Diet plays a profound role in shaping the gut microbiome, the vast community of microorganisms living within our digestive system. Recent research (Fackelmann et al) involving over 21,500 individuals across multiple countries has revealed significant differences in gut microbiome composition depending on dietary patterns, such as omnivorous, vegetarian and vegan diets.
These findings shed light on how food choices influence gut health and broader health outcomes, providing insights that could guide dietary recommendations and clinical interventions.
As ever, please talk to your doctor or medical practitioner most familiar with your medical history before implementing any changes in diet, exercise or lifestyle, especially if you are under treatment. Links to relevant studies at bottom of page.
Dietary Patterns and Gut Microbiomes
Each dietary pattern leaves a distinctive signature on the gut microbiome. For omnivores, species such as Alistipes putredinis, Bilophila wadsworthia, and Ruminococcus torques are prominent. These microbes are often linked to meat consumption, particularly red meat, and have been associated with inflammatory conditions, such as inflammatory bowel disease and colorectal cancer, as well as reduced production of short-chain fatty acids (SCFAs). SCFAs are beneficial compounds that support gut and metabolic health and their deficiency can negatively impact cardiometabolic outcomes.
In contrast, vegan diets foster gut microbes adept at breaking down dietary fibre, such as Lachnospiraceae, Butyricicoccus sp. and Roseburia hominis. These microbes are known producers of SCFAs and are associated with improved cardiometabolic health. Interestingly, microbes commonly found in soil and plants, such as Enterobacter hormaechei and certain strains of Klebsiella pneumoniae, are more prevalent in vegan gut microbiomes. These microbes may play a role in promoting plant growth through nitrogen fixation, raising intriguing possibilities about the interplay between agricultural practices and human gut health.
Diets rich in dairy products, such as those common among omnivores, show an abundance of lactic acid bacteria like Lactobacillus acidophilus and Streptococcus thermophilus. These microbes are considered beneficial to gut health and are a hallmark of dairy consumption.
While dietary patterns influence gut microbiomes, the quality of food choices within each pattern is equally important. For example, omnivores who consume a diverse range of plant-based foods exhibit gut microbial profiles more similar to vegetarians and vegans, suggesting that plant-based diversity can mitigate some of the negative effects associated with meat consumption. Increasing the intake of fruits, vegetables and other fibre-rich foods is a straightforward way to promote a healthier gut microbiome across all dietary patterns.
Final Thoughts
This research highlights the powerful role of diet in shaping gut microbiomes and, by extension, overall health. By choosing foods - rich in fibre and (not mentioned in this article, polyphenols) that support beneficial microbes, individuals can positively influence their gut health and cardiometabolic outcomes. While omnivores, vegetarians and vegans each exhibit distinct microbial profiles, incorporating a variety of plant-based foods into any diet is a universally beneficial strategy.
As plant-based diets gain popularity, further exploration of how dietary choices interact with gut microbiota will be key to developing personalised nutritional strategies and enhancing public health outcomes.
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Related Studies and Resources
The study in question... Fackelmann G, Manghi P, Carlino N, Heidrich V, Piccinno G, Ricci L, Piperni E, Arrè A, Bakker E, Creedon AC, Francis L, Capdevila Pujol J, Davies R, Wolf J, Bermingham KM, Berry SE, Spector TD, Asnicar F, Segata N. Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nat Microbiol. 2025 Jan 6. doi: 10.1038/s41564-024-01870-z. Epub ahead of print. PMID: 39762435.
Sun C, Li A, Xu C, Ma J, Wang H, Jiang Z, Hou J. Comparative Analysis of Fecal Microbiota in Vegetarians and Omnivores. Nutrients. 2023 May 18;15(10):2358. doi: 10.3390/nu15102358. PMID: 37242241; PMCID: PMC10221195.
Losasso C, Eckert EM, Mastrorilli E, Villiger J, Mancin M, Patuzzi I, Di Cesare A, Cibin V, Barrucci F, Pernthaler J, Corno G, Ricci A. Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study. Front Microbiol. 2018 Mar 5;9:317. doi: 10.3389/fmicb.2018.00317. PMID: 29556222; PMCID: PMC5844980.
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