Coffee is often studied for its effects on alertness, digestion and long-term health. Now a small human study suggests it may also influence the gut-brain axis, the communication system linking the digestive tract and the brain.
Researchers found that regular coffee drinkers showed differences in gut microbes and metabolites compared with non-drinkers, and some mood-related measures improved after coffee was reintroduced.
The study, published in Nature Communications, involved 62 adults and was funded by the Institute for Scientific Information on Coffee, an organization backed by major coffee companies. That does not invalidate the findings, but it does matter when interpreting them. The research was also small, short-term and focused on microbiome changes and self-reported psychological measures, not hard clinical outcomes.
Researchers compared 31 regular coffee drinkers with 31 non-coffee drinkers. The coffee drinkers first stopped drinking coffee for two weeks. They then resumed coffee on a blinded basis, with some receiving caffeinated coffee and others decaffeinated coffee. Throughout the study, researchers collected stool and urine samples and tracked mood, stress and other psychological measures.
After coffee was reintroduced, both the caffeinated and decaffeinated groups reported lower perceived stress and depression scores. The researchers also found shifts in gut metabolites and differences in certain bacteria among coffee drinkers compared with non-drinkers.
The results suggest that coffee may affect the gut microbiome in ways that could help explain some of its links to mood and cognition. But the study did not show that coffee directly treats stress, depression or other mental health concerns. It also did not show that the microbiome changes caused the mood changes researchers observed.
The caffeinated and decaffeinated groups did not look exactly the same, either. In this study, caffeinated coffee was associated with reduced feelings of anxiety and improved attention, while decaffeinated coffee was linked with better performance on some learning and memory measures. That raises the possibility that compounds in coffee other than caffeine, including polyphenols, may play a role. Still, this was an early-stage study, and the sample was too small to make broad claims.
“Coffee is more than just caffeine — it’s a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional wellbeing,” said senior author John Cryan.
That idea is plausible and worth studying further. Coffee contains hundreds of compounds, and researchers have been trying to sort out which ones may influence digestion, inflammation, metabolism and brain function. This study adds to that work by looking at both caffeinated and decaffeinated coffee and by pairing microbiome testing with psychological assessments.
Still, readers should be careful not to overread the findings. Mood and stress scores can shift for many reasons. Microbiome data can also be difficult to interpret cleanly, especially in small studies where many factors, including diet and daily routines, may influence the results. The paper offers an interesting clue about how coffee may interact with the body, but it does not settle the question.
The study was funded by the Institute for Scientific Information on Coffee, which is supported by major European coffee companies. APC Microbiome Ireland also receives public research support, and the paper lists additional support from European and Italian public funding sources. Several authors reported relationships with food, pharmaceutical and probiotic companies, including Nestle, Yakult, Bayer Healthcare, Nutricia, DuPont/IFF, Pharmavite, Fonterra and Tate and Lyle.