Coffee Drinkers Rejoice: Java May Boost Your Gut Health

Medically Reviewed by Melinda Ratini, MS, DO on April 15, 2025
7 min read

Donald Summerlin used to think putting actual cream in his coffee, rather than the powdered stuff, was "gourmet."

The 58-year-old had his first cup as a college freshman, harnessing the beverage's well-known exam-cram properties. Years later, he and his wife, Patti, traveled the world, where he was exposed to truly gourmet versions of the drink. At a high-end restaurant in Monte Carlo, Monaco, he had a cup of Guatemalan coffee after dinner. It was the best he'd ever had.

"Once you have a real cup of coffee, it stays with you," Summerlin says.

Still, back in the States, he had no issue with convenience store coffee. He has drunk five to six cups of brew a day for decades, gourmet and otherwise. Following a career in third-party logistics, he and Patti opened Donnie's Donuts in Atlanta in 2015. They wanted to serve only the finest java. He harkened back to that cup in Monte Carlo.

By then, he was familiar with research suggesting that coffee boosted brain health and reduced the risk of Alzheimer's and Parkinson's diseases. He also knows Kyoto-style cold brew, another favorite, is packed with higher levels of flavonoids and oils known for their antioxidant and anti-inflammatory properties, or as Summerlin puts it, "the gooey stuff in the bean that's good for your gut and brain."

So it came as no surprise when he read about a study released last year that linked coffee drinking with significantly higher levels of a bacteria that may contribute to a healthy gastrointestinal system. The research was the first in a series of studies aimed at "mapping the role of specific foods on the gut microbiome," the study says.

The gut microbiome is the collection of bacteria, fungi, viruses, and other microorganisms that can help predict your health, including your risk of disease and death. An imbalance in your microbiome – called dysbiosis – can contribute to chronic inflammation, inflammatory bowel disease, obesity, certain cancers, and other diseases.

Here's how your morning cuppa joe might be making your whole life better.

The paper, which was published in November, was based on research that began a few years earlier, when another study of more than 150 foods found that coffee had the "highest correlation with microbiome components."

Previous research linked coffee drinking with a host of health benefits, including lower risks of diseases of the heart and blood vessels, diabetes, nonalcoholic fatty liver disease, cancer, and other diseases, as well as all causes of death. A more recent study dubbed coffee "an elixir of youth," citing its anti-aging effects, ability to enhance mental function and metabolism, and its "role as a potent source of antioxidants."

These benefits led researchers to home in on coffee. They first took detailed dietary information and microbial DNA samples from almost 23,000 Americans and Britons and compared them to more than 54,000 samples from healthy people, those with various diseases, non-Westerners, ancient microbiome specimens, babies, and nonhuman primates. (If you're thinking, "Wait, infants and monkeys don't drink coffee," you're correct. They served as a control group to better gauge the effects on coffee drinkers.)

The people were sorted into categories: never drinkers, who consume fewer than three cups a month; moderate drinkers, who consume between three cups a month and three a day; and heavy drinkers, who consume more than three a day.

Researchers found that moderate and heavy coffee drinking were linked with an increase in several bacteria species in the gut – Lawsonibacter asaccharolyticus by far the strongest – and that "the gut microbiomes of coffee drinkers were clearly distinguishable from those of non-drinkers."

Knowing observational studies can be subject to biases, the researchers took their findings to a lab, says Mingyang Song, ScD, a senior author of the study and an associate professor of clinical epidemiology and nutrition at the Harvard T.H. Chan School of Public Health.

"Maybe the signal we captured was not driven by coffee, or it was something related to coffee, so we conducted an experiment to pour coffee into a culture to see how it affected the bacteria," he says. "Coffee was indeed promoting the growth of that bacteria."

The findings were stark: Moderate and heavy coffee drinkers showed far more L. asaccharolyticus in their microbiomes than did never-drinkers – sometimes as much as eight times the amount. The finding was supported by country-level studies that showed samples from Danes and Swedes, who tend to drink more coffee, had higher levels of the bacteria, compared to samples from China and India, where coffee consumption is lower.

More positive news: Cappuccinos and lattes appear to have the same benefits. Though nutritionists say black coffee is the healthiest, the findings were not altered by the inclusion of milk and sugar. Decaffeinated coffee also had the same results, leading researchers to believe the benefits come not from coffee's caffeine but rather from its elevated levels of polyphenols, compounds known for their prebiotic, antioxidant, and anti-inflammatory properties, as well as their ability to feed beneficial gut bacteria.

L. asaccharolyticus was first discovered in Japan in 2018 and is largely understudied. At least two polyphenols in coffee likely spur its growth, and the bacteria produces a fatty acid that seems to aid proper digestion and nutrition absorption. Outside of that, the bacteria remains largely a mystery, Song says.

"I don't think we know anything about its function. We're doing some solo studies to better understand it," he said. "In general, you can probably frame it as beneficial to the microbiome. I think we need more data to be more certain."

This holds true for the microbiome in general, says Bonnie Jortberg, PhD, an associate professor of family medicine at the University of Colorado Anschutz Medical Campus.

"We know relatively little, collectively, about our gut microbiome, and we're finding out a lot of interesting things. It's an exciting area of study," she says. "I never really thought about coffee in terms of affecting your gut microbiome until I read this study."

The study promises to open doors to further examine specific foods' effects on the gut microbiome. Jortberg remains cautiously optimistic "because we still don't know a lot," she says. She is particularly eager to see results from future studies aimed at determining why polyphenols – which are also found in fruits, vegetables, nuts, seeds, and fermented foods like yogurt and kombucha – seem so beneficial.

She's also looking forward to results from a study from Song's team examining the relationship between coffee and colon cancer. Patients are now being enrolled, and results from the trial should be available in two to three years, Song says.

Jortberg says she'd be suspicious of anyone trying to capitalize on these types of findings. She's wary of products such as at-home microbiome tests, for which people pay $100 or more to test their stool and learn if they need to eat more fruits and vegetables.

"You don't need to spend however much money to know that that's what you need to do," she says. "Don't get wrapped up into some of the commercialization of these types of things because I don't think we know enough."

There have been seemingly conflicting headlines over the years regarding coffee's health benefits. Song says there's "compelling evidence" coffee can improve a variety of health outcomes. But the risk of adverse effects goes up with consumption, so use caution if you drink more than three or four cups a day.

Jortberg recommends that most people drink moderate amounts of coffee. She stresses that we are all "an experiment of one." If your heart rate or blood pressure spikes or if you get jittery or lose sleep after drinking coffee, your body is communicating with you. Listen to it, she says. If you drink a lot of coffee, remember it's a diuretic, so you'll need to hydrate to counterbalance those effects, she says.

"But if the person is healthy and doesn't have high blood pressure or certain other chronic disease – yes, 100%, drink a couple cups of coffee a day, absolutely," she says.

Summerlin eventually found the Guatemalan coffee that he had enjoyed so much in Monte Carlo. He now serves it at Donnie's Donuts, along with Sumatran and Brazilian beans that fit the flavor profile he prefers. The beans come from a single farm, what's known as single origin, which makes it easier to guarantee they're farmed organically and cured consistently, while his roaster in Orlando, Florida, prepares them to his specifications weekly.

"That's how I went from trucker coffee to the stuff you see now," he says. "The downside is it's hard for us to find a good cup of coffee if we're not in our shop."