Researchers at APC Microbiome Ireland, a leading research center at University College Cork, have taken a major step towards understanding what coffee does for the body. For the first time, scientists have taken a closer look at how coffee interacts with the gut-brain axis, the communication network that connects the digestive system and the brain.
The survey results are nature communications Supported by the Institute for Scientific Information on Coffee (ISIC), research shows that drinking both caffeinated and decaf coffee regularly shapes the gut microbiome, which can influence mood and stress.
How coffee affects your gut microbiome and mood
Coffee has long been associated with digestive and mental health benefits, but the biological reasons behind these effects were not fully understood. The study focused on how coffee affects the microbiota-gut-brain axis (the two-way communication between the gut microbiome and the brain) using a wide range of biological and psychological measurements.
To investigate this, researchers compared 31 heavy coffee drinkers to 31 non-coffee drinkers. Participants completed psychological assessments, tracked their diet and caffeine intake, and provided stool and urine samples so scientists could analyze changes in gut bacteria and emotional states. In this study, a “coffee lover” was defined as an individual who typically consumes between 3 and 5 cups of coffee per day, a level considered safe and moderate by the European Food Safety Authority (EFSA).
Study design reveals changes in the microbiome
At the beginning of the experiment, coffee drinkers stopped drinking coffee for two weeks. During this period, researchers continued to collect biological samples and monitor mental health. This interruption led to clear changes in the metabolites produced by the gut microbes in regular coffee drinkers, distinguishing them from non-coffee drinkers.
After the abstinence phase, participants gradually reintroduced coffee without knowing whether they were drinking caffeinated or decaffeinated coffee. Half of them consumed decaf and the rest consumed regular coffee. Both groups reported improved mood, including lower levels of stress, depression, and impulsivity. These results suggest that coffee can have mood-enhancing effects even without caffeine.
Major intestinal bacteria associated with coffee intake
The study also identified specific bacteria commonly found in coffee drinkers. Levels of ‘Eggertella sp’ and ‘Cryptobacterium curtum’ were higher among those who regularly consumed coffee. These microorganisms play a role in processes such as acid production and bile acid synthesis in the digestive system, and are thought to help protect against harmful bacteria and infections. The researchers also observed an increase in the Firmicutes, a group of bacteria previously associated with positive emotions in women.
Effects of decaf and caffeine on brain function
Interestingly, improvements in learning and memory were only seen in participants who drank decaffeinated coffee. This finding suggests that compounds other than caffeine, such as polyphenols, may be involved in certain cognitive benefits.
On the other hand, caffeinated coffee showed clear benefits. Only participants who consumed caffeine experienced reduced anxiety along with improved alertness and alertness. Caffeine was also associated with a lower risk of inflammation.
Scientists explain coffee’s far-reaching effects
Professor John Cryan, corresponding author of the study and principal investigator at APC Microbiome Ireland at University College Cork, explained: “There is a huge public interest in gut health. 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 highlight 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 could also be leveraged as a further intervention as part of a healthy balanced diet.”
Professor Cryan added: “Coffee is more than just caffeine, it’s a complex dietary component that interacts with our gut bacteria, metabolism and even mental well-being.” “Our findings suggest that coffee, whether caffeinated or decaffeinated, may affect health in different, but complementary ways.”
