Drinking coffee regularly tends to alter the bacteria living in the human digestive system, which can affect a person’s mood, memory, and physical health, according to a new study. This study provides evidence that both caffeinated and decaf coffee have distinct benefits for psychological health and physical function. These findings were published in the journal nature communications.
Coffee is a complex beverage composed of many plant-based compounds, including caffeine and polyphenols. Polyphenols are naturally occurring phytochemicals known for their antioxidant properties. Growing evidence suggests that bacteria living in the human gut react to compounds found in coffee.
John Cryan, professor and chair of the Department of Anatomy and Neuroscience at University College Cork in Ireland, led the research team.
“This study builds on our long-standing interest in how diet interacts with the gut microbiome to influence brain function, the so-called microbiota-gut-brain axis,” Cryan said. “Coffee is one of the world’s most widely consumed beverages and one of the richest sources of dietary polyphenols, but most research has focused almost exclusively on caffeine. We wanted to understand how coffee as a whole affects the microbiome, metabolism, mood, cognition, and physiology.”
The human digestive system is home to trillions of microorganisms, collectively known as the gut microbiome. These microbes continuously communicate with the brain through a network called the microbiota-gut-brain axis. This two-way communication pathway helps regulate digestion, immune response, and even mood.
“It’s also noteworthy that a growing body of epidemiological research links moderate coffee consumption to healthy aging and reduced risk of neurodegenerative diseases such as dementia and Parkinson’s disease,” Cryan explained. “While our findings do not prove that coffee prevents these symptoms, they point to a possible biological mechanism through the gut microbiome and metabolism that may help explain some of their association.”
The researchers aimed to investigate how the timing of coffee habits affects mood and cognition through the lens of the gut microbiome. They recruited 62 healthy adults aged 30 to 50 living in Ireland. Half of the participants were moderate coffee drinkers, meaning they typically drink 3 to 5 cups a day, while the remaining 31 participants were non-coffee drinkers.
Scientists compared both groups at the beginning of the study. Participants completed psychological questionnaires to assess stress, impulsivity, and sleep quality. They also provided blood, saliva, urine, and stool samples. To ensure that diet was not causing the differences, participants kept detailed daily food records.
After this initial assessment, non-coffee drinkers terminated participation. Regular coffee drinkers were instructed to stop consuming any type of coffee or caffeinated beverages for two weeks. This period of abstinence allowed scientists to observe how the body and gut microbiome react if you suddenly stop drinking coffee.
After a two-week withdrawal phase, the coffee drinkers returned for a second test and sample collection. They were then randomly divided into two groups. For the next three weeks, 16 participants drank four cups of caffeinated instant coffee every day, and the other 15 participants drank four cups of decaf instant coffee every day.
At the end of this 3-week reintroduction phase, participants completed a final round of questionnaires, cognitive tests, and biological sampling. Cognitive tests included memory tasks and emotion recognition tasks. The scientists also induced a mild stress response by having participants place their hands in ice-cold water during the recordings.
When comparing the groups at the beginning of the study, the authors noted that heavy coffee drinkers scored higher on measures of impulsivity and emotional reactivity than non-coffee drinkers. During the two-week withdrawal period, these elevated levels of impulsivity and emotional reactivity decreased. Stress testing revealed that baseline stress hormones and physical stress tolerance were essentially the same for both regular coffee consumers and those who never drank coffee.
When reconsuming coffee, both the caffeinated and non-caffeinated groups reported lower levels of perceived stress and fewer symptoms of depression. The caffeinated coffee group experienced unique psychological benefits, reporting lower anxiety and less psychological distress. The caffeine group also showed reduced levels of certain inflammatory proteins in their blood after three weeks of drinking coffee.
Participants who drank decaffeinated coffee were found to sleep better and engage in more physical activity. The decaf group also showed improved performance on memory tests.
“One of the biggest surprises was that decaffeinated coffee had many of the same benefits as regular coffee,” Cryan said. “This suggests that caffeine is only part of the story, and that other coffee compounds, particularly polyphenols, may play a major role in shaping the gut-brain axis. We were also struck by how quickly the microbiome responds to changes in coffee intake. This system appears to be highly dynamic and sensitive to dietary input.”
“The main takeaway is that coffee is biologically much more complex than we think,” Cryan says. “This is more than just a stimulant; it appears to interact simultaneously with the gut microbiome, immune system, metabolism, and brain. Our findings suggest that both caffeinated and decaffeinated coffee can influence stress, mood, and cognition, likely through mechanisms involving the gut microbiome and microbial metabolites.”
Stool samples revealed that frequent coffee drinkers have a different composition of gut bacteria than non-coffee drinkers. Specifically, coffee drinkers had higher levels of several bacterial strains, including Cryptobacterium cultum and Eggertella. Stopping and restarting coffee intake caused changes in these specific bacterial populations, but the overall diversity of the gut microbiome remained unchanged.
Analysis of the participants’ urine revealed changes in compounds associated with the breakdown of caffeine and polyphenols. Interestingly, there was considerable individual variation in how polyphenols were processed. The authors linked this variation to differences in each person’s specific gut bacteria.
“This was a controlled experimental study of 62 healthy adults, so the results should not be interpreted as evidence that coffee dramatically alters personality or cognition,” Cryan cautioned. “The effects are subtle but measurable and are perhaps most meaningful in terms of understanding how habitual dietary exposure shapes physiology over time. This study is mechanistically important, perhaps not as a basis for immediate lifestyle recommendations, but because it shows that components of the daily diet can jointly influence the microbiome and brain.”
“This is a relatively small study in healthy participants, looking at associations and physiological responses rather than diagnosing clinical effects,” Cryan said. “Also, we cannot conclude that coffee is generally ‘good’ or ‘bad’ for cognition or mood. But as a frequent coffee drinker, I’m relieved that my habit can have a positive impact. ”
“Another important point is individual differences,” he added. “Response to coffee is likely to depend on a variety of factors, including genetics, sleep, baseline microbiome composition, habitual caffeine intake, and broader dietary patterns.”
“I think one of the broader messages is that the gut microbiome is not a static system,” Cryan explained. “It continually reacts to what we eat and drink, and those microbial changes can have effects far beyond digestion, including mood, stress resilience, and cognition.”
“We are very interested in understanding how certain dietary components, particularly polyphenols, interact with the microbiome to influence mental health and brain function,” Cryan said of next steps. “Future studies will investigate whether individual microbiome profiles can predict different responses to coffee, and whether these interactions may ultimately support more personalized nutritional strategies. We are particularly interested in how dietary components influence brain health via the microbiome. Further large-scale longitudinal studies are therefore needed.”
The study, “Habitual coffee consumption shapes the gut microbiota and alters host physiology and cognition,” was authored by Serena Boscaini, Thomaz FS Bastiaanssen, Gerard M. Moloney, Federica Bergamo, Laila Zeraik, Caroline O’Leary, Aimone Ferri, Maha Irfan, Maaike van der Rhee, and Thaïs IF. Lindeman, Elizabeth Schneider, Arti Chinna Meiyappan, Kirsten Belding Harrold, Caitriona M. Long-Smith, Karina Calvia, Kenneth J. O’Riordan, Jose Fernando Rinaldi de Alvarenga, Nicole Tosi, Daniele Del Rio, Alice Rossi, Leticia Bresciani, Pedro Mena, Gerald Clark, and John F. Cryan.
