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The power of your gut

The surprising effect of coffee on the microbiota

Diet
The gut microbiota What foods promote a balanced microbiota?

Can a single food cause a radical change in microbiota composition? Coffee sure can! According to a new study, coffee strongly stimulates the proliferation of a previously little-known gut bacterium. 1

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About this article

Created 13 February 2025
Updated 01 July 2026

The health benefits of coffee are well known. But how exactly does it affect the microbiota?

To answer these questions, researchers from Harvard University (USA) and the University of Trento (Italy) analyzed the gut microbiota and coffee consumption of more than 22,000 volunteers taking part in an Anglo-American research program. 

They divided the participants into three groups:

  • “Non-drinkers”, who consumed less than three cups of coffee per month;
  • “Moderate drinkers”, who drank between three cups per month and three cups per day.
  • “Heavy drinkers”, who drank more than three cups per day;
02.08.2021 The gut microbiota Read more

Non-drinkers vs. addicts, not the same effects

They found that the microbiota of coffee drinkers differs markedly from that of non-drinkers. The analysis showed that 115 bacterial species react positively to the beverage. 

How many coffees a day? ²

  • 1 cup of filtered coffee (200 ml) = 90 mg of caffeine
  • 1 espresso (60 ml) = 80 mg of caffeine
  • 1 cup of black tea (220 ml) = 50 mg of caffeine

Excessive consumption of caffeine (present in coffee and tea) is associated with cardiovascular problems, sleep disorders and delayed fetal development. What are safe doses?

  • Coffee is safe for all healthy adults up to 200 mg of caffeine per day (up to 400 mg if consumption is spread throughout the day, except for pregnant women).
  • From 100 mg of caffeine per day, sleep may be affected.

Surprisingly, Lawsonibacter asaccharolyticus, a bacterial strain in the microbiota little studied until now, is the microorganism most strongly linked to coffee consumption. The scientists calculated its level to be 4.5 to 8 times higher in the microbiota of “heavy drinkers” than in that of “non-drinkers” and 3.4 to 6.4 times higher in “moderate drinkers” than in “non-drinkers”.

By analyzing another dataset on several thousand individuals across 25 different countries the researchers confirmed that the presence of L. asaccharolyticus is indeed associated with coffee consumption and that the association exists regardless of country or lifestyle.

Virtues of coffee mediated by microbiota?

If there is one food whose beneficial effects have been proven, it is coffee. Studies show regular coffee consumption to be associated with a lower risk of:

  • diabetes 
  • cancer 
  • fatty liver disease 
  • cardiovascular disease
  • all-cause mortality 

The secret? Its polyphenol content, particularly that of chlorogenic acid, an antioxidant present in large quantities in the beverage. This molecule can be broken down and transformed by gut bacteria into multiple potentially beneficial metabolites. The microbiota may therefore be a mediator of the beneficial effects of coffee on health.

In a previous study on 1,000 individuals, the same researchers found that, of 150 foods, coffee had by far the greatest impact on gut microbiota composition.

Caffeine not to blame

To confirm that the exceptional growth of L. asaccharolyticus is directly linked to coffee, the scientists then cultivated the bacterium in vitro in a liquid medium either supplemented or not supplemented with coffee. They found that bacteria grow more quickly in the presence of coffee, even decaffeinated coffee, which removes caffeine from the equation. 

How to keep a healthy microbiota? 02.03.2023 How to keep a healthy microbiota? Read more

The stimulation of L. asaccharolyticus may be the work of chlorogenic acid, a polyphenol in coffee thought to contribute to its beneficial effects. Chlorogenic acid is metabolized by microbiota bacteria into various molecules, notably quinic acid. The researchers found more quinic acid in the blood of those with higher levels of L. asaccharolyticus.

The next step for researchers is to determine whether foods other than coffee specifically stimulate known beneficial bacteria. Thanks to tests that reveal the presence or absence of certain bacteria associated with a food, it may be possible to design personalized diets. 3

Sources

1. Manghi P, Bhosle A, Wang K, et al. Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. Nat Microbiol. 2024 Dec;9(12):3120-3134.

2. EFSA

3. Université de Trente

Tags
Gut microbiota Gut Diet Coffee Tea Sleep Bacteria Behavior Microbiome Flora

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