Researchers studying 62 healthy adults found that both caffeinated and decaffeinated coffee changed specific microbial populations and metabolites associated with communication between the digestive system and the brain. The findings suggest coffee’s influence on human physiology may arise partly from its polyphenols and other compounds rather than solely from its stimulant content.
The participants, aged between 30 and 50, included 31 people who regularly drank three to five cups of coffee a day and 31 who did not consume coffee. Regular drinkers stopped drinking it for two weeks before being assigned caffeinated or decaffeinated coffee for a three-week reintroduction period.
Researchers collected stool and urine samples, assessed diet and caffeine intake, and monitored blood pressure, inflammation, mood, sleep, stress and cognitive performance. The study was designed to examine the microbiota-gut-brain axis, the two-way communication network linking intestinal microbes with the nervous system.
Coffee withdrawal changed the regular drinkers’ metabolic profile until it began to resemble that of non-drinkers. Reintroducing either form of coffee restored several metabolites derived from polyphenols, while only caffeinated coffee restored compounds produced through caffeine metabolism.
Specific bacterial strains also responded to consumption and withdrawal. Regular coffee drinkers had higher levels of Cryptobacterium curtum and some Eggerthella strains, while non-drinkers had greater quantities of certain Veillonella strains. Reintroducing coffee produced further shifts regardless of whether caffeine was present.
The changes were concentrated among particular microorganisms rather than reflecting a broad increase in microbiome diversity. This distinction matters because a food or beverage can modify the activity of selected bacteria without necessarily making the entire microbial community more diverse.
Coffee contains chlorogenic acids, melanoidins and other phenolic compounds that can reach the large intestine and be processed by gut microbes. These substances may act in a prebiotic-like manner, influencing bacterial growth and the production of metabolites that interact with inflammation, metabolism and brain function.
Both groups receiving coffee recorded lower scores for perceived stress, depression and impulsivity during the intervention. The caffeinated group also showed reduced anxiety and psychological distress, improved attention and lower systolic blood pressure compared with participants receiving decaf.
Decaffeinated coffee produced a different pattern. Participants assigned decaf showed improvements in sleep quality, physical activity, learning and episodic memory. They also displayed reduced emotional reactivity, raising the possibility that non-caffeine compounds could affect cognition directly or indirectly through improved sleep and microbial metabolism.
The memory results require caution. Repeating cognitive tests can improve performance because participants become familiar with the tasks. The researchers acknowledged that this learning effect may have contributed to some of the gains, although the improvements were stronger among those receiving decaf.
The study does not establish that coffee will improve mood or memory for everyone. Its sample was small, drawn from healthy adults in Ireland and restricted to a relatively narrow age range. Participants also knew they were taking part in a coffee study, while several behavioural outcomes depended on self-reported questionnaires.
Baseline comparisons added further complexity. Habitual coffee drinkers initially recorded greater impulsivity and emotional reactivity than non-drinkers. Abstinence reduced both measures, suggesting that some apparent improvements after coffee was restored may reflect adaptation, withdrawal recovery or changes occurring across the full study period.
Inflammatory responses were also mixed. Coffee abstinence was associated with increases in some inflammatory markers, while both caffeinated and decaffeinated coffee reduced the production of interleukin-6 after immune stimulation. Other markers moved differently depending on caffeine content, preventing a simple claim that coffee uniformly reduces inflammation.
The project received support from the Institute for Scientific Information on Coffee, an organisation funded by major coffee companies. The published paper stated that the researchers retained scientific independence, but the financial connection remains relevant when assessing the findings and the need for independent replication.
Wider research has linked moderate coffee consumption with lower risks of several chronic conditions, but much of that evidence is observational and cannot prove cause and effect. Health outcomes may also vary with preparation method, serving size, added sugar, individual caffeine sensitivity, medication use and existing medical conditions.
The new work strengthens the case for studying coffee as a complex mixture rather than treating it as a delivery system for caffeine. It also suggests that decaf retains biologically active compounds capable of modifying microbial and metabolic activity, even when most of the stimulant has been removed.
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