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A study from APC Microbiome Ireland published in Nature Communications found that both caffeinated and decaffeinated coffee were associated with changes in the gut microbiome and improvements in stress, mood and, for decaf drinkers, learning and memory. The small sample size means the findings suggest biological pathways rather than proven cause and effect.
Scientists at APC Microbiome Ireland, a research center at University College Cork, have found that both regular and decaffeinated coffee are associated with changes in the gut microbiome and with 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 communication between the digestive system and the brain — and suggests that some of coffee’s effects on mood do not depend on caffeine.
The researchers recruited 31 regular coffee drinkers, defined as people consuming 3–5 cups per day — an amount the European Food Safety Authority (EFSA) classifies as safe and moderate for most people — alongside 31 people who did not normally drink coffee. Participants completed psychological assessments and kept records of caffeine intake and diet, while researchers collected stool and urine samples to track changes in gut microbes, metabolism, mood and perceived stress.
Regular coffee drinkers first stopped consuming coffee for two weeks, repeatedly completing assessments and providing samples during that period. When coffee was removed, researchers observed substantial shifts in gut metabolite profiles — the small molecules produced or altered during metabolism, including compounds created by gut microbes — compared with the non-coffee-drinking group. Coffee was then reintroduced without participants knowing whether they were receiving caffeinated or decaffeinated coffee; half received each type.
After coffee returned to participants’ diets, both groups reported lower perceived stress, depression and impulsivity scores, according to the study. The researchers also identified differences in gut bacteria: Eggertella sp. and Cryptobacterium curtum were more abundant among coffee drinkers, and higher levels of Firmicutes bacteria — a group previously associated with positive emotions in females — were observed. Caffeinated coffee was associated with reduced anxiety, improved vigilance and attention, and a reduced risk of inflammation. Improved learning and memory were observed only among participants drinking decaffeinated coffee.
Why Decaf Results Change the Coffee Conversation
The decaf findings matter because they challenge the common assumption that coffee’s effects are mainly caffeine effects. If mood and cognitive changes appear — and in the case of learning and memory, appear only — with decaffeinated coffee, then other components are likely involved. 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 study also adds mechanistic detail to long-standing observational associations between coffee and health. By focusing on the microbiota-gut-brain axis — the two-way communication system linking gut microorganisms with the brain via immune activity, hormones, nerves and microbe-produced chemicals — the researchers offer possible biological pathways that could help explain results reported in earlier coffee research.
How the Study Was Designed
Scientists have long studied coffee for possible effects on digestion, mood and overall health, but exactly how those effects arise has remained unclear. This study addressed that gap with a controlled withdrawal-and-reintroduction design: a two-week coffee-free period followed by blinded reintroduction, with caffeinated and decaffeinated coffee randomly assigned so participants did not know which they received.
The ‘coffee drinker’ threshold of 3–5 cups per day follows EFSA’s definition of moderate, safe consumption for most adults. The research was sponsored by ISIC, a body funded by coffee companies, which the authors disclose; the peer-reviewed findings were published in Nature Communications.
“Coffee is more than just caffeine — it’s a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional well-being.”
— Professor John Cryan, Principal Investigator at APC Microbiome Ireland, University College Cork
Small Sample, Industry Funding, Open Questions
The study involved a relatively small number of participants — 31 coffee drinkers and 31 non-drinkers — and the researchers themselves state that the findings do not establish that coffee directly causes the observed changes in mood, cognition or gut health. Associations reported here may reflect other dietary or lifestyle factors.
Several mechanisms remain unconfirmed. The roles of Eggertella sp. in acid secretion and Cryptobacterium curtum in bile acid production are described as thought to or potentially involved, not proven. It is also unclear why improved learning and memory appeared only in the decaf group, or how long the observed microbiome shifts persist. The sponsorship by ISIC, a coffee-industry-funded body, is another factor readers may weigh when interpreting the conclusions.
Larger Trials and Caffeine-Free Compounds
The authors frame the work as providing new clues about biological pathways rather than final answers. Follow-up research would need larger and longer trials to test whether coffee — and specifically its non-caffeine compounds such as polyphenols — causally affects the gut-brain axis, and whether effects differ reliably between caffeinated and decaffeinated coffee, between individuals, and by sex, given the prior link between Firmicutes and positive emotions in females.
The researchers suggest that identifying which coffee compounds drive the observed changes could eventually inform dietary guidance or targeted interventions for digestive and mental health, though any such application remains speculative at this stage.
Key Questions
Does this study prove coffee improves mood and gut health?
No. The study found associations between coffee consumption and changes in gut microbes, mood and stress, but because of the small sample size the authors state it does not establish that coffee directly causes these changes.
Did decaffeinated coffee have the same effects as regular coffee?
Not exactly. Both types were linked to lower perceived stress, depression and impulsivity, but improved learning and memory were observed only with decaf, while reduced anxiety and better vigilance and attention were associated with caffeinated coffee.
How much coffee did participants drink?
‘Coffee drinkers’ in the study regularly consumed 3–5 cups per day, the amount the European Food Safety Authority defines as safe and moderate for most people.
How could coffee affect the brain through the gut?
The researchers focused on the microbiota-gut-brain axis, a two-way communication system in which signals travel between gut microbes and the brain via immune activity, hormones, nerves and microbe-produced chemical compounds.
Who funded the research?
The study was sponsored by the Institute for Scientific Information on Coffee (ISIC), an industry-funded body, and conducted by scientists at APC Microbiome Ireland, University College Cork. It was peer-reviewed and published in Nature Communications.
Source: rss
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