More and more research is unpacking the health benefits of drinking coffee. Drinking just one cup may fight off unhealthy fat, ease inflammation associated with obesity, or even protect the brain into old age.

Furthermore, drinking at least three cups of coffee every day may keep arteries healthy and supple by preventing a calcium buildup and staving off the risk of clogging.

Coffee could also help fight off diabetes by improving blood sugar control and can keep the liver healthy and “happy.”

But how exactly coffee yields all of these wonderful health benefits has remained somewhat of a mystery.

New research shines some light on the mechanisms behind coffee’s effects by looking at the links between coffee and the health of the gut microbiota.

Dr. Li Jiao is the senior and corresponding author of the study. Dr. Jiao is an associate professor of medicine–gastroenterology at the Baylor College of Medicine in Houston, TX, and a researcher at the Center for Innovations in Quality, Effectiveness, and Safety at the Michael E. DeBakey VA Medical Center.

Dr. Shawn Gurwara, also from Baylor College, who is the first author of the paper, presented the findings at the American College of Gastroenterology (ACG) 2019 Annual Scientific Meeting, which took place in San Antonio, TX.

Looking into the gut microbiota

“The beneficial roles of coffee consumption in metabolic diseases have previously been shown,” Dr. Jiao told Medical News Today. “We set out to examine whether phytochemical ‘caffeine’ in coffee would account for this beneficial effect.”

Dr. Jiao and team looked at “the association between caffeine consumption and the composition and structure of the colonic-gut microbiota.”

To do so, the scientists asked 34 participants to undergo a screening colonoscopy and endoscopy to confirm the health of their colons.

The researchers obtained 97 “snap-frozen colonic mucosa biopsies” from various segments of these individuals’ colons, extracted microbial DNA, and performed 16s rRNA sequencing analysis.

The participants answered a self-administered food frequency questionnaire to evaluate the daily intake of coffee. The team divided coffee intake into high coffee consumption — that is, at least 82.9 milligrams (mg) per day — and low coffee consumption, that is, less than 82.9 mg daily.

The effects of coffee on the gut

The analyses revealed that high caffeine consumers had high levels of the bacterial genera Faecalibacterium and Roseburia, but low levels of Erysipelatoclostridium — a “potentially harmful” bacterial genus.

The research team found these associations regardless of the participants’ age or the quality of their diets.

Although part of a normal healthy gut, excessive levels of Erysipelatoclostridium ramosum (E. ramosum) may be harmful.

Previous studies in humans have linked E. ramosum with metabolic syndrome, and animal studies found links with “upregulation of small intestinal glucose and fat transporters,” which enhanced diet-induced obesity.

Furthermore, the researchers of this present study found higher levels of other bacteria “commonly detected in gut microbiomes” in high coffee consumers. These bacteria included OdoribacterDialisterFusicatenibactorAlistipesBlautia, and various strains of Lachnospiraceae.

The authors conclude:

Higher caffeine consumption was associated with increased richness and evenness of the mucosa-associated gut microbiota, and higher relative abundance of anti-inflammatory bacteria, such as Faecalibacterium and Roseburia and lower levels of potentially harmful Erysipelatoclostridium.”

Strengths and limitations of the study

Dr. Jiao also commented on the strengths and limitations of the research. The fact that the study examined the mucosa-associated gut microbiome set it apart from most studies, which center on the fecal microbiome, she said.

However, she cautioned, “the study was conducted in 34 adult men who had [a] normal colon in a single hospital. It is unknown whether these preliminary results can be applied to women or other populations.”

Furthermore, said Dr. Jiao, “We used the 16S rRNA gene sequencing that cannot tell which bacterial species are important.”

Also, the self-reported diet data did not give the researchers information about how the coffee was made or which brands the participants used.

Finally, “We cannot tease out whether polyphenol or other compounds in coffee may also partially explain the association,” said Dr. Jiao.

“We need [to] learn more about the interaction between the host and gut microbiome in diverse populations,” Dr. Jiao added. “More research is needed to understand what these bacteria (such as Alistipes) do in our body.”