Dairy and Your Gut Microbiome: What a 2025 Study Found

Most microbiome research looks at stool. Researchers at Baylor College of Medicine looked somewhere more informative.

A 2025 study published in Nutrients (Chen et al.) analyzed 97 colonic biopsies from 34 polyp-free individuals, correlating their dairy intake with the composition of the mucosa-associated microbiome: the bacteria embedded directly in the colon wall rather than floating in gut contents. The distinction matters because mucosal bacteria have a more direct relationship with the intestinal epithelium and the immune system than luminal bacteria do. Getting at them requires biopsy, which is why this data is harder to come by.

The findings were consistent with the idea that dairy, and specifically milk, supports a more beneficial microbial environment in the colon.

What They Found

Microbial diversity. Higher total dairy and milk consumption was associated with greater alpha-diversity in the mucosa-associated microbiome (adjusted p < 0.05). Alpha-diversity measures the richness and balance of species in a microbial community. A more diverse microbiome is generally more resilient, and lower diversity is associated with inflammatory bowel disease, metabolic dysfunction, and colorectal cancer risk.

More Faecalibacterium. Higher dairy and milk intake was linked to greater relative abundance of Faecalibacterium, a butyrate-producing bacterium with well-established anti-inflammatory effects. Butyrate is the primary energy source for colonocytes, the cells lining the colon, and reduced Faecalibacterium levels are associated with IBD, colorectal cancer, and metabolic disease.

More Akkermansia. Higher milk intake specifically was independently associated with greater relative abundance of Akkermansia muciniphila, a bacterium linked to gut barrier integrity, healthier glucose and lipid metabolism, and reduced age-related mucosal thinning. Akkermansia has attracted significant research attention in recent years for its apparent role in metabolic and immune health.

Less Bacteroides. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides, a genus linked to pro-carcinogenic metabolic activity and colorectal cancer.

Overall community composition. Dairy consumption influenced beta-diversity, the overall makeup of the microbial community, across all dairy subtypes: milk, cheese, and yogurt. Not just one form of dairy, all of them.

What This Study Can and Can't Establish

This is a cross-sectional study with a relatively small sample. It can identify associations but can't establish that consuming more dairy directly causes these microbial profiles, and the authors are clear about that. It's a preliminary investigation, not a definitive causal trial.

The fact that it specifically measures mucosal bacteria, rather than the more commonly studied luminal bacteria, is a methodological strength. Mucosal bacteria are more directly relevant to immune function. The sample size is a real limitation and the findings should be interpreted accordingly.

How It Connects to the Protein Research

The Faecalibacterium finding doesn't exist in isolation. Faecalibacterium is one of the primary producers of butyrate in the gut, the same short-chain fatty acid that the A2 versus A1 controlled trials tracked directly. Both Sheng et al. (2019) and Jianqin et al. (2016) found that milk from A2 cows was associated with significantly higher fecal butyrate and total SCFA concentrations compared to conventional A1/A2 milk. The Chen et al. study offers a plausible microbial explanation for why: milk consumption promotes the colonization of the bacteria that produce those acids in the first place.

Dairy supports the microbiome. The protein variant in that dairy influences what those bacteria can do.

Sources

Chen LA, Ajami NJ, White DL, Liu Y, Gurwara S, Hoffman K, Graham DY, El-Serag HB, Petrosino JF, Jiao L. (2025). Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans: A Preliminary Investigation. Nutrients, 17, 567. https://doi.org/10.3390/nu17030567

Sheng M, Li Y, Ni L, Yelland G. (2019). Effects of Conventional Milk Versus Milk Containing Only A2 β-Casein on Digestion in Chinese Children: A Randomized Study. Journal of Pediatric Gastroenterology and Nutrition, 69(3):375–382. https://doi.org/10.1097/MPG.0000000000002437

Sun Jianqin, Xu Leiming, Xia Lu, Yelland GW, Ni J, Clarke AJ. (2016). Effects of Milk Containing Only A2 Beta Casein Versus Milk Containing Both A1 and A2 Beta Casein Proteins on Gastrointestinal Physiology, Symptoms of Discomfort, and Cognitive Behavior of People with Self-Reported Intolerance to Traditional Cows' Milk. Nutrition Journal, 15:35. https://doi.org/10.1186/s12937-016-0147-z