Regularly drinking coffee tends to modify the bacteria living in the human digestive system, which in turn influences a person’s mood, memory, and physical health, according to a new study. The research provides evidence that both caffeinated and decaffeinated coffee offer distinct benefits for psychological well-being and bodily functions. These findings were published in the journal Nature Communications.
Coffee is a complex beverage made up of many plant-based compounds, including caffeine and polyphenols. Polyphenols are naturally occurring plant chemicals known for their antioxidant properties. A growing body of evidence suggests that the bacteria living in the human gut respond to the 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 most widely consumed beverages in the world and one of the richest sources of dietary polyphenols, yet most research has focused almost exclusively on caffeine. We wanted to understand how coffee as a whole influences 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 communicate continuously with the brain through a network called the microbiota-gut-brain axis. This two-way communication pathway helps regulate digestion, immune responses, and even mood.
“It is also worth noting that a growing body of epidemiological research links moderate coffee consumption with healthier aging and a reduced risk of neurodegenerative disorders such as dementia and Parkinson’s disease,” Cryan explained. “Our findings do not prove that coffee prevents these conditions, but they do provide possible biological mechanisms through the gut microbiome and metabolism that may help explain some of those associations.”
The researchers aimed to explore how the timing of coffee habits affects mood and cognition through the lens of the gut microbiome. They recruited 62 healthy adults living in Ireland, ranging in age from 30 to 50 years old. Half of the participants were moderate coffee drinkers, meaning they typically drank three to five cups per day, while the other 31 participants were non-coffee drinkers.
The 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 diet was not causing differences, participants kept detailed daily food logs.
Following this initial assessment, the non-coffee drinkers concluded their participation. The habitual coffee drinkers were instructed to stop drinking any type of coffee or caffeinated beverage for two weeks. This abstinence period allowed the scientists to observe how the body and gut microbiome reacted to the sudden absence of coffee.
After the two-week withdrawal phase, the coffee drinkers returned for a second round of tests and sample collections. They were then randomly divided into two groups. For the next three weeks, 16 participants drank four daily cups of caffeinated instant coffee, while the other 15 participants drank four daily cups of decaffeinated instant coffee.
At the end of this three-week reintroduction phase, the participants completed the final round of questionnaires, cognitive tests, and biological sampling. The cognitive tests included memory tasks and an emotional recognition task. The scientists also induced a mild stress response by having participants hold their hand in ice-cold water while being recorded.
When comparing the groups at the beginning of the study, the authors noted that regular 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 dropped. The stress testing revealed that baseline stress hormones and physical stress resilience were essentially the same for both regular coffee consumers and those who never drank it.
Upon reintroducing coffee, both the caffeinated and decaffeinated groups reported lower levels of perceived stress and fewer symptoms of depression. The caffeinated coffee group experienced unique psychological benefits, reporting reduced anxiety and decreased psychological distress. The caffeinated group also showed lower levels of certain inflammatory proteins in their blood after drinking the coffee for three weeks.
Participants who drank decaffeinated coffee showed improvements in sleep quality and engaged in more physical activity. The decaffeinated group also demonstrated enhanced performance on memory tests.
“One of the biggest surprises was that decaffeinated coffee produced many of the same effects as regular coffee,” Cryan noted. “That suggests 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 rapidly the microbiome responded to changes in coffee intake. The system appears to be highly dynamic and sensitive to dietary inputs.”
“The main takeaway is that coffee is much more biologically complex than we tend to think,” Cryan said. “It is not simply a stimulant; it appears to interact with the gut microbiome, immune system, metabolism, and brain simultaneously. 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.”
The stool samples revealed that regular coffee drinkers hosted a different composition of gut bacteria compared to non-coffee drinkers. Specifically, coffee drinkers had higher levels of several bacterial strains, such as Cryptobacterium curtum and Eggerthella. Stopping and restarting coffee intake caused shifts in these specific bacterial populations, but it did not change the overall diversity of the gut microbiome.
Analysis of the participants’ urine showed changes in compounds related to the breakdown of caffeine and polyphenols. Interestingly, there was a high degree of variation in how individuals processed polyphenols. The authors linked this variation to differences in each person’s specific gut bacteria.
“This was a controlled experimental study in 62 healthy adults, so the findings should not be interpreted as evidence that coffee dramatically changes personality or cognition,” Cryan warned. “The effects were subtle but measurable, and are probably most meaningful in terms of understanding how habitual dietary exposures shape physiology over time. The study is perhaps more important mechanistically, showing that everyday dietary components can influence the microbiome and brain together, than as a basis for immediate lifestyle recommendations.”
“This was a relatively modest-sized study in healthy participants, and we are observing associations and physiological responses rather than diagnosing clinical effects,” Cryan said. “We also cannot conclude that coffee is universally ‘good’ or ‘bad’ for cognition or mood. However, as a frequent coffee drinker, I am reassured that there may be positive consequences of my habit.”
“Another important point is individual variability,” he added. “Responses to coffee likely 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 responds continuously to what we eat and drink, and those microbial changes may have consequences far beyond digestion, including for mood, stress resilience, and cognition.”
“We are very interested in understanding how specific dietary components, especially polyphenols, interact with the microbiome to influence mental health and brain function,” Cryan said regarding next steps. “Future work will explore whether individual microbiome profiles can predict different responses to coffee and whether these interactions may eventually support more personalized nutritional strategies. We are particularly interested in how dietary components can affect brain health via the microbiome. Thus much more large-scale longitudinal studies are needed.”
The study, “Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition,” was authored 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 & John F. Cryan.
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