21 April 2026: New research from APC Microbiome Ireland, a world leading research centre at University College Cork , has comprehensively explored the mechanisms behind coffee’s positive effects on the gut-brain axis for the first time 1 .
The study published in Nature Communications and sponsored by the Institute for Scientific Information on Coffee (ISIC), reveals how regular consumption of both caffeinated and decaffeinated coffee can affect the gut microbiome, and in turn influence mood and stress levels.
The benefits of coffee for both digestion and mood have been widely studied, but the exact mechanisms behind these effects have remained unclear. This research investigated how coffee consumption affects the microbiota-gut-brain axis – the bidirectional communication between the gut microbiome and the brain - through a wide range of measures.
31 coffee drinkers and 31 non-coffee drinkers were closely studied through a series of psychological tests, caffeine and food diaries, and stool and urine samples to understand changes in their microbiome and perceived mood or stress. ‘Coffee drinkers’ were set as those who regularly consume 3-5 cups of coffee a day – defined by the European Food Safety Authority (EFSA) as a safe and moderate amount for most people 2 .
Participants first abstained from coffee for two-weeks, with regular psychological assessments, as well as stool and urine samples throughout. This period of abstinence for coffee-drinkers corresponded with significant changes in metabolite profiles in the gut microbiome, compared to non-coffee drinkers.
Coffee was reintroduced to regular drinkers on a blinded basis, with half of participants consuming decaffeinated coffee and the other half caffeinated coffee. Both groups reported lower perceived stress, depression and impulsivity scores, suggesting that drinking coffee significantly improved mood, regardless of caffeine content.
Bacteria, such as ‘Eggertella sp’ or ‘Cryptobacterium curtum ’ , were notably increased in coffee-drinkers compared to non-coffee drinkers. The former is thought to contribute to gastric and intestinal acid secretion, while the latter is thought to be involved in bile acid synthesis - both of which may play a role in eliminating unhealthy gut bacteria and stomach infections. Increased ‘Firmicutes’ bacteria were also observed, which has been associated with positive emotions in females.
A notable improvement in learning and memory was found only in those who consumed decaffeinated coffee, suggesting that components other than caffeine, such as polyphenols, are responsible for these cognitive benefits. However, in this study the researchers found that only caffeinated coffee was associated with reduced feelings of anxiety, as well as improved vigilance and attention. Caffeine was also linked to a reduced risk of inflammation.
Corresponding author of the study, Professor John Cryan, Principal Investigator at APC Microbiome Ireland, University College Cork, commented: “ Public interest in gut health has risen hugely. The relationship between digestive and mental health is also increasingly being better understood, but 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. Coffee may modify what microbes do collectively, and what metabolites they use. As the public continues to think about dietary changes for the right digestive balance, coffee has the potential to also be harnessed as a further intervention as part of a healthy balanced diet”.
“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 Prof. Cryan. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”
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Notes to editors
Corresponding author
About ISIC
The Institute for Scientific Information on Coffee (ISIC) is dedicated to contributing and consolidating balanced scientific information on coffee consumption – providing a reference for professionals and authorities who address health and wellbeing.
It’s activities include:
ISIC respects scientific research ethics in all its activities. ISIC’s communications are based on sound science and rely on scientific studies derived from peer-reviewed scientific journals and other publications.
ISIC members are five of the major European coffee companies: illycaffè , JDE Peet’s , Lavazza , Paulig and Tchibo .
About APC Microbiome Ireland
APC Microbiome Ireland is a world leading research centre based in University College Cork. It was formed in 2003 with funding from Science Foundation Ireland and in conjunction with key industry partners. APC represents a seamless collaboration between University College Cork and Teagasc (the Irish Agriculture and Food Development Authority).
It is widely recognised that the gut microbiota plays an important role in human health and has become one of the most dynamic, complex, and exciting areas of research in both food and pharmaceutical arenas. Over the last decade APC has established itself as one of the leading global centres in gut microbiota research.
APC has made several landmark discoveries and has published over 3,000 research articles in peer-reviewed journals, generating many journal covers and associated editorials. Recent research areas being led by APC include the development of new diagnostics or biomarkers of health or risk of disease (e.g. colon cancer) based on analysis of the microbiota; exploring the mechanisms by which the microbiota may be favourably mobilised or manipulated (e.g. by bacteriophage) to promote health and ‘mining’ the microbiota for new drugs (e.g. smart antibiotics) and functional food ingredients.
About Coffee & Health
Coffee & Health is a science-based resource developed for healthcare and other professional audiences and provides the latest information and research into coffee, caffeine and health.
References
Nature Communications
People
21-Apr-2026