Frequent coffee drinkers show more diverse gut microbiomes, Danish study suggests

Researchers at the Danish University of Copenhagen link regular coffee drinking to a more diverse gut microbiome and differences in gut physiology, in an eight-day observational study. The team believes the findings could help address constipation. 

Researchers analyzed the human digestive tract by asking healthy Danish adults to swallow a small electronic capsule called a SmartPill. As it traveled through the digestive tract, the capsule recorded variables such as its transit time through the gastrointestinal system, as well as intestinal temperature, pH levels, and contractions.

“Frequent coffee consumption appears to affect the physiology of the gut itself, in other words, how the gut functions,” says first author Francesca Bucci, a Ph.D. student at the university’s Department of Nutrition, Exercise and Sports.

Habitual coffee drinking and physical gut differences

The researchers note that previous research has linked moderate coffee consumption to a reduced risk of cardiovascular-related mortality, type 2 diabetes, depression, and several types of cancer. 

Regular coffee consumption is linked to increased colon contractions and a lower pH in the small intestine, pointing to physiological changes in how the gut functions.However, they say much less is known about how habitual coffee consumption relates to physiological conditions within the gut.

The study published in Gut Microbiology categorized participants into two groups: frequent coffee drinkers, who drank coffee on more than three of the eight study days, and those who drank coffee less often. 

All 61 participants recorded everything they ate and drank over eight days, while 50 of them also swallowed the SmartPill.

In addition to the SmartPill measurements, the researchers recorded coffee-related biomarkers, specifically, caffeine metabolites in urine, to objectively measure participants’ coffee consumption. They also collected and analyzed stool samples to assess the composition and abundance of gut bacteria.

Beneficial differences or not?

The primary finding is consistent with earlier research suggesting that coffee affects the composition of gut bacteria.

In a previous study by APC Microbiome Ireland at University College Cork, published in Nature Communications in April 2026 and sponsored by the Institute for Scientific Information on Coffee, researchers found that changes in the gut microbiome associated with caffeinated and decaffeinated coffee consumption may benefit mood and stress levels.

The authors of the new paper report that frequent coffee drinkers had a significantly lower pH in the small intestine than those who drank coffee less often. They also found that higher urinary levels of caffeine metabolites were linked to more colon contractions.

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

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

They also stress that the study cannot establish whether the differences are caused solely by coffee consumption. Nevertheless, senior author Henrik Munch Roager, associate professor and research group leader at the Department of Nutrition, Exercise and Sports, believes there is evidence that 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,” he notes.

“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.”

Roager is a member of Nestlé Europe’s Healthier Eating Advisory Council, the paper discloses.

Need for follow-up research

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

“A great many people struggle with constipation and irregular bowel movements,” he notes. “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.”