Sixty-one healthy Danish adults kept eight-day food diaries, gave stool and urine samples, and most of them swallowed a wireless capsule that recorded pressure and acidity on its way through the gut. The people who drank coffee on most of those days had a richer mix of gut bacteria, more contractions in the colon, and a more acidic small intestine than the people who rarely drank it. The paper, from the University of Copenhagen, appeared online in the Elsevier journal Gut Microbiology in September 2026 (volume 3, article 100018) and the university announced it on November 10, 2026.

What the capsule and the stool samples showed

The study is cross-sectional: one snapshot of 61 adults, with no coffee assigned and no follow-up. Coffee intake came from two directions, the diaries and caffeine metabolites measured in urine, so the result does not rest on self-report alone. Frequent drinkers were defined as anyone who logged coffee on more than three of the eight diary days; the university's release puts their intake at one to five cups on those days. Rare drinkers logged it on fewer than three days. According to the release, 50 of the 61 participants also swallowed the motility capsule.

Frequent drinkers had higher microbial richness, meaning more distinct bacterial types in their stool, and the amount of caffeine metabolite in urine tracked with total bacterial load. Three groups were more abundant in frequent drinkers: Lawsonibacter, Slackia and an unclassified branch of the Eggerthellaceae family, with Lawsonibacter rising in step with coffee intake. On the physiology side, caffeine metabolites were associated with more colonic contractions, and both habitual intake and caffeine metabolites were associated with a lower pH in the small intestine. The funder recorded with the paper is the Novo Nordisk Foundation.

Where it sits against earlier coffee microbiome work

The Lawsonibacter signal is the part that lines up with the biggest study on this question. In Nature Microbiology in November 2024, a multi-cohort analysis of 22,867 adults in the United States and the United Kingdom with detailed diet records, extended with public data from 211 cohorts totaling 54,198 people, found that coffee was the single food most tightly linked to gut microbiome composition, with a model telling coffee drinkers from non-drinkers at an area under the curve of 0.89. One species, Lawsonibacter asaccharolyticus, carried most of that signal: its median abundance was 4.5 to 8 times higher in high coffee drinkers than in people who never drank it, and 3.4 to 6.4 times higher in moderate drinkers than never drinkers, while moderate and high drinkers barely differed. The authors grew the bacterium in the lab and found coffee stimulated it, and the association held in two cohorts for decaffeinated coffee as well. That work was supported by the nutrition company ZOE and by TwinsUK, and several authors are founders, employees or consultants of ZOE, which the paper discloses.

A smaller trial added the other half of the picture in April 2026. In Nature Communications, researchers at University College Cork compared 31 healthy adults aged 30 to 50 who never drank coffee with 31 who drank three to five cups a day, then had the drinkers stop for 14 days and restart for 21 days with either caffeinated (16 people) or decaffeinated (15 people) instant coffee. Drinkers had more Cryptobacterium and Eggerthella species and lower levels of several microbial metabolites, including indole-3-propionic acid and the neurotransmitter GABA. Some of the metabolite changes reversed during the two weeks off, and restarting coffee shifted the microbiome whether or not it contained caffeine. That trial was funded through Science Foundation Ireland's APC Microbiome Ireland center and the European Research Council. Its authors name the lack of a direct transit-time measurement as a limitation, which is exactly the gap the Copenhagen capsule data begin to fill.

What the new study does not show

It does not show that coffee causes any of these differences. People who drink coffee most days differ from people who do not in many other ways, and a cross-sectional design cannot separate coffee from the rest of a diet or a daily routine. The authors say as much, and propose an intervention trial in which coffee intake is controlled as the next step. Sixty-one people is a small sample.

It also does not say whether a more acidic small intestine or a richer microbiome is good for anyone. The researchers state they cannot yet tell whether the lower pH is beneficial or harmful. The study measured no health outcome, symptom or disease. Nothing in it tests coffee against constipation, bloating or any digestive condition, and nothing in it compares caffeinated with decaffeinated coffee, so the caffeine question that the Cork trial addressed stays open here.

Reading the results in a training week

For an active reader the practical content is narrow: regular coffee drinking is associated with a different gut environment, measured for once with an instrument inside the gut rather than inferred from stool alone, and the bacterium that keeps turning up across 2024, April 2026 and now September 2026 is Lawsonibacter. Whether changing coffee intake changes that environment, and whether that matters for digestion, performance or health, waits on the controlled trial the Copenhagen group says it wants to run. The paper is open access at the DOI below; the question to bring to a clinician is whether a coffee habit matters for any digestive symptom or medication a reader already has.

This article reports research and expert guidance. It is not medical advice. Talk to your clinician before changing medication, treatment or a medical diet.

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