Scientists in Ireland have reported new evidence that coffee may influence the gut-brain axis — the two-way signaling system linking digestion and brain function. The research suggests that both caffeinated and decaffeinated coffee can shape gut microbes and may be associated with changes in mood-related measures.
The study, led by APC Microbiome Ireland at University College Cork and published in Nature Communications, compared 31 regular coffee drinkers with 31 non-coffee drinkers. Researchers combined diet records, psychological questionnaires, and stool and urine samples to examine links between coffee intake, microbiome activity and wellbeing.
Regular coffee drinkers were first asked to stop consuming coffee for two weeks, allowing scientists to observe what changed when coffee was removed from the diet. During this abstinence period, researchers reported shifts in microbe-related metabolites that helped distinguish habitual coffee drinkers from non-drinkers.
Coffee was then reintroduced in a blinded manner, meaning participants did not know whether they were receiving caffeinated or decaffeinated coffee. According to the findings, both groups showed improvements across several mood-related measures, including lower reported stress levels and fewer depressive symptoms.
One of the more closely watched findings was that improvements in learning and memory were observed in the decaffeinated group. The authors suggest this points to coffee compounds beyond caffeine — such as polyphenols and other bioactive substances — as possible contributors to some brain-related effects.
Meanwhile, the caffeinated group showed changes consistent with caffeine’s known effects, including improved alertness and attention, alongside reduced anxiety in the study’s assessments. The paper also described differences in biological markers associated with inflammation, although researchers did not present coffee as a treatment.
The researchers identified specific bacterial signals associated with coffee consumption, including higher levels of Eggertella species and Cryptobacterium curtum among coffee drinkers. They also observed shifts in broader bacterial groups that have been linked in previous studies to metabolic and emotional health outcomes.
Experts caution that microbiome research often identifies associations rather than direct cause-and-effect relationships, and larger studies are still needed. Nevertheless, the findings add to growing evidence suggesting that everyday dietary habits — including coffee consumption — may influence both gut activity and mental wellbeing.
In Europe, moderate caffeine intake is generally considered safe for most healthy adults, with recommendations commonly placing the upper limit at around 400 mg of caffeine per day from all sources. People who are pregnant, highly sensitive to caffeine, or managing anxiety, reflux or sleep disorders are usually advised to discuss caffeine intake with a healthcare professional.
