Coffee may affect far more than alertness. New research suggests that both regular and decaffeinated coffee can alter the gut microbiome and may influence mood, stress, memory, and attention through the gut brain connection.
Scientists at APC Microbiome Ireland, a research center at University College Cork, investigated in detail how coffee may influence communication between the digestive system and the brain.
The study published in Nature Communications and sponsored by the Institute for Scientific Information on Coffee (ISIC), found that both caffeinated and decaffeinated coffee were associated with changes in the gut microbiome as well as differences in mood and stress.
How Coffee May Affect the Gut-Brain Connection
Scientists have long studied coffee for possible effects on digestion, mood, and overall health, but exactly how these effects arise has remained less clear.
The new research focused on the microbiota-gut-brain axis, the two-way communication system linking microorganisms in the digestive tract with the brain. Signals can travel between the gut and brain through immune activity, hormones, nerves, and chemical compounds produced by microbes.
Researchers examined 31 regular coffee drinkers and 31 people who did not normally drink coffee. Participants completed psychological assessments and kept records of caffeine intake and diet. Researchers also collected stool and urine samples to track changes in gut microbes, metabolism, mood, and perceived stress.
For the study, ‘Coffee drinkers’ were set as those who regularly consume 3-5 cups of coffee a day, defined by the European Food Safety Authority (EFSA) as a safe and moderate amount for most people.
What Happened When Coffee Was Removed
The regular coffee drinkers first stopped consuming coffee for two weeks. During that period, participants repeatedly completed psychological assessments and provided stool and urine samples.
When coffee drinkers stopped drinking coffee, researchers observed substantial shifts in their gut metabolite profiles compared with people who did not normally consume coffee. Metabolites are small molecules produced or altered during metabolism, including compounds created by gut microbes as they process food and other substances.
Coffee was then reintroduced without participants knowing whether they were receiving caffeinated or decaffeinated coffee. Half received decaf, while the other half received caffeinated coffee.
After coffee returned to their diets, both groups reported lower perceived stress, depression and impulsivity scores. The findings suggest that some of coffee’s effects on mood may not depend entirely on caffeine.
Coffee Was Linked to Changes in Gut Bacteria
Researchers also found differences in several types of gut bacteria.
Bacteria, such as ‘Eggertella sp.‘ or ‘Cryptobacterium curtum‘, were more abundant among coffee drinkers than non-coffee drinkers. ‘Eggertella sp‘ is thought to contribute to acid secretion in the stomach and intestines, while ‘Cryptobacterium curtum‘ may participate in bile acid production.
Both processes could potentially help create an intestinal environment that discourages certain harmful bacteria and infections.
Researchers also observed higher levels of ‘Firmicutes’ bacteria, a broad group of microbes that has previously been associated with positive emotions in females.
Decaf and Caffeinated Coffee Showed Different Effects
One of the most intriguing findings was that caffeinated and decaffeinated coffee did not appear to affect participants in exactly the same way.
Improved learning and memory were observed only among participants drinking decaffeinated coffee. That finding suggests that substances other than caffeine may contribute to some of coffee’s effects on cognition.
Coffee contains thousands of chemical compounds, including polyphenols. These plant derived substances can act as antioxidants and can also interact with gut microbes, potentially influencing metabolism and other biological processes.
Caffeinated coffee, meanwhile, was associated with reduced feelings of anxiety as well as improved vigilance and attention. Caffeine was also linked to a reduced risk of inflammation.
Because the study involved a relatively small number of participants, the findings do not establish that coffee directly causes these changes in mood, cognition, or gut health. However, they provide new clues about the biological pathways that could help explain associations reported in earlier coffee research.
Coffee Is More Than Caffeine
Corresponding author of the study, Professor John Cryan, Principal Investigator at APC Microbiome Ireland, University College Cork, commented: “Public interest in gut health has risen hugely. 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. 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.”
The findings add to growing evidence that coffee should not be viewed simply as a source of caffeine. Its many other components may interact with the microbiome, metabolism, and nervous system in different 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,” said Professor Cryan. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”
