Scientists Just Discovered a Hidden Benefit of Coffee That Has Nothing to Do With Caffeine

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 Irelanda 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 wellbeing,” said 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.