People who drink coffee regularly appear to have a more diverse community of gut bacteria and measurable differences in how their digestive tract works, according to a small new study led by University of Copenhagen scientists.
Bucci et al. provide integrated evidence linking habitual coffee intake, not only to gut microbiota, but also to direct measurements of gastrointestinal physiology. Image credit: Sci.News.
“Coffee is one of the most consumed beverages worldwide and has been present in the human diet for centuries,” said University of Copenhagen Ph.D. student Francesca Bucci and her colleagues.
“Its consumption has been linked to a range of health benefits, including reduced risk of all-cause and cardiovascular-related mortality, type 2 diabetes, cognitive decline, depression, and certain types of cancer.”
“Coffee is a complex beverage that contains more than 1,000 bioactive compounds, including methylxanthines, phenolic acids, diterpenes, vitamins, volatile compounds, and polysaccharides like galactomannans and type II arabinogalactans.”
“Some physiologically active compounds present in coffee, such as phenolic acids and fibers, can reach the large intestine unmetabolized and act as prebiotics-like compounds, serving as substrates for gut microbes,” they said.
“Consequently, coffee intake has been associated with microbiota composition and function in population studies, suggesting a potential role in the modulation of host-microbe interactions.”
In the study, the researchers followed 61 healthy adults for nine days, tracking what they ate and drank, and analyzing urine for caffeine and its breakdown products.
Fifty of the participants also swallowed a wireless capsule that measured acidity, pressure and movement as it traveled through the gut.
Participants who drank coffee on more than three of eight recorded days, about 48 of the 61, showed greater microbial richness in stool samples than those who rarely drank it.
Three groups of bacteria, including Lawsonibacter and Slackia, were more abundant among frequent drinkers. The Lawsonibacter finding echoes earlier research linking that microbe to coffee.
Higher levels of caffeine byproducts in urine were associated with more contractions in the colon. The small intestine was also less acidic in frequent coffee drinkers than in rare ones.
“We already know from other studies that coffee can influence a range of processes in the digestive system, including acid secretion in the stomach,” said Dr. Henrik Munch Roager, a researcher at the University of Copenhagen.
“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.”
The findings were published September 15 in the journal Gut Microbiology.
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Francesca Bucci et al. 2026. Habitual coffee consumption is linked to differences in gut microbiota and gut physiology. Gut Microbiology 3: 100018; doi: 10.1016/j.gutmic.2026.100018
