A recent study of humans suggests that regular coffee drinking is linked to shifts in gut microbes and metabolites that might ripple all the way to the brain, affecting mood, memory and stress.
The research, published April 21 in Nature Communications, comes from a team at APC Microbiome Ireland, a leading gut microbiome research center at University College Cork.
The authors positioned the work as a comprehensive human study of how coffee affects what scientists call the microbiota-gut-brain axis — the two-way communication system linking the gut microbiome and the brain.
The gut microbiome is the vast community of bacteria, yeasts and other microorganisms living in the digestive tract. Evidence increasingly suggests it can shape not only digestion and immunity but also mood, cognition and stress response. In this study, coffee intake was linked to measurable shifts in gut microbes, metabolites and some behavioral and cognitive measures.
“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,” study co-author John Cryan of University College Cork said in an announcement of the study. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”
What the Study Did
Researchers recruited 62 healthy adults between the ages of 30 and 50, including 31 regular coffee drinkers and 31 non-coffee drinkers. The two groups were similar on baseline measures of diet, BMI, education, alcohol consumption and predicted IQ.
Coffee drinkers first abstained from coffee for two weeks, then were randomly assigned to reintroduce either caffeinated or decaffeinated instant coffee for 21 days.
Throughout each phase, participants submitted stool and urine samples, completed detailed psychological questionnaires and kept seven-day food diaries. Researchers used a DNA-sequencing technique called shotgun metagenomics to profile gut bacteria, and two types of chemical analysis to track hundreds of compounds in feces and urine.
The Findings on Mood, Stress and Memory
After coffee was reintroduced to habitual coffee drinkers, both the caffeinated and decaffeinated groups reported lower perceived stress, lower depression scores and lower impulsivity than at the start of the intervention.
Some effects appeared to differ by coffee type. Only the caffeinated group showed reduced anxiety and better attention and vigilance scores, while the decaffeinated group showed improved sleep quality and gains on some memory and learning measures.
While the UCC press release and much of the subsequent coverage emphasize potential benefits, the paper itself presents a more complicated picture.
At baseline, habitual coffee drinkers showed higher impulsivity and emotional reactivity than non-coffee drinkers, while non-coffee drinkers performed better on memory measures.
During the two-week abstinence, impulsivity and emotional reactivity fell among habitual drinkers. After coffee was reintroduced, some mood measures improved again, but the paper suggests that part of that change may reflect reversal of withdrawal-related effects rather than a simple across-the-board benefit.
The authors also note that non-coffee drinkers appeared to avoid caffeine-withdrawal symptoms altogether.
Context
DCN previously covered a 2024 Nature Microbiology study linking coffee consumption to higher levels of a beneficial gut bacterium called Lawsonibacter asaccharolyticus across more than 54,000 participants. More recently, a mouse study from China suggested caffeine may help prevent depression via gut microbiota regulation.
The Cork study examined the mechanism in healthy human adults using simultaneous microbiome profiling, metabolomics and cognitive testing, while also isolating the effects of caffeine from other coffee compounds. However, the human sample size was limited to 62 people, all of whom were in Ireland.
Funding Disclosure
The study was sponsored by the Institute for Scientific Information on Coffee (ISIC), an organization whose members are five major European coffee companies: Illycaffè, JDE Peet’s, Lavazza, Paulig and Tchibo.
The paper says ISIC funded the research, and it also discloses outside speaking, consulting or research relationships for several authors, including research funding from pharmaceutical companies and Nestlé.
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