Researchers at APC Microbiome Ireland, a research centre at University College Cork, have found that coffee may influence far more than alertness by altering the gut microbiome and potentially shaping mood, stress, memory and attention through the gut-brain axis. The study, published in Nature Communications and funded by the Institute for Scientific Information on Coffee, examined both caffeinated and decaffeinated coffee’s effects on the body’s digestive and nervous systems.
The project involved 62 adults, split into 31 regular coffee drinkers and 31 individuals who did not normally drink coffee. Regular drinkers were defined as those who typically consume 3 to 5 cups of coffee a day, a level described by the European Food Safety Authority as safe and moderate for most people.
When the regular coffee drinkers abandoned caffeine for two weeks, researchers observed substantial shifts in their gut metabolite profiles compared with those who did not habitually drink coffee. Metabolites are small molecules produced or altered during metabolism, including compounds produced by gut microbes as they process food and other substances.
Coffee was then reintroduced without participants knowing whether they were receiving caffeinated or decaffeinated coffee. Half of the participants received decaf, while the other half received caffeinated coffee. After coffee returned to their diets, both groups reported lower perceived stress, depression and impulsivity, suggesting that some mood effects may not arise solely from caffeine.
In addition, researchers noted changes in several types of gut bacteria. Bacteria such as Eggerthella sp. and Cryptobacterium curtum were more abundant among coffee drinkers than non-drinkers. Eggerthella sp is thought to contribute to acid secretion in the stomach and intestines, while Cryptobacterium curtum may participate in bile acid production, possibly fostering an intestinal environment unfavourable to certain harmful microbes. The team also observed higher levels of Firmicutes, a broad group of microbes that has previously been associated with positive emotions in females.
One of the study’s more striking findings was that caffeinated and decaffeinated coffee did not appear to affect participants in exactly the same way. Improved learning and memory were observed only among those who drank decaffeinated coffee, while caffeinated coffee was associated with reduced anxiety and improved vigilance and attention. Caffeine was also linked to a reduced risk of inflammation. The researchers stressed that the relatively small participant pool means the study cannot prove causation, but it offers new clues about the biological pathways that may underpin associations seen in earlier coffee research.
Corresponding author 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,” he added.
The findings add to growing evidence that coffee should not be viewed simply as a source of caffeine. Its many other components may interact with the microbiome, metabolism, and nervous system in different ways, according to Cryan. “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,” he said. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”
