Regular coffee consumption alters gut bacteria and digestive physiology

If you drink coffee regularly, it appears to alter not only your gut bacteria but also the physiology of the gut itself. That is the conclusion of a study from the University of Copenhagen, which may help point the way towards better treatments for constipation.

It may be a slightly awkward topic, but many of us know the feeling: that cup of coffee that gets things moving.

Research now suggests that regular coffee consumption affects how our digestive system functions.

A research team from the University of Copenhagen asked a group of Danish participants to swallow a small electronic capsule. As it travelled through the digestive tract, the capsule measured, among other things, transit time through the gastrointestinal system, temperature, pH levels and intestinal contractions.

The participants were categorized into frequent coffee drinkers, defined as consuming between one and five cups a day on more than three of the eight study days, and those who drank coffee less often.

The results first and foremost confirmed that coffee affects the composition of gut bacteria, as previous studies have suggested. Frequent coffee drinkers had a greater diversity of microorganisms in their gut than those who drank coffee less often.

But perhaps more importantly, frequent coffee consumption appears to affect the physiology of the gut itself, in other words how the gut functions."

Francesca Bucci, first author, PhD student, Department of Nutrition, Exercise and Sports, University of Copenhagen

It is already well established that moderate coffee consumption is associated with a reduced risk of cardiovascular disease, diabetes, depression and several types of cancer. However, much less is known about how habitual coffee consumption relates to physiological conditions within the gut.

Stimulates contractions in the gut

The researchers found that frequent coffee drinkers had a significantly lower pH in the small intestine than those who drank coffee less often. They also observed that higher coffee consumption was associated with more contractions in the colon.

So are these physiological differences beneficial or not?

"Contractions in the gut can support healthy digestion, help prevent constipation and keep the intestinal muscles in good condition," says Francesca Bucci.

The researchers cannot yet determine whether the lower pH is beneficial or harmful to health. However, the pH level in the small intestine plays an important role in the activity of digestive enzymes and in how food is broken down.

The researchers also stress that the study cannot establish whether the differences are caused solely by coffee consumption. Nevertheless, senior author Henrik Munch Roager believes there is good reason to think coffee plays a key role.

"For example, we already know from other studies that coffee can influence a range of processes in the digestive system, including acid secretion in the stomach. So there are good reasons to believe that what we are seeing is not merely coincidence. Anecdotally, many people also report that coffee affects their digestion," says Henrik Munch Roager, Associate Professor and Research Group Leader at the Department of Nutrition, Exercise and Sports.

Calls for further studies

According to Roager, the natural next step would be an intervention study in which researchers control how much coffee participants drink and examine what happens to gut physiology during periods of high coffee consumption compared with periods without coffee.

The researchers hope that these and future findings can help address a widespread problem.

" A great many people struggle with constipation and irregular bowel movements. If we can understand how coffee affects digestion and intestinal contractions, it may be possible to use that knowledge to stimulate gut motility in a natural way. That would be extremely valuable," says Henrik Munch Roager.

Source:
Journal reference:

Bucci, F., et al. (2026). Habitual coffee consumption is linked to differences in gut microbiota and gut physiology. Gut Microbiology. DOI: 10.1016/j.gutmic.2026.100018. https://www.sciencedirect.com/science/article/pii/S3051172026000149?via%3Dihub

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