Habitual coffee consumption has been found to affect mood and stress through gut bacteria.
Many people feel that drinking coffee 'clears their head' or 'lifts their mood,' but the mechanism behind this has not been fully understood until now. A study published by an international research team consisting of researchers from
Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition | Nature Communications
https://www.nature.com/articles/s41467-026-71264-8
Previous research has linked moderate coffee consumption to various health benefits and has shown evidence that coffee directly affects the brain, shaping both neural activity and cognitive outcomes. Furthermore, a 2024 metagenomics study involving over 1,000 participants examined the relationship between more than 150 dietary components and gut microbiome composition, finding coffee to be the food with the highest correlation to microbiome components.
Experts explain the various benefits of drinking coffee - GIGAZINE
On the other hand, the temporal changes associated with coffee consumption, discontinuation, and resumption have not been fully elucidated, and the role of gut bacteria as a mediating factor between coffee consumption and brain function has not been established. Therefore, a study published in the academic journal Nature Communications on April 21, 2026, investigated the effects of coffee on the 'gut microbiota-gut-brain axis,' which is a bidirectional communication pathway between the gut microbiome and the brain.
A research team at University College Cork and others investigated the temporal effects of coffee consumption, discontinuation, and reintroduction on cognition, mood, and behavior through self-report questionnaires. They then integrated the measurement of 'gut microbiota composition,' 'gut metabolome,' 'cognitive function and behavior,' and 'mood and stress indicators' using stool and urine samples, psychological tests, and questionnaires in healthy adults during periods of coffee consumption, temporary discontinuation, and reintroduction. To evaluate whether coffee has effects independent of caffeine, they also compared decaffeinated and caffeinated coffee. While the paper doesn't specify the type or temperature of the coffee, it's likely that the coffee was served without milk or sugar, given the focus on components like caffeine and polyphenols.
As a result, it was found that coffee drinkers had a significantly increased relative abundance of certain gut bacteria involved in the secretion of gastric and intestinal acids, and decreased levels of certain metabolites. While coffee consumption did not significantly alter the composition of gut bacteria itself, changes were observed in the profile of metabolites produced by the microorganisms. In terms of behavior, coffee drinkers showed strong improvements in impulsivity and emotional reactivity, while only those who consumed decaffeinated coffee showed significant improvements in memory and learning ability.
By comparing the levels of non-targeted fecal metabolites in participants, researchers confirmed that caffeine and polyphenols in coffee significantly contribute to the overall excretion of metabolites. Therefore, the researchers concluded that 'coffee consumption alters specific microbial populations without changing the overall diversity of the gut microbiota.'
Based on questionnaires administered before and after the intervention, both those who consumed caffeinated and decaffeinated coffee showed improvements in the BDI (a measure of stress and depression) and the UPPS-P (a measure of impulsive behavior). However, only the group that reintroduced caffeinated coffee showed improvement in anxiety and psychological distress. In particular, there was evidence that coffee consumption regulated the balance of tryptophan , a precursor of serotonin, which is related to mood, via gut bacteria. This is thought to be part of the mechanism by which anxiety and psychological distress improved with the reintroduction of caffeinated coffee.
To further investigate the effects of coffee on stress coping abilities, cortisol, a stress hormone, was also tested. The results showed that cortisol levels were remarkably similar between coffee drinkers and non-drinkers, suggesting that coffee may support mental health not by reducing the source of stress, but by mitigating 'emotional reactivity,' or how the brain perceives stress.
Overall, the researchers concluded that coffee has been found to affect impulsivity and emotional reactivity. They also suggested that different types of coffee offer different benefits: caffeinated coffee improves anxiety and cognitive function, while decaffeinated coffee enhances memory, sleep quality, and physical activity. These differences suggest that coffee consumption may independently alter the gut microbiota, influencing brain function through the gut environment.
Professor John Cryan of University College Cork, who led the study, said, 'Public interest in gut health has increased dramatically. We are also gaining a better understanding of the relationship between digestive and mental health, but the mechanisms by which coffee affects the gut-brain axis remain unclear. Our findings reveal the effects of coffee on the microbiome and nervous system, and its potential long-term effects on a healthier microbiome. Coffee may alter the collective function of microorganisms and the metabolites they utilize. As people continue to explore dietary improvements for proper digestive balance, coffee has the potential to be used as an additional intervention as part of a healthy, balanced diet.'
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