A new study from APC Microbiome Ireland, a world-leading research center at University College Cork, has comprehensively investigated the mechanisms behind coffee’s positive effects on the gut-brain axis for the first time.
The study, published in Nature Communications and sponsored by the Institute for Coffee Science Information (ISIC), reveals how regular consumption of both caffeinated and decaffeinated coffee affects the gut microbiome, which in turn affects mood and stress levels.
Coffee’s benefits for both digestion and mood have been widely studied, but the exact mechanisms behind these effects remain unclear. This study investigated how coffee consumption affects the microbiota-gut-brain axis (the two-way communication between the gut microbiome and the brain) through a range of measurement methods.
Thirty-one coffee drinkers and 31 non-coffee drinkers were studied in-depth through a battery of psychological tests, caffeine and food diaries, and stool and urine samples to understand changes in their microbiome and perceived mood and stress. A “coffee lover” was defined as someone who regularly consumed 3 to 5 cups of coffee per day. This is defined by the European Food Safety Authority (EFSA) as a safe and adequate amount for most people.
Participants first refrained from drinking coffee for two weeks and underwent regular psychological evaluations and stool and urine samples. This period of abstinence in coffee drinkers was consistent with greater changes in the metabolite profile of the gut microbiota compared to non-coffee drinkers.
Coffee was reintroduced to regular coffee drinkers in a blinded manner, with half of the participants consuming decaffeinated coffee and the other half consuming caffeinated coffee. Both groups reported lower scores for perceived stress, depression, and impulsivity, suggesting that drinking coffee significantly improved mood, regardless of caffeine content.
Bacteria such as “Eggertella sp” and “Cryptobacterium curtum”‘significantly increased in coffee drinkers compared to non-coffee drinkers. The former is thought to contribute to the secretion of stomach and intestinal acids, and the latter is thought to be involved in the synthesis of bile acids, both of which may play a role in eliminating unhealthy gut bacteria and stomach infections. An increase in the Firmicutes bacteria, which is associated with positive emotions in women, was also observed.
Significant improvements in learning and memory were observed only in those who consumed decaffeinated coffee, suggesting that components other than caffeine, such as polyphenols, are responsible for these cognitive benefits. However, in this study, researchers found that only caffeinated coffee was associated with reduced anxiety and increased vigilance and attention. Caffeine was also associated with a lower risk of inflammation.
Professor John Cryan, lead researcher on the APC microbiome at University College Cork, Ireland, and corresponding author of the study, commented:Society’s interest in intestinal health is increasing significantly. The relationship between the digestive system and mental health is also becoming increasingly understood, but the mechanisms behind coffee’s effects on this gut-brain axis remain unclear.
“Our findings reveal microbiome and neurological responses to coffee, as well as potential long-term benefits for a healthier microbiome. Coffee can change what microbes do collectively and the metabolites they use. As the public continues to think about dietary changes for proper digestive balance, coffee may also be leveraged as a further intervention as part of a healthy balanced diet.”
“Coffee is more than just caffeine. It’s a complex dietary element that interacts with gut bacteria, metabolism and even mental health,” Professor Cryan said. “Our findings suggest that coffee, whether caffeinated or decaffeinated, may affect health in different, but complementary ways.”
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Reference magazines:
Boscaini, S. others. (2026). Habitual coffee consumption shapes the gut microbiota and alters host physiology and cognition. Nature Communications. DOI: 10.1038/s41467-026-71264-8. https://www.nature.com/articles/s41467-026-71264-8
