet patterns were distinguishable using machine learning, with the highest predictability between vegans and omnivores.

When examining microbial signatures, omnivores had more abundant species associated with meat digestion, while vegans had more fiber-degrading and butyrate-producing species. Dairy consumption notably influenced microbial composition, with dairy-linked species being more prevalent in omnivores and vegetarians.

The study also showed that major food groups, particularly dairy, meat, vegetables, and fruits, played a key role in shaping the microbiome. For instance, meat consumption was linked to species in omnivores, while plant-based foods were more strongly associated with vegetarians and vegans.

Additionally, the research found that dietary diversity, particularly plant-based food intake, influences gut microbial composition. Vegans showed fewer food-derived microbes, likely due to the absence of meat and dairy in their diets. The study also linked gut microbiome signatures to cardiometabolic health, with omnivores having less favorable outcomes compared to vegetarians and vegans.

Omnivores had microbial species like Alistipes putredinis, Bilophila wadsworthia, and Ruminococcus torques associated with meat consumption, particularly red meat, which were associated with inflammatory diseases and poor cardiometabolic health. In contrast, vegan diets had microbes such as Lachnospiraceae, Butyricicoccus sp., and Roseburia hominis, linked to fiber breakdown from vegetables and fruits, and were associated with better cardiometabolic health.

Dairy-heavy diets showed signatures of lactic acid bacteria, such as Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, and Lactococcus lactis, beneficial for gut health. Vegan microbiomes also contained microbes shared with soil and plant microbiomes, suggesting a potential connection between agriculture and gut health.

Conclusions

This study explored how different diets, specifically omnivore, vegetarian, and vegan, impact the gut microbiome through an analysis of data from 21,561 individuals. The researchers found distinct microbiome signatures for each diet.

Their findings highlighted how dietary choices, especially increasing plant-based foods in omnivore diets, can improve gut health. Researchers also found evidence of the harms associated with red meat consumption in terms of cardiometabolic health and inflammatory disease. The study emphasizes the need for further research on food-to-gut transmission and the relationship between diet and microbiome health.