Share and Follow
Your daily cup of coffee might do more than just energize you—it could significantly affect your digestive system, even if you opt for decaffeinated versions.
Scientists at APC Microbiome Ireland have discovered that regular coffee drinking can alter the trillions of microorganisms residing in your gut. These changes create a chemical feedback loop that may directly impact your mood, stress levels, and mental alertness.
The study monitored 62 individuals to explore the interaction between coffee and the microbiome.
This group was split evenly between 31 coffee drinkers and 31 non-coffee drinkers. Participants underwent various psychological evaluations and meticulously recorded their dietary habits and coffee intake.
The researchers classified “coffee drinkers” as those who consume between three and five cups daily, a range considered safe and moderate by the European Food Safety Authority.
After people stopped drinking coffee for two weeks and then started drinking it again, the bacteria in their digestive systems behaved differently than the non-drinkers, according to a press release.

“Coffee is more than just caffeine,” study author John Cryan, principal investigator at APC Microbiome Ireland, said in a statement.
“It’s a complex dietary factor that interacts with our gut microbes, our metabolism and even our emotional well-being.”
The coffee drinkers were found to have higher levels of specific beneficial bacteria, such as Eggertella and Cryptobacterium curtum.

These microbes play a vital role in releasing gastric acids and creating bile, both of which help the body eliminate harmful bacteria and manage inflammation, the researchers noted.
Both caffeinated and decaf drinkers reported lower levels of perceived stress, depression and impulsivity. This suggests that the non-caffeine components of coffee, like polyphenols and antioxidants, are doing the heavy lifting for mental health.
However, the two types of brew offer different perks. Caffeinated coffee was specifically linked to reduced anxiety and better focus, while decaf was shown to lead to significant improvements in learning and episodic memory.
Researchers believe these cognitive gains in decaf drinkers may be tied to better sleep quality and increased physical activity.
The study’s findings are limited by a small sample size, which may not accurately represent the diverse microbiome profiles found across different global populations.
Because the research relied heavily on self-reported data regarding participants’ coffee habits and mood levels, the results are subject to memory errors and subjective bias, the researchers noted.
The study also did not strictly control for other dietary variables, such as sugar and dairy additives, which could independently influence gut health and cloud the specific impact of the coffee bean itself.
The research was published in the journal Nature Communications.