A new study published in Nature Communications found that drinking coffee, whether caffeinated or decaf, actually changes the bacteria living in your gut in ways that can boost your mood and possibly your brain power.

Researchers at APC Microbiome Ireland, a global leader in microbiome research, found that both caffeinated and decaffeinated coffee altered the gut microbiome in ways that lifted mood, eased stress, and in some cases, sharpened cognitive performance.

While this built on previous findings that link the drink to a range of health benefits, until now, the exact mechanisms behind many of those effects have long remained unclear.

The Gut-Brain Connection
“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,” John Cryan, PhD, principal investigator at APC and co-author of the study, told The Independent. “Our findings suggest that coffee, whether caffeinated or decaffeinated, can influence health in distinct but complementary ways.”

To do this, they focused on the gut-brain axis, a bidirectional communication pathway between the gut microbiome and the brain, and assessed whether these effects occur independently of caffeine in healthy participants.

How the Study Was Conducted
The study followed 31 regular coffee drinkers, defined as those consuming three to five cups a day, and 31 non‑coffee drinkers through psychological assessments, food and caffeine diaries, and stool and urine sampling.

After a two-week period where regular drinkers abstained from coffee entirely, both groups were reintroduced to coffee on a blinded basis, with half receiving caffeinated and half decaffeinated. This allowed researchers to isolate the effects of coffee on the gut microbiome and measure any changes in mood, stress, and cognitive performance.

Key Benefits: From Lower Stress to Sharper Memory
The study found that both caffeinated and decaffeinated coffee were linked to a range of mental and physical benefits, including:

Significant shifts in gut microbiome activity, specifically in the substances the body produces when breaking down food.

Lower perceived stress, depression, and impulsivity upon reintroduction of coffee to both regular and non-coffee drinkers.

Improved mood and concentration with regular consumption.

Reduced anxiety and lower inflammation risk (caffeinated).

Sharper learning and memory (decaffeinated).

Positive shifts in gut bacteria linked to digestion and emotional well-being.

Specifically, researchers noted increases in beneficial bacteria, including Eggertella sp and Cryptobacterium curtum, both linked to digestive health and the elimination of harmful microbes. They also observed a rise in Firmicutes, a group of bacteria associated with positive emotions in women.

Why Decaf Drinkers Benefit Too
Since the two types of coffee produced distinct effects, the findings suggest that natural compounds in coffee—the researchers theorize polyphenol—may be responsible for some of its cognitive benefits rather than caffeine alone.

“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,” Cryan said.

“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,” he said.