New Study Links Coffee Intake to Microbiome Changes and Improved Mental Well-Being

New research from scientists at University College Cork suggests that caffeinated and decaffeinated coffee reshapes the gut microbiome in ways that reduce stress and improve psychological well-being, offering clues to the drink’s long-suspected health effects.

Boscaini and others. reveal previously unrecognized effects of coffee on the microbiota-gut-brain axis, suggesting that microbiome profiles could potentially predict coffee consumption patterns and highlighting a close association between coffee consumption and gut microbial composition. Image credit: Sci.News.

Coffee is a plant-based beverage produced from processed coffee beans, whose flavor and chemical profile are determined by factors such as bean variety, maturity, processing techniques, roasting and brewing methods.

It contains a range of bioactive compounds including alkaloids like caffeine, polyphenols such as phenolic acids, diterpenes, and melanoidins formed during roasting.

Moderate coffee consumption has been linked to a lower risk of several chronic diseases, including type 2 diabetes, liver disease, cardiovascular disorders and certain cancers.

Additionally, higher consumption was consistently associated with lower risk of Parkinson’s disease in a dose-dependent manner.

Coffee drinkers are less likely to develop depression, while one analysis found regular consumption was associated with a 27% lower incidence of Alzheimer’s disease.

In a new study, Professor John Cryan from University College Cork and colleagues explored the effects of coffee consumption, withdrawal and reintroduction on cognition, mood and behavior in the context of microbiota-gut-brain – the two-way communication between the gut microbiome and the brain.

Researchers studied 31 coffee drinkers and 31 non-coffee drinkers through a series of psychological tests, caffeine and food diaries, and stool and urine samples to understand changes in their microbiome and perceived mood or stress.

Coffee drinkers have been defined as those who regularly consume 3 to 5 cups of coffee per day – defined by the European Food Safety Authority (EFSA) as a safe and moderate amount for most people.

Participants initially abstained from coffee for two weeks, with regular psychological assessments, as well as stool and urine samples taken throughout.

This period of abstinence for coffee drinkers corresponded to significant changes in metabolite profiles in the gut microbiome, compared to non-coffee drinkers.

Coffee was reintroduced to regular drinkers in a blinded manner, with half of the participants consuming decaffeinated coffee and the other half consuming caffeinated coffee.

Both groups reported lower perceived stress, depression, and impulsivity scores, suggesting that coffee consumption significantly improved mood, regardless of caffeine content.

Bacterial species such as Eggertelle sp. Or Cryptobacteria curtum were particularly increased in coffee drinkers compared to non-coffee drinkers.

The former is thought to contribute to stomach and intestinal acid secretion, while the latter is believed to be involved in the synthesis of bile acids, both of which could play a role in eliminating unhealthy gut bacteria and stomach infections.

Increase Firmicutes bacteria were also observed, which was associated with positive emotions in women.

Noticeable improvement in learning and memory was only seen in those who consumed decaffeinated coffee, suggesting that components other than caffeine, such as polyphenols, are responsible for these cognitive benefits.

However, scientists found that only caffeinated coffee was associated with reduced feelings of anxiety, as well as improved alertness and attention. Caffeine was also associated with a reduced risk of inflammation.

“Public interest in gut health has increased significantly,” Professor Cryan said.

“The relationship between digestive and mental health is also increasingly understood, but the mechanisms behind coffee’s effects on this gut-brain axis remain unclear.”

“Our results reveal the microbiological and neurological responses to coffee, as well as their potential long-term benefits for a healthier microbiome.”

“Coffee may change what microbes do collectively and the metabolites they use.”

“As the public continues to think about dietary changes for healthy digestive balance, coffee has the potential to also be leveraged as an additional intervention within a healthy, balanced diet.”

“Coffee is much more than caffeine: it is a complex dietary factor that interacts with our gut microbes, our metabolism and even our emotional well-being.”

“Our results suggest that coffee, whether caffeinated or decaffeinated, may influence health in distinct but complementary ways.”

The team’s findings appear today in the journal Natural communications.

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S. Boscaini and others. 2026. Habitual coffee consumption shapes the gut microbiome and alters host physiology and cognition. Nat Common 17, 3439; doi: 10.1038/s41467-026-71264-8