Deep Cut: Colon Biopsies Reveal Dairy’s Influence on Gut Microbiota

Written by: Lauren Milligan Newmark, Ph.D. | Issue # 127 | 2025

“Abs are made in the kitchen” is a fitness mantra referring to the relationship between your diet and the visibility of your abdominal muscles. Whether or not you have a six pack depends on more than just the foods you eat. But the saying may have some validity if you go a little deeper than muscle tissue—all the way down to the intestines. 

“Your gut microbiome is made in the kitchen” may not be destined for mantra status, but it highlights a well known association between diet and the composition of the bacteria that reside in your gut. The foods we eat influence the types, function, and diversity of the trillions of gut microbes, which in turn influence our overall health [1, 2]. 

Foods that positively impact gut health—by promoting the growth of beneficial bacteria or inhibiting the growth of harmful pathogens—are considered functional foods because they improve human health beyond their nutritional components [1-3]. Dairy foods, particularly milk, yogurt, kefir, and cheese, are nutrient-rich and are considered functional foods because of their positive influence on human health, including reduced risk of diabetes and inflammation, and improved cognition and heart health. Many of these health benefits are modulated by gut bacteria [1-3]. Could improving gut health be yet another function of dairy? 

A new study [4] by researchers from Baylor University investigated dairy’s status as a functional food group using a novel approach. Most studies that analyze the composition of gut bacteria collect fecal samples from their study subjects. Although non-invasive and easy to collect, bacteria from fecal samples only represent the bacteria found on the surface of the intestinal cavity, or lumen. To get a more comprehensive and accurate representation of the gut microbiota, the Baylor researchers went straight to the source and collected biopsies from the mucosal (or inner) layer of the colon [4]. 

Getting volunteers to willingly undergo a colonoscopy that involves collecting a biopsy is not an easy feat, so the researchers enrolled study subjects who already had a scheduled colonoscopy at a veterans’ medical facility in Houston, Texas [4]. After excluding study participants due to factors known to influence the composition of the gut microbiota (such as cancer, colorectal polyps, recent hepatitis infection, or antibiotic use within three months of the colonoscopy), the researchers had a total of 34 people (33 men and one woman between 55 and 71 years old) and 97 colonic biopsies. Each biopsy sample underwent microbiome profiling, where the researchers used a series of genomic tools to identify and characterize the different types of microorganisms.

Collecting information on participant diet was (thankfully) much less invasive. Each participant completed a food frequency questionnaire (FFQ) that calculated daily servings of nutrients and foods over the previous year from a series of recall questions about the individual’s recent food consumption. 

This study was cross-sectional in design, which means the researchers collected data on the relationship between diet and the gut microbiota at a single point in time. They didn’t select participants based on their dairy intake, nor did they control how much dairy each participant was consuming prior to their colonoscopy. When all the FFQ data were analyzed, it turned out that this group of veterans had a considerably lower median intake of dairy foods than the recommended daily intake. After adjusting for total calories, the median daily intake was 0.57 servings of total dairy, 0.24 cups of milk, 0.27 servings of cheese, and only 0.002 cups of yogurt [4]. However, if the researchers were able to identify significant differences in microbial types and frequencies based on dairy intake despite the relatively low intake of their study population, it would indicate that dairy foods have a strong potential to impact the structure of the gut microbiome.

And that’s precisely what they found. Dividing their study subjects into categories of high and low intake (using the median daily intake to divide these two groups), those with high total dairy, high milk, and low cheese intake had a more diverse population of microbes. More variety in the types of bacteria that make up your gut microbiota is a good thing—diverse microbiomes have been associated with improved immune function and reduced risk of certain diseases [5]. 

When looking at the data at the level of the genus, the research team found high and low dairy intake groups had significant differences in the composition of their bacterial communities [4]. Study participants in the high total dairy and high milk intake group had a higher relative abundance of Faecalibacterium. High milk consumption was associated with a greater relative abundance of Akkermansia. These bacterial genera are associated with positive health outcomes. Faecalibacterium produces buryate and other short-chain fatty acids as metabolites and has recognized anti-inflammatory properties and Akkermansia has been associated with improved glucose and lipid metabolism, improved gut barrier function, reduced inflammation, and improved colon health [4].

Importantly, when the researchers adjusted their statistical models to account for total lactose intake, this reduced the significance of the association between total dairy and milk intake and the relative abundance of Faecalibacterium and Akkermansia [4]. This finding supports the idea that lactose may have prebiotic properties.

The reduced amount of lactose in cheese could explain why cheese consumption was not associated with higher levels of Faecalibacterium and Akkermansia like milk. Instead, high cheese consumption was associated with a lower relative abundance of Bacteriodes. Low levels of bacteria from this genus in the gut have previously been associated with inflammatory bowel disease. On the other hand, the study authors point out that Bacteriodes species have also been associated with the production of toxins linked to colon cancer. Because of these potentially conflicting functions, it is not clear whether high levels of this bacterial genus are harmful or helpful. 

Cheese lovers take note—the jury is still out on the association between cheese consumption and gut microbes, and clearly further research with a population that consumes higher amounts of all types of dairy is needed. This is especially true of yogurt. As a cross-sectional study, the researchers had to work with what they had, and unfortunately, they had a group of participants who rarely ate yogurt, making it impossible to identify any statistically significant relationships. However, cross-sectional studies are still worthwhile because they establish associations that can be tested in randomized studies. Cross-sectional studies cannot establish causality, but this study does indicate that dairy consumption influences the structure of the mucosa-associated gut microbiota in humans. The specific nature of this influence and what this means for human health will be exciting topics to look for in future research studies. 

References

1. Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C. The interplay between diet and the gut microbiome: implications for health and disease. Nature Reviews Microbiology. 2024 Nov;22(11): 671-86.
2. Zhang P. Influence of foods and nutrition on the gut microbiome and implications for intestinal health. International Journal of Molecular Sciences. 2022 Aug 24;23(17):9588.
3. Banerjee A, Somasundaram I, Das D, Jain Manoj S, Banu H, Mitta Suresh P, Paul S, Bisgin A, Zhang H, Sun XF, Duttaroy AK. Functional foods: a promising strategy for restoring gut microbiota diversity impacted by SARS-CoV-2 variants. Nutrients. 2023 Jun 5;15(11): 2631.
4. Chen E, Ajami NJ, White DL, Liu Y, Gurwara S, Hoffman K, Graham DY, El-Serag HB, Petrosino JF, Jiao L. Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans—A Preliminary Investigation. Nutrients. 2025 Feb 2;17(3):567.
5. Manor O, Dai CL, Kornilov SA, Smith B, Price ND, Lovejoy JC, Gibbons SM, Magis AT. Health and disease markers correlate with gut microbiome composition across thousands of people. Nature Communications. 2020 Oct 15;11(1): 5206.

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