How Coffee Might Change Your Gut, According to New Research

A new study underscores that drinking coffee may alter the composition of your gut microbiome, the environment of microorganisms like bacteria inhabiting your intestinal tract. 

Researchers specifically found that regular coffee drinkers had higher levels of a specific strain of bacteria—Lawsonibacter asaccharolyticus—than people who don’t usually drink the beverage. 

“This study further establishes the fact that there is a specific link between the food we eat and the microbes in our gut,” Kelsey Russell-Murray, MS, RD, a clinical dietitian and founder of the Gut Healthy Dietitian, a virtual private clinic, told Health.

Though scientists know little about L. asaccharolyticus, said study author Nicola Segata, PhD, a professor and head of the laboratory of occupational metagenomics at the University of Trento, it’s possible that the microbe contributes to coffee’s potential ability to protect the heart, brain, and other aspects of health.

Evidence increasingly shows that the bacteria and other microbes in our gut strongly influence overall health, including the development of chronic conditions. “Gut microbiome research continues to be fascinating, and the more we learn only further establishes how wide-reaching the impact of the microbiome is on every aspect of our health,” Russell-Murray said.

The new study, conducted by the nutrition company ZOE and published in the journal Nature Microbiology, builds on previous research finding that coffee has the strongest food-microbiome association of more than 150 food and drinks. “The single food having the biggest impact on the composition of the gut microbiome was—by far—coffee,” Segata, who was also involved in that research, told Health. 

Intrigued by this finding, the research group designed a study examining how coffee might interact with the gut microbiome in more detail. (“The fact that we love coffee in my lab also helped,” Segata added.)

The team looked at 23,115 participants from the United States and the United Kingdom involved in the ZOE PREDICT research program, the Mind–Body Study, and the Men’s Lifestyle Validation Study. The group was diverse in terms of health status.

Participants had their gut flora analyzed via metagenomics, a technique that can glean insights into gut microbiome composition based on sequencing the genetic content of stool samples. They also filled out questionnaires about their coffee intake.

“One advantage we have when working on coffee, but not for most other foods, is that it’s relatively easy to obtain accurate information about coffee drinking habits,” Segata explained. “Most of us either never drink coffee or drink coffee one or more times every single day—and usually the same type of coffee.”

Researchers divided participants by coffee intake: People who drank less than three cups per month were categorized in the “never” group, those who drank more than three cups daily were considered “high,” and everyone in between was in the “moderate” group.

After analyzing the gut flora of participants in each group, the team isolated L. asaccharolyticus as the microbe most associated with coffee intake. Levels ranged from 4.5 to eight times higher in the “high” group compared to the “never” group and 3.4 to 6.4 times higher in the “moderate” group versus the “never” group. The difference between the “high” and “moderate” groups was only 1.4-fold and not statistically significant in most cohorts. 

These links were consistent regardless of the health status of participants and across the U.S. and U.K. populations, meaning the findings are “rather independent from the type of coffee and the composition of the general diet,” Segata explained.

Additionally, the researchers validated the results through test-tube experiments, where they isolated L. asaccharolyticus and analyzed its growth when supplemented with coffee. The bacteria grew with caffeinated and decaffeinated coffee, suggesting the findings aren’t necessarily related to caffeine. 

“[With] growing this bacterium in vitro, we have seen that it grows faster if you add coffee to the culture medium,” study author Paolo Manghi, PhD, said in a press release.

While the study answers one question—the microbe with the strongest relationship to coffee intake—it raises many more. 

Scientists only discovered L. asaccharolyticus a few years ago, according to Segata, and there’s still much to learn about it. “We do not know its possible roles in host-microbe interaction, and thus on human health,” he said. “Preliminary data point us to a rather ‘neutral’ role, but we are just at the very beginning of this specific line of research.” 

One avenue to explore is how specific coffee components biochemically interact with L. asaccharolyticus and how they do so.

It’s possible that chlorogenic acid, a polyphenol found in coffee believed to contribute to its health benefits, may be behind coffee’s encouragement of L. asaccharolyticus growth, the study noted. After being metabolized, chlorogenic acid produces metabolites like caffeic acid and quinic acid, which stimulate the growth of microbes like Bifidobacterium animalis, Bifidobacterium lactis, and Escherichia coli. Researchers found more quinic acid in the blood of coffee drinkers with higher L. asaccharolyticus levels, suggesting that chlorogenic acid may also help that microbe thrive. 

“There are many lifestyle factors that impact gut health, including sleep, stress, environment, exercise, alcohol intake, and smoking,” Russell-Murray said. “But diet remains the most impactful.” 

Russell-Murray said your best bet for maintaining a healthy gut is to eat a diet filled with various plant foods. These foods offer prebiotic (or soluble) fiber that healthy gut bacteria consume. While most plant-based foods contain at least small amounts of fiber, rich sources include garlic, oats, bananas, onion, asparagus, artichoke, wheat, apples, flax, and legumes. 

If the study has inspired you to start drinking coffee, Russell-Murray suggests easing into it so that you can figure out if it agrees with you. “From a digestive perspective, coffee stimulates colonic motility and, therefore, can stimulate bowel movements,” she said. “For this reason, people with diarrhea, irritable bowel syndrome with diarrhea (IBS-D), or urgency issues may want to avoid or limit coffee.”