Milk, cheese, and other dairy products are both good and bad for your gut health

Most of us have heard that the gut is full of bacteria that help with digestion, immunity, and even mood. What you eat and drink shapes that microbial community.

Dairy sits in the middle of the conversation because it provides nutrients and, sometimes, live cultures, yet researchers don’t always agree on its effects. A careful study that sampled the colon lining directly adds useful clues.

Diet studies often rely on stool samples. That’s helpful, but it doesn’t always reflect the bacteria that stick to the gut wall.

This project looked at those wall-attached microbes, which sit directly against our tissues. The goal was straightforward: see whether everyday dairy habits show up in that community of bacteria.

Understanding the microbiome

Think of your gut microbiome as a bustling neighborhood of trillions of microbes – mostly bacteria, plus some fungi and viruses – that live mainly in your large intestine.

They help break down parts of food you can’t digest on your own, especially fiber, producing short-chain fatty acids like butyrate that feed your colon cells and help keep inflammation in check.

These microbes also train your immune system, make certain vitamins, and interact with your nervous system through chemical signals. That’s where we get the term “gut feeling.”

Everyone’s microbiome is a little different, shaped by birth, diet, environment, sleep, stress, and medicines like antibiotics.

Diversity tends to be a good sign: a wider variety of species usually means a more stable, resilient community.

There’s no single “perfect” microbiome, but you can nudge yours in a healthy direction with balanced meals, regular movement, enough sleep, and cautious antibiotic use when medically needed.

Learning how dairy shapes gut bacteria

Adults undergoing routine colonoscopies at a veterans’ hospital in Houston participated. Their colons appeared normal, and none had major conditions that could confound the results.

During the procedure, doctors collected pinhead-sized biopsies from the colon lining for lab analysis.

In total, the team analyzed 97 biopsies from 34 people. Beforehand, participants completed a food questionnaire that covered the past year, including milk, cheese, yogurt, and total dairy intake.

In the lab, the group used 16S rRNA sequencing to identify which bacteria were present and in what amounts.

Two basic yardsticks apply. “Alpha diversity” refers to how many kinds of bacteria are in a single sample. “Beta diversity” compares how different two people’s communities are.

The analysis adjusted for age, body size, smoking, alcohol use, health conditions, overall diet quality, and which part of the colon the sample came from. That helps separate signals that are likely true associations from those created by other factors.

What the scientists learned

People who drank more milk – and those who consumed more total dairy – tended to have higher alpha diversity in the bacteria attached to the colon lining.

Beta diversity also differed between higher and lower consumers of total dairy, milk, cheese, and yogurt, indicating that intake patterns were associated with broader shifts in community structure.

Two familiar bacteria stood out. Faecalibacterium is often considered beneficial because it makes butyrate, a short-chain fatty acid that fuels colon cells and can calm inflammation. People who consumed more total dairy and more milk had more Faecalibacterium on the colon lining.

Akkermansia, frequently linked to a strong gut barrier and better metabolic markers, also appeared at higher levels with milk intake.

Dairy products and bacteria

When the team accounted for dietary lactose, the milk-microbe links weakened. That points to lactose as a possible prebiotic – food for specific bacteria – that may help certain microbes grow.

It also fits a simple nutrition fact: milk contains lactose, while many hard cheeses have very little.

Cheese didn’t follow milk’s pattern. Higher cheese intake was associated with lower amounts of certain bacteria in adjusted models, including Bacteroides and Subdoligranulum.

Scientists don’t treat Bacteroides as purely good or bad; it depends on the species and context.

Subdoligranulum can produce butyrate, which is usually beneficial, so seeing lower levels with higher cheese intake raises questions about which cheese components might shift the balance. Turning milk into cheese changes nutrients in ways that could matter.

Yogurt intake here was very low on average – approximately a few sips per day – so the study couldn’t draw firm conclusions.

The researchers didn’t see clear links between yogurt and diversity, and classic yogurt cultures like Lactobacillus and Bifidobacterium appeared at very low levels on the colon lining in these samples.

Colon lining yields clues

Most data we see come from stool samples, which reflect what exits the body. The mucosa – the gut’s surface – can look different.

Studying the wall-attached community gives a closer view of the microbes that interact with the gut barrier and immune cells. It reflects the mucosal surface rather than only what is present in stool.

Gut bacteria, dairy, and health

If you tolerate dairy and already drink milk, your gut’s surface community may be more diverse.

If cheese is your main dairy, the effects likely depend on the type of cheese, your overall diet – especially fiber – and your individual microbiome.

If you don’t tolerate lactose well, prebiotic fibers from beans, oats, bananas, onions, and asparagus can nourish beneficial bacteria by another route.

Different dairy foods appear to influence the gut’s wall-attached community in distinct ways.

Larger, longer studies in more diverse groups will help test which dairy components do what, and for whom. For now, what goes in your glass and on your plate shows up in your gut in measurable ways.

The full study was published in the journal Nutrients.

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