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New Study Finds Coffee Supercharges Good Gut Bacteria — Even Decaf

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Ever wondered why coffee makes you go to the bathroom more often?

Research on coffee’s beneficial effects on intestinal health continues to emerge. Coffee has been scientifically shown to enhance the balance of intestinal microorganisms and aid in the growth of beneficial bacteria. Its well-known awakening effect and metabolism-promoting properties also contribute to general health.

The Gut-Boosting Power of Coffee

A recent study published in the international academic journal Nature Microbiology analyzed the correlation between intestinal microorganisms and coffee consumption across a large population group. Researchers from the University of Trento in Italy studied the eating habits and gut flora of approximately 22,000 adults across the U.S. and U.K.

As a result, it was found that the beneficial bacteria called Rosonibacter asaccharolyticus increased up to 8 times in the intestines of people who frequently consumed coffee.

It’s Not the Caffeine—It’s the Antioxidants

Surprisingly, coffee’s gut benefits appear to come not from the caffeine but from its rich mix of plant compounds—particularly chlorogenic acid and quinic acid. These antioxidants in both regular and decaf coffee help fuel the growth of beneficial bacteria and reduce gut inflammation.

Chlorogenic acid is converted in the body into quinic acid, which acts like a prebiotic—feeding good gut microbes and supporting microbial diversity. These compounds help maintain intestinal balance, reduce inflammation, and strengthen the gut lining, a barrier against harmful substances.

You’ll also find quinic acid in fruits like apples, blueberries, and cherries—but coffee remains one of the easiest and most concentrated sources in the average diet.

Coffee and That Morning Bathroom Trip

Of course, coffee’s most immediate and noticeable effect is its ability to get your digestive system going. Coffee stimulates intestinal contractions by directly activating the colon or triggering the gastrocolic reflex—a normal reaction that makes the colon move after eating or drinking.

And yes, this effect happens with both caffeinated and decaffeinated coffee.

Iced coffee / bibistudio-shutterstock.com
Iced coffee / bibistudio-shutterstock.com

What Kind of Coffee Is Best?

Not all coffee is created equal when it comes to health. Sugary lattes, flavored syrups, and heavy cream can cancel out the benefits by adding empty calories and spiking blood sugar. Nutrition experts recommend sticking to black coffee or an Americano with a splash of milk. One to two cups per day is considered the sweet spot.

For those with sensitive stomachs or digestive issues, it’s best to enjoy coffee with a light snack or meal to minimize discomfort.

Small Habit, Big Benefits

According to a family medicine professor at Seoul National University College of Medicine, coffee’s effects build up over time because it’s a habitual beverage. Drinking a cup or two daily not only aids digestion but can also support immune health, reduce inflammation, and boost mental clarity.

So the next time your coffee sends you on a bathroom break, remember—it’s doing more than waking you up. It’s also helping to keep your gut in check.

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