For millions of people worldwide, the morning routine begins with the familiar aroma and comforting warmth of a freshly brewed cup of coffee. Beyond providing a much-needed jolt of alertness to start the day, coffee may be working behind the scenes in ways scientists are only just beginning to understand. New research suggests that both regular and decaffeinated coffee can actively alter the human gut microbiome, potentially influencing mood, stress levels, memory, and attention through the intricate communication network known as the gut-brain axis.
The study, which was conducted by scientists at APC Microbiome Ireland—a prominent research center located at University College Cork—provides a detailed look at how coffee interacts with the digestive system and how those digestive changes might communicate with the brain. Published in the scientific journal Nature Communications and sponsored by the Institute for Scientific Information on Coffee (ISIC), the research revealed that both caffeinated and decaffeinated varieties of coffee are associated with distinct shifts in the gut microbiome, alongside measurable differences in human mood and stress.
How Coffee May Affect the Gut-Brain Connection
For decades, researchers have investigated coffee for its potential physiological effects on digestion, mood, and overall human health. However, the exact biological mechanisms that give rise to these effects have historically remained elusive.
The new research focused heavily on the microbiota-gut-brain axis, a complex, two-way communication system that links the vast community of microorganisms living in the human digestive tract directly with the brain. Biological signals travel back and forth along this axis through a variety of pathways, including immune system activity, hormonal fluctuations, direct nerve signaling, and chemical compounds produced directly by microbes as they process what we eat and drink.
To explore these pathways, researchers recruited 31 regular coffee drinkers and compared them against a control group of 31 individuals who did not normally consume coffee. Throughout the study period, participants completed detailed psychological assessments and kept thorough records of their daily caffeine intake and overall dietary habits. Additionally, researchers collected biological samples, including stool and urine, to meticulously track changes in gut microbes, metabolic processes, psychological mood states, and perceived stress levels.
For the parameters of this study, regular coffee drinkers were defined as individuals who routinely consume between three and five cups of coffee per day. This consumption level aligns with the guidelines set by the European Food Safety Authority (EFSA), which considers this a safe and moderate amount for the general population.
What Happened When Coffee Was Removed
To observe the baseline shifts caused by coffee consumption, the regular coffee drinkers participating in the study were first asked to completely stop consuming coffee for a duration of two weeks. During this withdrawal and abstinence period, participants repeatedly completed psychological evaluations and continued to provide regular stool and urine samples for analysis.
When the regular coffee drinkers eliminated coffee from their diets, researchers observed substantial, striking shifts in their gut metabolite profiles when compared against the group of people who did not normally consume coffee. Metabolites are small, bioactive molecules produced or altered during metabolic processes, including specialized compounds created by gut microbes as they break down food, beverages, and other ingested substances.
Following the two-week abstinence period, coffee was reintroduced to the participants’ diets in a blinded fashion, meaning participants did not know whether they were receiving caffeinated or decaffeinated coffee. Half of the participants were randomly assigned to receive decaf, while the other half received caffeinated coffee.
Once coffee returned to their daily diets, participants in both groups reported lower perceived stress scores, alongside decreases in reported depression and impulsivity. These fascinating findings strongly suggest that some of coffee’s beneficial effects on human mood may not depend entirely on caffeine, pointing instead toward other chemical constituents found within the beverage.
Coffee Was Linked to Changes in Gut Bacteria
As researchers analyzed the biological samples collected during the various phases of the study, they also uncovered notable differences in several specific types of gut bacteria among the participants.
Certain bacterial strains, such as Eggertella sp. and Cryptobacterium curtum, were found to be significantly more abundant among regular coffee drinkers than among non-coffee drinkers. Eggertella sp. is widely thought by microbiologists to contribute to acid secretion processes within the human stomach and intestines, while Cryptobacterium curtum may play an active role in the production of bile acids.
Both of these biological processes could potentially help create a specialized intestinal environment that discourages the colonization of certain harmful bacteria and protects against various gastrointestinal infections.
Furthermore, researchers observed higher relative levels of Firmicutes bacteria, which constitute a broad and diverse group of microbes that has previously been linked in scientific literature to positive emotional states, particularly in females.
Decaf and Caffeinated Coffee Showed Different Effects
One of the most intriguing and unexpected findings to emerge from the research was that caffeinated and decaffeinated coffee did not appear to impact participants in exactly the same physiological or cognitive ways.
For instance, measurable improvements in learning and memory were observed exclusively among the participants who were drinking decaffeinated coffee during the intervention period. This specific finding strongly reinforces the hypothesis that chemical substances other than caffeine are actively contributing to some of coffee’s profound effects on human cognition.
Coffee is a remarkably complex dietary beverage containing thousands of distinct chemical compounds, including a high concentration of polyphenols. These plant-derived substances function naturally as powerful antioxidants and are also known to interact directly with gut microbes, potentially influencing human metabolism and a wide array of other biological processes within the body.
Meanwhile, caffeinated coffee was associated with distinct outcomes, including reduced feelings of anxiety, as well as noticeably improved vigilance and attention among participants. Furthermore, caffeine consumption was linked directly to a reduced risk of inflammation.
Because the study involved a relatively small number of human participants, the researchers emphasize that these findings do not definitively establish that coffee directly causes these changes in mood, cognition, or gut health on their own. Instead, the research provides valuable new clues regarding the biological pathways that could help explain the positive associations reported in numerous earlier epidemiological coffee studies.
Coffee Is More Than Caffeine
Professor John Cryan, Principal Investigator at APC Microbiome Ireland at University College Cork and the corresponding author of the study, noted the shifting landscape of public health interest regarding the digestive system.
"Public interest in gut health has risen hugely," Professor Cryan commented. "The relationship between digestive and mental health is also increasingly being better understood, but the mechanisms behind coffee’s effects on this gut-brain axis have remained unclear."
"Our findings reveal the microbiome and neurological responses to coffee, as well as their potential long-term benefits for a healthier microbiome," he continued. "Coffee may modify what microbes do collectively, and what metabolites they use. As the public continues to think about dietary changes for the right digestive balance, coffee has the potential to also be harnessed as a further intervention as part of a healthy balanced diet."
These findings add significantly to the growing body of scientific evidence demonstrating that coffee should not be viewed simply as a convenient vehicle for a caffeine fix. Its many other chemical components interact with the human microbiome, metabolic processes, and nervous system in diverse and fascinating ways.
"Coffee is more than just caffeine—it’s a complex dietary factor that interacts with our gut microbes, our metabolism, and even our emotional well-being," Professor Cryan concluded. "Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways."