Meat-eaters vs. vegans: how their guts compare

The gut microbiome is one of the most powerful, yet often overlooked, forces shaping our health. It’s a vast ecosystem of bacteria, fungi, and other microbes living in our digestive tract, influencing everything from digestion to immune function, mental health, and even the risk of chronic diseases.¹ But does what we eat determine the kind of microbes that thrive inside us? And do meat-eaters, vegetarians, and vegans have fundamentally different microbiomes?

Looking at the science

A new large-scale international study, involving over 21,000 participants across the U.K., U.S., and Italy, sought to find out whether diets affect microbiomes differently.¹ Researchers examined stool samples to map out the gut microbiome of omnivores (people who eat both plants and meat), vegetarians, and vegans, linking the data to detailed dietary habits. The findings suggest that our gut bacteria are significantly shaped by what we eat, but the key to a healthy microbiome lies in increasing diversity in plant-based foods.¹

The microbial dietary divide

Omnivores tend to have gut bacteria suited for digesting meat. But while these microbes help break down animal proteins, they’ve also been linked to inflammation, higher risks of colon cancer, and even cardiovascular disease due to their role in producing trimethylamine N-oxide (TMAO), a compound associated with heart disease.^1,2

However, that’s not to say that an omnivore’s microbiome is all bad, as diversity in diet can often lead to a more resilient microbiome. But the key issue is balance. A typical Western diet heavy in processed meats and low in fibre can create a microbiome that leans towards inflammation and poor gut health. On the other hand, an omnivore who eats plenty of plant-based foods alongside meat may share many of the gut health benefits seen in vegetarians and vegans.¹

Vegetarians and vegans have microbiomes enriched with bacteria known for breaking down dietary fiber and producing short-chain fatty acids (SCFAs), which are compounds that support gut health, reduce inflammation, and even enhance immune function.³ The key microbes in the diets of those who are plant-based are known for their role in breaking down fibre into gut-friendly metabolites.⁴

Can a meat-eater have a vegan-like microbiome?

Just because vegan and vegetarian diets seem to offer more benefits to your gut microbiome, you shouldn't assume that the only path to a healthy gut is through strict plant-based eating. In the 2025 study, the healthiest omnivore microbiomes looked remarkably similar to those of vegetarians and vegans, so long as they ate a wide variety of plant-based foods.¹

The study found that omnivores who consumed a high diversity of vegetables, fruits, nuts, seeds, and legumes had microbial profiles comparable to their plant-based counterparts. It wasn’t necessarily about eliminating meat; rather, the microbiome benefits were driven by adding more plant diversity to the diet.¹

Plant diversity matters more than diet labels

Research suggests that what you add to your diet is just as important as what you remove.¹ A 2018 study found that people who ate more than 30 different types of plant-based foods per week had significantly more diverse gut microbiomes than those who ate fewer plants.⁵ Diversity in diet fuels diversity in gut bacteria, and a varied microbiome is associated with better digestion, stronger immune function, and even improved mental health.

What’s the best diet for a healthy gut?

There’s no single “perfect” microbiome, but the research suggests that a gut-friendly diet is one that maximises microbial diversity while fostering beneficial bacteria, regardless of whether you eat meat or not. Here’s what that looks like in practical terms:

• Prioritise fibre-rich foods: Increasing your intake of plant-based foods like vegetables, fruits, legumes, and whole grains is key to supporting beneficial gut bacteria.⁵

• Limit processed and red meats: Studies suggest that frequent consumption of red and processed meats can encourage the growth of bacteria linked to inflammation and chronic disease risk.⁶

• Eat a diverse range of foods: Microbial diversity is linked to better gut health, so the more variety in your diet, the better.⁷ This means incorporating different types of plant-based foods, fermented foods, and, if you consume animal products, choosing high-quality sources in moderation.

• Include fermented foods: Foods like yoghurt, kefir, sauerkraut, kimchi, and miso contain probiotics that can help maintain a healthy gut balance.⁸

• Stay hydrated: Water improves digestion and helps move fibre through the digestive system, supporting overall gut health.

The conversation around diet and gut health is often framed as an ‘either-or’ decision; meat versus no meat. But the science suggests that instead of focusing solely on cutting out meat or dairy, a more effective strategy is to focus on adding a greater diversity of plant-based foods to your diet.

The numan take

Whether you’re a steak lover, a devoted vegan, or somewhere in between, the most important shift you can make for your gut health is to eat the rainbow. More plants, more diversity, and a fibre-rich diet feeds your microbes the nutrients they need to support you in return.

References

1. ^{Fackelmann G, Manghi P, Carlino N, Heidrich V, Piccinno G, Ricci L, et al. Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. Nat Microbiol [Internet]. 2025;10(1):41–52. Available from: http://dx.doi.org/10.1038/s41564-024-01870-z}

2. ^{Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat Med [Internet]. 2019;25(4):667–78. Available from: http://dx.doi.org/10.1038/s41591-019-0405-7}

3. ^{de Vos WM, Tilg H, Van Hul M, Cani PD. Gut microbiome and health: mechanistic insights. Gut [Internet]. 2022;71(5):1020–32. Available from: http://dx.doi.org/10.1136/gutjnl-2021-326789}

4. ^{Sidhu SRK, Kok CW, Kunasegaran T, Ramadas A. Effect of plant-based diets on gut Microbiota: A systematic review of interventional studies. Nutrients [Internet]. 2023;15(6):1510. Available from: http://dx.doi.org/10.3390/nu15061510}

5. ^{McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, et al. American gut: An open platform for citizen science microbiome research. mSystems [Internet]. 2018;3(3). Available from: http://dx.doi.org/10.1128/msystems.00031-18} 

6. ^{Wang Y, Uffelman CN, Bergia RE, Clark CM, Reed JB, Cross T-WL, et al. Meat consumption and gut Microbiota: A scoping review of literature and systematic review of randomized controlled trials in adults. Adv Nutr [Internet]. 2023;14(2):215–37. Available from: http://dx.doi.org/10.1016/j.advnut.2022.10.005} 

7. ^{Heiman ML, Greenway FL. A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol Metab [Internet]. 2016;5(5):317–20. Available from: http://dx.doi.org/10.1016/j.molmet.2016.02.005} 

^{Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented foods, health and the gut microbiome. Nutrients [Internet]. 2022;14(7):1527. Available from: http://dx.doi.org/10.3390/nu14071527}