If you drink coffee every morning, your gut microbiome may differ from that of non-coffee drinkers, and people who drink decaf may experience some of the same changes.
Change in Microbiome
Researchers at University College Cork wanted to understand how coffee affects the gut-brain axis. The study followed 62 healthy adults in Ireland, half of whom drank three to five cups of caffeinated coffee every day.
Throughout the study, researchers tracked cognition, mood, stress, sleep, inflammation, and gut microbiome composition.
Habitual coffee drinkers had distinctly different gut microbiome profiles compared with non-coffee drinkers. Certain bacteria became more abundant among coffee drinkers, including Cryptobacterium curtum and Eggerthella, both involved in digestive processes, such as recycling bile acids that help digest fats.
“Coffee changes the physiology of people who drink it,” Stefano Gaburro, who holds a doctorate in neuropharmacology and neuroscience and was not involved in the study, told The Epoch Times.
Many of these physiological changes were associated with improvements in mood, cognition, immune function, and gut health, though some effects differed between caffeinated and decaffeinated coffee.
Change in Metabolite
Metabolite patterns also differed between the two groups. Metabolites—small molecules generated when the body and gut microbes break down substances found in foods and beverages such as coffee—are compounds that can affect inflammation, hormones, immune signaling, and brain activity.
Among habitual coffee drinkers, researchers found higher levels of several coffee-related metabolites, including paraxanthine, known to have neuroprotective and antioxidant effects, and theophylline, a compound associated with anti-inflammatory activity and a lower risk of Parkinson’s disease.
Some of the coffee-related metabolites identified in the study appeared alongside certain gut bacteria and cognitive patterns, suggesting that coffee may influence the brain partly through microbiome-related pathways: Coffee changes gut microbes, and gut microbes produce compounds linked to mood and cognition.
“The fact that coffee influences mental health and quality of life may surprise some people,” Douglas Kalman, a nutrition researcher and scientific expert in sports nutrition and nutritional neuroscience who wasn’t part of the study, told The Epoch Times.
This positive effect may stem from how coffee influences neurotransmitter production through the gut microbiome.
Caffeine is already known to promote alertness by blocking adenosine, a brain chemical that builds up throughout the day and makes you feel sleepy. Blocking adenosine also indirectly enhances the activity of mood-related neurotransmitters such as dopamine and serotonin.
Researchers also found differences in gut compounds linked to mood and brain signaling, including GABA. However, some potentially beneficial compounds were actually lower in coffee drinkers, a reminder that the relationship between coffee and brain health is not straightforwardly positive.
When habitual coffee drinkers stopped drinking coffee for two weeks, they showed reductions in blood pressure, impulsivity, and emotional reactivity. Their microbiome and metabolite profiles also shifted significantly, suggesting that coffee’s effects on the microbiome may be ongoing and dynamic rather than permanent.
The Decaf Finding
One of the study’s main findings, Gaburro noted, was that several gut-related markers changed similarly in both the caffeinated and decaffeinated groups, suggesting that some of coffee’s biological effects may come from compounds other than caffeine.
Caffeinated and decaffeinated coffee produced both distinct and overlapping effects—and decaf performed surprisingly well.
Only caffeinated coffee was linked to lower morning levels of cortisol, a hormone involved in the body’s wake-up response, and its effects on alertness, attention, and arousal align with caffeine’s well-documented influence on the brain. On the other hand, participants drinking decaffeinated coffee showed improvements in sleep quality, physical activity, and learning performance.
Both groups showed lower stress, depression, and inflammatory responses. Lab tests also showed weaker inflammatory responses in immune cells from both groups.
The study suggests that decaffeinated coffee may also positively affect learning and memory. “This may relate to coffee’s polyphenols,” Kalman said.
Coffee contains hundreds of biologically active compounds in addition to caffeine, including polyphenols and phenolic acids. These plant compounds have antioxidant and anti-inflammatory properties and are thought to contribute to many of coffee’s health benefits. Some also act as food for beneficial gut microbes.
“This is not only a caffeine story. It is a coffee story,” Gaburro said.
For people who are sensitive to caffeine, that is meaningful news. “People who switch to decaf still get most of the polyphenol-related signals,” he said.
Not a Supplement
Experts cautioned against treating coffee as a supplement for gut or brain health.
The effects observed in the study were modest—it involved only healthy adults between 30 and 50, and statistical associations are not the same as demonstrated biological pathways. Gaburro pointed out, for example, that GABA measured in stool samples is not equivalent to GABA activity in the brain.
“Coffee is a food. It is not a supplement, and it is not a prescription,” Gaburro said.
The findings offer reassurance that moderate coffee consumption appears compatible for most healthy adults, and those who have made the switch to decaf may be giving up less than they thought.