Study Reveals How Coffee Affects Gut Microbiome and Brain Function

Your daily cup of coffee may be quietly reshaping your brain through your gut. A new study published in Nature Communications reveals that coffee, both caffeinated and decaffeinated, can influence the gut-brain axis, altering microbes linked to mood, stress, and cognition.

Researchers from APC Microbiome Ireland at University College Cork explored how regular coffee intake affects the microbiome and mental health. The gut-brain axis, a complex communication network between the digestive system and the brain, has become a major focus in understanding emotional and cognitive well-being.

The study compared regular coffee drinkers (3–5 cups daily) with non-drinkers. After a two-week break from coffee, habitual drinkers showed noticeable shifts in gut-derived metabolites—chemical signals produced by microbes—highlighting how dependent the microbiome is on dietary habits. When coffee was reintroduced, participants unknowingly consumed either regular or decaffeinated versions.

Surprisingly, both groups experienced improved mood, including reduced stress, depression, and impulsivity. This suggests that coffee’s mental health benefits extend beyond caffeine. In fact, decaffeinated coffee showed unique cognitive advantages, improving learning and memory—likely due to bioactive compounds such as polyphenols.

Caffeinated coffee, however, had its own strengths. It enhanced attention, alertness, and reduced anxiety, while also showing links to lower inflammation. These findings highlight that different components of coffee may act through distinct biological pathways.

On the microbial level, coffee drinkers had higher levels of specific bacteria that are associated with digestive processes and protection against harmful microbes. An increase in beneficial bacterial groups like Firmicutes was also observed, potentially linked to positive emotional states.

While more long-term studies are needed, these findings suggest that your coffee habit could be playing a subtle but meaningful role in shaping both your microbiome and your mind.

REFERENCE: 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, John F. Cryan. Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition. Nature Communications, 2026; 17 (1) DOI: 10.1038/s41467-026-71264-8