How might drinking coffee alter your gut microbiome?

Researchers conducted what they believe to be the largest study to date on the connection between coffee consumption and the human gut microbiome.

They utilized data from several sources, including:

• five ZOE PREDICT cohorts
• the Mind–Body Study (MBS)
• the Men’s Lifestyle Validation Study (MLVS).

They analyzed over 22,000 “shotgun metagenomic” samples, a technique used to detect and measure the abundance of all microbial DNA in a sample.

They also assessed participants’ nutritional habits through food frequency questionnaires from four PREDICT cohorts, MBS, and MLVS.

Participants were then categorized into three levels of coffee consumption:

1. never-consumers, if they had up to 20 grams (g) of coffee a day, or less than 3 cups a month
2. moderate consumers, if they had between 21–599 g of coffee per day
3. high consumers, if they had 600 g or more of coffee per day, or more than 3 cups a day.

They ended up with 22,867 participants after excluding those whose coffee intake was in the top 1% in the PREDICT groups, considering them outliers.

A total of 5,730 individuals were categorized as “never” coffee drinkers, 14,647 as “moderate” coffee drinkers, and 2,490 as “high” coffee drinkers.

The study also incorporated public data on microbial genetic material (metagenomics) from stool samples from 211 cohorts, totaling 54,198 samples across various countries.

Additionally, it utilized active gene data from 364 stool samples and blood metabolite data from 438 samples, both from the MBS and MLVS cohorts.

The researchers then used machine learning to see how coffee drinking relates to the types and levels of bacteria in our gut. They trained a computer program to identify differences in the gut bacteria in people who never drink coffee, those who drink it moderately, and those who consume a lot.

Consistent with earlier studies, the current study witnessed a strong relationship between coffee consumption and increases in specific microbiome species, particularly L. asaccharolyticus.

The median abundance of L. asaccharolyticus was shown to be significantly greater in the high coffee consumption group, with values ranging from 4.5 to 8 times more than in the never group.

Similarly, the moderate consumption group exhibited 3.4 to 6.4-fold greater levels than the never group.

Analyses of blood metabolites showed that compounds like quinic acid and trigonelline were also particularly prevalent in coffee drinkers, correlating with higher L. asaccharolyticuslevels.

There was a smaller difference in the effect of coffee on the microbiome between people who drank a moderate amount and those who drank a high amount, and for three of the cohorts the difference was not significant.

This suggests that increasing coffee intake beyond moderate consumption might not have a strong impact on the microbiome.

In other words, you may not have to drink large amounts of coffee to see changes in your gut microbiome.

The researchers also conducted in vitro experiments, adding caffeinated and decaffeinated coffee to L. asaccharolyticus cultures, with both boosting the bacteria’s growth. This suggests that compounds in coffee, other than caffeine, may be responsible for the growth stimulation.

They further validated the link between L. asaccharolyticus and coffee consumption by correlating estimated per capita coffee intakes with L. asaccharolyticus prevalence in 25 countries, using a re-analysis of thousands of publicly available data sets.

Overall, this research adds to the evidence that coffee alters the gut microbiome’s composition, with L. asaccharolyticus being particularly responsive to coffee intake.

However, more research is needed to fully understand this relationship’s mechanisms and potential health implications.

As coffee consumption has been linked to a lower risk of all-cause mortality, the study authors suggest future studies should investigate whether L. asaccharolyticus may mediate this relationship.

Alyssa Simpson, RDN, CGN, CLT, adigestive health dietitian in Phoenix, AZ, not involved in the study, told Medical News Today that “while we don’t fully understand the mechanism yet, L. asaccharolyticus might play a role in metabolizing coffee’s polyphenols, like quinic acid, into bioactive compounds that contribute to coffee’s known benefits.”

Thomas M. Holland, MD, MS, a physician-scientist and assistant professor at the RUSH Institute for Healthy Aging, RUSH University, College of Health Sciences, also not involved in the study, agreed that while we don’t know for sure, L. asaccharolyticus is “likely associated with coffee’s known health benefits through its involvement in metabolizing coffee-derived compounds, such as quinic acid.”

He further explained how this might benefit health:

“These metabolites, and other compounds like the polyphenols chlorogenic acid and the catechins (a flavonoid subclass) may influence gut health, inflammation, or metabolic processes, potentially contributing to reduced risks of chronic diseases like cardiovascular disease or improved gut microbiome diversity.”

Additionally, Holland noted, “other studies have linked coffee consumption to increased microbial diversity and beneficial gut bacteria.”

“Coffee’s polyphenols and chlorogenic acids are known to act as prebiotics, substances that help create a favorable environment for certain gut microbes,” he said.

Simpson similarly explained that coffee may “positively impact the gut microbiome by increasing microbial diversity and supporting beneficial bacteria through its polyphenols and prebiotic-like effects.”

Simpson highlighted that “while it’s too early to recommend coffee specifically for gut health, moderate consumption can be a healthy choice for most people, offering potential microbiome benefits alongside its metabolic and anti-inflammatory properties.”

“For the most potential benefits,” she said, “enjoy your coffee black or with minimal additions like unsweetened plant-based milk.”

“If you prefer it sweetened, opt for natural, low-calorie sweeteners like stevia, monk fruit, or allulose, which are gentler on blood sugar levels,” she advised.

And finally, Simpson noted, “stick to moderate consumption — 1–3 cups daily —a nd choose high-quality, organic coffee to reduce exposure to pesticides and maximize its health benefits.”

“While coffee is the primary known enhancer of Lawsonibacter asaccharolyticus, other foods may have similar effects,” Simpson said.

For example, she said, “aronia berries contain chlorogenic acid and polyphenols like those in coffee.”

Holland also mentioned aronia berries, and explained why you may not have heard of them yet.

“They are a relatively new food crop that are traditionally grown in Russia and Eastern Europe but have made their way to be grown commercially in the Midwest and other regions of North America due to their ‘superfood’ status,” he said.

He likewise explained that, similar to coffee, aronia berries are rich in polyphenols and may promote the growth of L. asaccharolyticus.

“Foods rich in chlorogenic acid, such as blueberries, apples, and pears, may also support its growth,” Simpson added.

Holland agreed but noted that the direct impacts of chlorogenic acid-rich foods on L. asaccharolyticus require further study.

Simpson concluded by emphasizing that, although not directly associated with L. asaccharolyticus, consuming fermented foods can also promote overall gut microbiome diversity, supporting a healthy gut.