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Researchers at APC Microbiome Ireland (University College Cork) found that both caffeinated and decaffeinated coffee were associated with changes in the gut microbiome, metabolites, mood and stress in a 62-person study published in Nature Communications. Decaf was linked to improved learning and memory, while caffeinated coffee was linked to reduced anxiety and better attention. The small sample size means the findings do not establish causation.
Scientists at APC Microbiome Ireland, a research center at University College Cork, have found that both caffeinated and decaffeinated coffee are associated with changes in the gut microbiome as well as differences in mood, stress and cognition. The study, published in Nature Communications and sponsored by the Institute for Scientific Information on Coffee (ISIC), examined how coffee influences the microbiota-gut-brain axis, the two-way communication system linking gut microbes with the brain.
The researchers followed 31 regular coffee drinkers, defined as people consuming 3–5 cups per day — the amount the European Food Safety Authority (EFSA) considers safe and moderate for most people — alongside 31 non-coffee drinkers. Participants completed psychological assessments and kept records of caffeine intake and diet, and provided stool and urine samples so researchers could track gut microbes, metabolites, mood and perceived stress.
During a two-week coffee abstinence period, the regular drinkers showed substantial shifts in their gut metabolite profiles compared with people who did not normally drink coffee. Coffee was then reintroduced without participants knowing whether they were receiving caffeinated or decaffeinated coffee; half received each type. After coffee returned to their diets, both groups reported lower perceived stress, depression and impulsivity scores, suggesting that some of coffee’s effects on mood may not depend entirely on caffeine.
The study also found differences in gut bacteria. Bacteria such as Eggertella sp. and Cryptobacterium curtum were more abundant among coffee drinkers; the researchers say the first may contribute to acid secretion in the stomach and intestines, while the second may participate in bile acid production — processes that could potentially create an intestinal environment that discourages certain harmful bacteria. Higher levels of Firmicutes, a group previously associated with positive emotions in females, were also observed. Caffeinated and decaf coffee did not act identically: improved learning and memory were observed only in the decaf group, while caffeinated coffee was associated with reduced anxiety, improved vigilance and attention, and a reduced risk of inflammation.
Why Coffee’s Effects May Go Beyond Caffeine
The results add to growing evidence that coffee should not be viewed simply as a caffeine delivery system. Coffee contains thousands of chemical compounds, including polyphenols, plant-derived substances that can act as antioxidants and interact with gut microbes, potentially influencing metabolism. The suggestion that decaf improved learning and memory while caffeinated coffee affected anxiety and attention points to different compounds acting through different pathways.
For readers, the study offers a possible biological explanation — via the gut-brain axis — for associations between coffee and mood or cognition reported in earlier research. It does not, however, provide grounds for changing coffee habits for health reasons, because the study involved a relatively small number of participants and does not establish that coffee directly causes the observed changes.
The Gut-Brain Axis and the Study Design
Scientists have long studied coffee for possible effects on digestion, mood and overall health, but exactly how those effects arise has remained unclear. The new research focused on the microbiota-gut-brain axis, the communication system through which gut microorganisms and the brain exchange signals via immune activity, hormones, nerves and microbially produced chemical compounds.
The study’s design — a washout period followed by blinded reintroduction of caffeinated or decaffeinated coffee — allowed the researchers to separate effects of habitual coffee consumption from the effects of removing and restoring it, and to compare caffeine-dependent and caffeine-independent outcomes. The work was sponsored by ISIC, a coffee-industry-funded body, and published in a peer-reviewed journal.
“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.”
— Professor John Cryan, corresponding author, Principal Investigator at APC Microbiome Ireland, University College Cork
Small Sample and Open Questions
Because the study involved only 62 participants, the findings do not establish that coffee causes the observed changes in mood, cognition or gut health. Several reported associations — such as the roles of Eggertella sp. and Cryptobacterium curtum in acid and bile acid processes — are described by the researchers as possibilities rather than demonstrated mechanisms, and the link between Firmicutes and positive emotions comes from earlier research in females, not this study.
It is also unclear how long the observed metabolite and microbiome shifts persist, whether the mood and cognitive effects would appear in larger and more diverse populations, and which specific coffee compounds drive the decaf-associated learning and memory effects. The study’s industry sponsorship by ISIC is a further factor readers may weigh when interpreting the conclusions.
Larger Trials and Compound Identification
The researchers describe the work as providing new clues about biological pathways that could explain associations reported in earlier coffee research. Follow-up studies are expected to test the findings in larger groups, identify which of coffee’s thousands of compounds interact with gut microbes, and examine whether the observed microbiome and metabolite changes translate into durable effects on mood, stress and cognition over the long term. No further trial results or timelines were announced with the publication.
Key Questions
Does this study prove coffee improves mood or brain function?
No. The study found associations between coffee consumption and changes in gut microbes, metabolites, mood and stress in a small sample of 62 people. The researchers state that the findings do not establish that coffee directly causes these changes.
Was decaffeinated coffee also linked to effects?
Yes. Both caffeinated and decaf coffee were associated with lower perceived stress, depression and impulsivity scores after reintroduction, and improved learning and memory were observed only in the decaf group, suggesting non-caffeine compounds play a role.
How much coffee did participants drink?
Regular coffee drinkers in the study consumed 3–5 cups per day, an amount the European Food Safety Authority defines as safe and moderate for most people.
What is the gut-brain axis?
It is the two-way communication system linking microorganisms in the digestive tract with the brain, with signals traveling through immune activity, hormones, nerves and compounds produced by gut microbes.
Who funded the research?
The study was sponsored by the Institute for Scientific Information on Coffee (ISIC), a coffee-industry-funded body, and conducted by scientists at APC Microbiome Ireland, University College Cork. It was published in the peer-reviewed journal Nature Communications.
Source: rss
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