Scientists have found new evidence that coffee may do more than boost energy, suggesting it can also influence gut bacteria and affect mood, stress levels and brain function.

The research, carried out by APC Microbiome Ireland at University College Cork, is among the first to closely examine how coffee interacts with the “gut-brain axis”, the communication system linking the digestive system and the brain. The study was published in *Nature Communications* and supported by the Institute for Scientific Information on Coffee.

Researchers say both caffeinated and decaffeinated coffee may help shape the gut microbiome and bring changes in emotional wellbeing.

Study looks at coffee, gut bacteria and mental health

The study compared 31 regular coffee drinkers with 31 people who do not drink coffee. Participants underwent psychological tests, recorded diet and caffeine intake, and provided stool and urine samples so scientists could study changes in gut bacteria and mental state.

Regular coffee drinkers were defined as people consuming around 3 to 5 cups a day, a level considered moderate and safe by European food safety guidelines.

At the beginning of the experiment, coffee drinkers stopped consuming coffee for two weeks. During this period, researchers observed noticeable changes in gut microbial activity and related compounds, separating them from non-coffee drinkers.

Mood improvements seen in both decaf and regular coffee

After the break, coffee was gradually reintroduced without participants knowing whether they were drinking caffeinated or decaffeinated coffee.

Both groups reported improved mood, including lower stress, reduced depression symptoms and less impulsive behaviour. Researchers say this suggests coffee may improve mood even without caffeine.

Gut bacteria linked with coffee intake

The study also found that certain gut bacteria were more common among coffee drinkers, including ‘Eggertella’ species and ‘Cryptobacterium curtum’. These bacteria are believed to play roles in digestion and protecting against harmful microbes.

Higher levels of another group of bacteria, ‘Firmicutes’, were also observed, which earlier research has linked with positive emotional effects in women.

Different effects of caffeine and decaf

Interestingly, improvements in learning and memory were seen only in those who drank decaffeinated coffee. Researchers suggest that plant compounds like polyphenols, rather than caffeine, may be responsible for these cognitive benefits.

Caffeinated coffee, however, showed different advantages. It was linked with reduced anxiety, better focus and increased alertness. It was also associated with lower signs of inflammation.

Researchers say coffee interacts with gut and brain

Lead researcher Professor John Cryan said growing interest in gut health is helping scientists better understand the connection between digestion and mental wellbeing, though the exact role of coffee had remained unclear until now.

He said the findings show that coffee can influence gut microbes and the substances they produce, which may have wider health effects.

“Coffee is more than just caffeine. It interacts with our gut microbes, metabolism and even emotional wellbeing,” he said, adding that both regular and decaf coffee may offer different but complementary benefits.

Researchers say the findings could help guide future understanding of how diet, especially coffee, may support both digestive and mental health.