Study Shows Habitual Coffee Intake Alters Gut Microbiome and Influences Cognition, Mood in Adults

Habitual coffee consumption shapes the gut microbiome and modifies host physiology and cognition, according to a study published in Nature Communications. Researchers led by S. Boscaini investigated whether these effects occur independently of caffeine in healthy adults.

1038/s41467-026-71264-8. Sixty-two healthy adults aged 30-50 from Ireland participated. Thirty-one were non-coffee drinkers, labeled NCDs, while the other 31 were moderate coffee drinkers, or CDs, who consumed 3-5 cups daily.

Participants with a history of acute or chronic coexisting illness were excluded, as were those under any medication, habitual consumers of high quantities of fermented foods, and pregnant or lactating individuals. At baseline, participants underwent a physical exam, provided blood and fecal samples, and completed questionnaires and cognitive tasks. The majority of participants were female.

CDs consumed more caffeine than NCDs, but other lifestyle factors and genetic profiles were similar between the groups. No significant dietary differences emerged, and dietary intake remained largely stable throughout the study. General well-being assessments showed no differences between groups.

Before the intervention, CDs abstained from coffee, other caffeinated beverages, and dark chocolate for two weeks. They were then randomly assigned to either a caffeinated group of 16 or a decaffeinated group of 15 in a double-blind, parallel design. The intervention lasted three weeks, with participants consuming four sachets per day of their assigned coffee.

During the intervention, coffee abstinence led to lower blood pressure in CDs. Caffeinated coffee reduced systolic blood pressure compared to decaffeinated coffee. CDs exhibited higher impulsivity and emotional reactivity scores than NCDs at baseline.

Coffee abstinence reduced impulsivity and emotional reactivity in CDs and improved cognitive performance. Caffeinated coffee reduced anxiety and enhanced cognitive performance, while decaffeinated coffee improved memory, sleep quality, and physical activity.

Only caffeinated coffee resulted in lower salivary cortisol after the intervention. Both coffee types reduced perceived stress, depression, and impulsivity, but neither affected stress resilience. Caffeinated coffee improved self-concept and coping abilities, whereas decaffeinated coffee increased positive affect.

Memory performance was comparable between groups at baseline, but only decaffeinated coffee led to significant improvements in episodic memory. During coffee withdrawal, cravings remained stable, while withdrawal symptoms decreased rapidly. These symptoms included reductions in drowsiness, headaches, and fatigue, with energy levels increasing.

Decaffeinated coffee led to greater drowsiness and fatigue, whereas caffeinated coffee improved mood and mitigated withdrawal symptoms. Caffeinated coffee reduced IL-10 and IL-6, while decaffeinated coffee raised C-reactive protein and tumor necrosis factor alpha. NCDs exhibited a greater IL-6 response at baseline.

Both coffee types lowered IL-6 following the intervention, and decaffeinated coffee reduced TNFα secretion. These changes suggest coffee modulates immune responses in context-dependent ways. CDs exhibited higher fecal concentrations of caffeine, theophylline, 1,7-dimethylxanthine, and hippuric acid compared to NCDs, along with lower levels of indoles and gamma-aminobutyric acid in feces.

Coffee abstinence reduced fecal metabolites in CDs. Reintroduction of coffee produced shifts in metabolites depending on the type consumed. CDs excreted higher levels of caffeine metabolites and phenolic compounds in urine compared to NCDs.

After coffee abstinence, urinary metabolite profiles of CDs resembled those of NCDs, except for a few unchanged metabolites. CDs had higher fecal concentrations of certain benzoic and cinnamic acid derivatives, which decreased during abstinence and rose after reintroduction, independent of caffeine content.

Urinary polyphenol metabolites correlated with specific microbial species and other metabolites, and were strongly associated with cognitive outcomes.

Coffee abstinence and reintroduction resulted in dynamic shifts in microbial populations, regardless of caffeine content. Microbiota diversity differed between NCDs and CDs but remained stable within the CD group after the intervention, indicating coffee influences specific microbial strains rather than overall diversity. The study was authored by Boscaini, S.

Et al. and published in 2026. An article summarizing the research, written by Dr. net.