How Might Drinking Coffee Alter Your Gut Microbiome?

Coffee is one of the most popular beverages consumed globally. It’s a daily staple for many, known for its potential metabolic and health advantages.

Recent studies suggest that coffee may also have a direct relationship with our gut microbiome.

In fact, in 2021, researchers found that out of more than 150 foods studied, the popular beverage showed the strongest link to gut microbiome composition, particularly levels of Lawsonibacter asaccharolyticus, in about 1,000 people.

Now, to better understand the effects of coffee consumption on the gut microbiome, this research team analyzed diet and medical data from over 22,800 individuals in the United States and United Kingdom, in addition to publicly available information from nearly 54,200 people worldwide.

They compared data from stool samples collected from coffee drinkers and non-drinkers to identify differences in their gut bacteria.

The study observed several correlations, the strongest being between coffee intake and L. asaccharolyticus: Coffee drinkers had up to eight times higher levels of the bacteria than non-drinkers. This pattern was seen across the Globe.

While the exact health effects of this bacteria are still unknown, the researchers believe they could be linked to the effects attributed to drinking coffee.

Impact of coffee on the 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.

Drinking coffee may change your gut, but how much coffee do you have to drink?

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 mortalityTrusted Source, the study authors suggest future studies should investigate whether L. asaccharolyticus may mediate this relationship.