The findings, published in Nature Communications and supported by the Institute for Scientific Information on Coffee (ISIC), show that regularly drinking both caffeinated and decaffeinated coffee can shape the gut microbiome and influence mood and stress.

How Coffee Affects the Gut Microbiome and Mood

Coffee has long been associated with digestive and mental health benefits, but the biological reasons behind these effects have not been fully understood. This study focused on how coffee impacts the microbiota-gut-brain axis — the bidirectional communication between the gut microbiome and the brain — using a wide range of biological and psychological measurements.

To explore this, researchers compared 31 regular coffee drinkers with 31 people who do not drink coffee. 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 state. In this study, “coffee drinkers” were defined as individuals who typically consume 3-5 cups of coffee per day, a level considered safe and moderate by the European Food Safety Authority (EFSA).

Study Design Reveals Microbiome Changes

At the start of the experiment, coffee drinkers stopped consuming coffee for two weeks. During this period, researchers continued to collect biological samples and monitor mental health. This break led to clear shifts in the metabolites produced by gut microbes in regular coffee drinkers, setting them apart from non-coffee drinkers.

After the abstinence phase, coffee was gradually reintroduced without participants knowing whether they were drinking caffeinated or decaffeinated coffee. Half received decaf, while the others consumed regular coffee. Both groups reported improvements in mood, including lower levels of stress, depression, and impulsivity. These results suggest that coffee can enhance mood even without caffeine.

Key Gut Bacteria Linked to Coffee Consumption

The study also identified specific bacteria that were more common in coffee drinkers. Levels of ‘Eggertella sp’ and ‘Cryptobacterium curtum’ were higher among those who regularly consumed coffee. These microbes are believed to play roles in processes such as acid production in the digestive system and bile acid synthesis, which may help protect against harmful bacteria and infections. Researchers also observed an increase in ‘Firmicutes’, a group of bacteria previously linked to positive emotions in females.

Decaf vs Caffeine Effects 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 responsible for certain cognitive benefits.

On the other hand, caffeinated coffee showed distinct advantages. Only participants consuming caffeine experienced reduced anxiety along with better attention and alertness. Caffeine was also associated with a lower risk of inflammation.

Scientists Explain Coffee’s Broader Impact

Corresponding author of the study, Professor John Cryan, Principal Investigator at APC Microbiome Ireland, University College Cork, explained: “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.”

He added: “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.”