Coffee alters gut bacteria and improves mood and cognition, with both caffeinated and decaf offering distinct mental health benefits.
Researchers at APC Microbiome Ireland, a leading research center at University College Cork, have, for the first time, closely examined how coffee produces positive effects on the gut-brain axis.
The study, published in Nature Communications and supported by the Institute for Scientific Information on Coffee (ISIC), shows that regularly drinking both caffeinated and decaffeinated coffee can shape the gut microbiome and influence mood and stress.
Although coffee’s benefits for digestion and mental well-being are well known, the biological processes behind these effects have not been fully understood. This study explored how coffee affects the microbiota-gut-brain axis, the two-way communication system linking the gut microbiome and the brain, using a wide range of measurements.
Study Design and Participant Analysis
The research followed 31 coffee drinkers and 31 non-coffee drinkers using psychological evaluations, caffeine and diet logs, and stool and urine samples to track changes in gut microbes and self-reported mood and stress. “Coffee drinkers” were defined as individuals who regularly consume 3-5 cups per day, an amount considered safe and moderate for most people by the European Food Safety Authority (EFSA).
Participants then avoided coffee for two weeks while continuing psychological assessments and biological sampling. During this period, regular coffee drinkers showed clear shifts in gut metabolite profiles compared to non-coffee drinkers.
After this phase, coffee was reintroduced in a blinded setup. Half of the participants received decaffeinated coffee, while the others consumed caffeinated coffee. Both groups reported lower levels of stress, depression, and impulsivity, indicating that coffee improved mood regardless of caffeine content.
Microbiome Changes and Beneficial Bacteria
Certain bacteria, including Eggertella sp and Cryptobacterium curtum, were found in higher levels among coffee drinkers than non-coffee drinkers. Eggertella sp is believed to support gastric and intestinal acid production, while Cryptobacterium curtum plays a role in bile acid synthesis. These functions may help remove harmful gut bacteria and reduce stomach infections. Higher levels of Firmicutes bacteria were also observed, which have been linked to positive emotional states in females.
Only participants who consumed decaffeinated coffee showed clear improvements in learning and memory, suggesting that compounds other than caffeine, such as polyphenols, may drive these cognitive effects. In contrast, caffeinated coffee was associated with reduced anxiety along with better alertness and attention. Caffeine was also linked to a lower risk of inflammation.
Expert Insights on Coffee and Health
Corresponding author of the study, Professor John Cryan, Principal Investigator at APC Microbiome Ireland, University College Cork, commented, “Public interest in gut health has risen hugely. The relationship between digestive and mental health is also increasingly being better understood, but the mechanisms behind coffee’s effects on this gut-brain axis have remained unclear.
“Our findings reveal the microbiome and neurological responses to coffee, as well as their potential long-term benefits for a healthier microbiome. Coffee may modify what microbes do collectively and what metabolites they use. As the public continues to think about dietary changes for the right digestive balance, coffee has the potential to also be harnessed as a further intervention as part of a healthy, balanced diet.”
“Coffee is more than just caffeine—it’s a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional well-being,” said Professor Cryan. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”
Reference: “Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition” by Serena Boscaini, Thomaz F. S. Bastiaanssen, Gerard M. Moloney, Federica Bergamo, Laila Zeraik, Caroline O’Leary, Aimone Ferri, Maha Irfan, Maaike van der Rhee, Thaïs I. F. Lindemann, Elizabeth Schneider, Arthi Chinna Meyyappan, Kirsten Berding Harold, Caitríona M. Long-Smith, Carina Carbia, Kenneth J. O’Riordan, José Fernando Rinaldi de Alvarenga, Nicole Tosi, Daniele Del Rio, Alice Rosi, Letizia Bresciani, Pedro Mena, Gerard Clarke and John F. Cryan, 21 April 2026, Nature Communications.
DOI: 10.1038/s41467-026-71264-8
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