Coffee in the gut and brain was analyzed by researchers from University College Cork, who observed changes in the microbiome, mood, stress, attention, and memory, showing that the drink acts through pathways that go beyond caffeine.
Coffee in the gut and brain underwent a detailed analysis in a study conducted by researchers from APC Microbiome Ireland, a research center at University College Cork. The investigation examined how the beverage interacts with the gut-brain axis, a communication network that links the digestive system to the brain.
The findings were published in the journal Nature Communications and indicate that regular consumption of regular and decaffeinated coffee can shape the gut microbiome and influence mood and stress. The research was supported by the Institute for Scientific Information on Coffee.
The study evaluated the so-called gut-brain microbiota, a bidirectional communication between gut bacteria and the brain. The objective was to understand biological mechanisms associated with digestive and mental effects already linked to coffee consumption.
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Participants underwent a consumption break
The research compared 31 regular coffee drinkers with 31 non-coffee drinkers. Participants underwent psychological evaluations, recorded diet and caffeine intake, and provided stool and urine samples for analysis of gut bacteria and emotional state.
In the study, coffee consumers were defined as people who drank 3 to 5 cups per day, a level considered safe and moderate by the European Food Safety Authority. The study design allowed for observing changes before, during, and after withdrawal from the beverage.
At the beginning of the experiment, habitual consumers stopped consumption for two weeks. During this period, researchers continued collecting biological samples and monitoring mental health, which revealed changes in metabolites produced by gut microbes.
Coffee in the gut showed changes in bacteria
After the abstinence phase, coffee was gradually reintroduced, without participants knowing whether they were drinking the regular or decaffeinated version. Half received decaffeinated, while the other half consumed caffeinated coffee.
Both groups reported improved mood, with lower levels of stress, depression, and impulsivity. This result indicates that coffee in the gut may be associated with effects on emotional state even when there is no caffeine in the beverage.
The analysis also identified bacteria more common among regular coffee drinkers. Levels of Eggertella sp and Cryptobacterium curtum appeared higher in this group, microorganisms linked to processes such as acid production in the digestive system and bile acid synthesis.
These processes can help protect against harmful bacteria and infections. Researchers also observed an increase in Firmicutes, a bacterial group previously linked to positive emotions in women.
Decaffeinated and caffeine had different effects
Improvements in learning and memory appeared only among participants who drank decaffeinated coffee. This data suggests that compounds other than caffeine, such as polyphenols, may be involved in some of the observed cognitive benefits.
Caffeinated coffee showed its own effects in other areas. Only participants who consumed caffeine experienced reduced anxiety, improved attention, and increased alertness, in addition to an association with a lower risk of inflammation.
According to Professor John Cryan, corresponding author of the study and principal investigator at APC Microbiome Ireland, coffee is a complex dietary factor. The beverage interacts with gut microbes, metabolism, and emotional well-being, with distinct and complementary effects in both regular and decaffeinated versions.
The study reinforces that coffee in the gut does not act merely as a source of caffeine. The beverage can alter the collective functioning of microbes and the metabolites they use, expanding the understanding of its relationship with digestion, mood, stress, and cognition.
Click here to access the study.

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