Scientists Discover How Coffee Affects the Gut and Mood

A new study by researchers from the APC Microbiome Ireland research center at University College Cork has shown that coffee influences the gut–brain axis by altering the composition of the microbiome and related processes, which in turn affect mood, stress levels, and cognitive functions.

The study was published in the journal Nature Communications and is among the first to подробно explain the mechanisms behind this effect.

The study involved 62 participants—31 regular coffee drinkers and 31 non-drinkers. Participants completed psychological assessments, kept food diaries, and provided stool and urine samples, allowing researchers to track changes in the microbiome and subjective well-being. Regular consumers were defined as those who drink 3–5 cups of coffee per day—a level the European Food Safety Authority considers moderate and safe for most people.

In the first phase, all participants abstained from coffee for two weeks. Among habitual drinkers, this led to noticeable changes in gut microbiome metabolites, indicating the sensitivity of gut flora to regular coffee consumption.

Coffee was then reintroduced into the diet, with some participants receiving caffeinated coffee and others decaffeinated coffee, in a blinded setup. In both cases, participants reported reduced stress levels, fewer depressive symptoms, and lower impulsivity, suggesting a positive effect of coffee on mood regardless of caffeine content.

However, differences in effects were also observed. Coffee consumption was associated with an increase in certain bacteria, including Eggerthella and Cryptobacterium curtum, which are linked to digestion and bile acid metabolism and may play a role in protecting against harmful microorganisms. There was also an increase in bacteria from the Firmicutes group, which in some studies are associated with more positive emotional states.

Interestingly, improvements in learning and memory were observed only in participants who received decaffeinated coffee, suggesting the role of other components such as polyphenols. At the same time, caffeinated coffee was linked to reduced anxiety, as well as improved attention and alertness. In addition, caffeine showed an association with lower levels of inflammation.

The authors emphasize that coffee acts as a complex dietary factor, influencing not only the microbiome but also metabolism and nervous system function. In their view, regular coffee consumption may be considered one of the factors supporting gut health and psycho-emotional well-being as part of a balanced diet.

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