Coffee and the Gut: What’s Brewing in the Microbiome?

 Every morning, Javier follows the same ritual: two black coffees before leaving the house. He has long believed caffeine is what prompts his bowels to move within minutes. During a recent visit, however, his gastroenterologist explained that coffee’s effects may extend beyond stimulating intestinal motility to altering the gut microbiota, with potential implications for gastrointestinal and metabolic health.

For years, coffee’s effect on intestinal transit has been attributed primarily to activation of the gastrocolic reflex, which increases colonic motility and transient hormonal stimulation. Emerging evidence suggests that this explanation is incomplete. Recent studies indicate that the effect of coffee on intestinal function cannot be explained by caffeine alone and may instead involve interactions between bioactive coffee compounds and the gut microbiota.

Researchers previously reported that patients who consumed coffee after gastrointestinal surgery recovered bowel function sooner than those who did not consume coffee. Administration of caffeine alone did not produce the same benefit, suggesting that other constituents of coffee contribute to its physiologic effects.

These findings are consistent with earlier preclinical studies. In 2022, researchers reported that both caffeinated and decaffeinated coffee stimulated ileal and colonic contractions in vitro. The findings suggested activation of muscarinic pathways independent of caffeine. Together, these observations indicate that coffee contains bioactive compounds, including polyphenols, and roasting-derived substances, such as melanoidins, that affect the gut microbiota.

Coffee-Responsive Bacteria

Evidence supporting a direct interaction between coffee and the gut microbiota comes primarily from a study published in Nature Microbiology in 2024. Researchers analyzed metagenomic data from more than 54,000 stool samples collected from European and US cohorts together with dietary information from more than 22,000 participants.

The study identified a consistent association between coffee consumption and an increased abundance of Lawsonibacter asaccharolyticus, a bacterial species whose biological role remains poorly understood. The association was replicated across multiple independent cohorts with different dietary patterns and was also observed among individuals who consumed decaffeinated coffee.

Participants with the highest coffee intake had a substantially greater abundance of L asaccharolyticus than noncoffee drinkers. The in vitro experiments further demonstrated that coffee promoted bacterial growth in culture, supporting the possibility of direct biological interaction rather than a purely epidemiologic association.

Beyond Caffeine

Researchers believe the observed effects are unlikely to be explained by caffeine alone.

The polyphenols in coffee, particularly chlorogenic acid derivatives, reach the colon, where they are metabolized by intestinal bacteria into bioactive compounds. Melanoidins formed during coffee roasting are also partially fermentable and may exert prebiotic effects.

These compounds may selectively promote bacterial species associated with favorable metabolic profiles. However, the underlying mechanisms and the functional role of L asaccharolyticus remain uncertain.

Another study published in Nutrients in 2024 found that coffee consumption in moderation was associated with greater abundance of Bifidobacterium species together with lower levels of Enterobacteriaceae, a bacterial family associated with intestinal dysbiosis when present in excess. Coffee drinkers also had greater microbial diversity, a characteristic generally considered a marker of a more resilient gut ecosystem.

The researchers concluded that the effect of coffee extends beyond gastrointestinal motility and may involve interactions among the gut microbiota, polyphenol-derived metabolites, and gut-brain signaling. However, they also noted that consumption of more than five cups of coffee daily has been associated with an increased risk for gastroesophageal reflux disease and progression of Crohn’s disease.

A population-based study published in 2025 also reported an association between excessive caffeine intake and chronic constipation.

Gut-Brain Axis

Recent research has further expanded understanding of the biological effects of coffee.

A recent study published in Nature Communications examined how consumption of coffee influences the microbiota-gut-brain axis — the bidirectional communication pathway between the gut microbiota and the central nervous system. Regular coffee drinkers had distinct microbial profiles compared with noncoffee drinkers, along with differences in microbial metabolites involved in intestinal function and communication between the gut and the central nervous system.

Importantly, some of these changes were also observed after consumption of decaffeinated coffee and changed when coffee consumption was stopped, suggesting that bioactive compounds other than caffeine contribute to these effects.

The researchers proposed that coffee may act as a modulator of the microbiota-gut-brain axis by influencing microbial composition and gut metabolism and affecting specific cognitive performance and behavioral markers.

Clinical Perspective

These findings are consistent with the principles of precision gastroenterology, in which dietary recommendations are increasingly tailored to individual biological profiles rather than applied universally. In this context, coffee may benefit some individuals, such as those with functional constipation, while being less tolerated by others, including certain patients with irritable bowel syndrome. However, current clinical guidelines do not yet include microbiota-based recommendations.

In Javier’s case, coffee may be doing more than stimulating bowel movements. Emerging evidence suggests that it could also influence the composition and function of the gut microbiota, modulate the abundance of specific bacterial species, and influence systemic metabolic pathways that affect digestive health.

https://www.medscape.com/viewarticle/coffee-and-gut-whats-brewing-microbiome-2026a1000mlo