Coffee’s Hidden Gut Benefits: How It Supports Microbiome Health

Recent research suggests that coffee may offer another health benefit: supporting gut microbiome diversity. A study published in Nature Microbiology found that coffee drinkers have an increased abundance of a gut bacterium known as Lawsonibacter asaccharolyticus. Interestingly, even decaffeinated coffee was linked to higher levels of this specific bacterium, and lab tests confirmed that coffee stimulates its growth.

Although L. asaccharolyticus was only discovered in 2018, scientists have associated it with higher levels of quinic acid, a compound with antioxidant properties that help reduce oxidative stress and inflammation.

Is Coffee Good for Gut Health

Coffee contains polyphenols—plant compounds that are widely recognized for their health benefits. Among these polyphenols is chlorogenic acid, which gut bacteria break down into quinic acid, delivering antioxidant effects. Coffee’s polyphenols also have prebiotic properties, promoting the growth of beneficial gut bacteria that aid digestion, regulate the immune system, and support overall gut health.

Dr. David M. Poppers, a professor of medicine and gastroenterology expert at NYU Langone Health, highlighted the importance of a diverse gut microbiome for general health. "A wider variety of bacterial species is associated with good gut health, anti-inflammatory properties, and potentially even longevity," he said.

However, experts caution that coffee should not be seen as the sole solution for gut health. Foods like fermented products—kimchi, sauerkraut, kefir, yogurt, and kombucha—are equally important for maintaining a healthy microbiome. "Coffee is potentially part of an arsenal for gut health, but not in isolation," Poppers added.

Does Coffee Explain Why You Poop After Drinking It

Coffee’s impact on gut motility may explain why many people experience bowel movements shortly after consuming it. While caffeine has a laxative effect, decaffeinated coffee can also promote regularity through mechanisms such as polyphenol activity and quinic acid’s support of gut movement.

A diverse gut microbiome similarly contributes to bowel regularity, and coffee’s compounds play a reinforcing role. Despite these benefits, experts caution against excessive coffee consumption, encouraging moderation. Drinking too much caffeine can lead to unpleasant side effects such as anxiety, heart palpitations, and headaches. According to Poppers, approximately 400 mg of caffeine daily is considered safe for most individuals.

"In moderation, coffee can help with gut regularity, energy levels in the morning, and improved inflammation markers," Poppers said.

Can You Get Similar Benefits from Other Foods

Coffee provides numerous health benefits, but it is not the only source of polyphenols and antioxidants. There are many fruits and vegetables that contain chlorogenic acid, the compound responsible for antioxidant effects and gut health support. Tea, zucchini, broccoli, okra, and eggplant are examples of foods that also provide health benefits similar to coffee.

Diana Roopchand, a food science associate professor at Rutgers University, noted that other plant-based options can supplement coffee’s role in gut health. "This is great because people who choose not to consume coffee can consume other plant foods for similar benefits," she said.

For instance, Aronia berries—commonly known as black chokeberries—have been shown to increase the presence of L. asaccharolyticus in the gut microbiome, offering a viable alternative for those who prefer not to drink coffee.

Whether through coffee or other nutrient-rich foods, adding polyphenols to your diet can enhance gut health, improve digestion, and contribute to overall well-being. However, moderation and diversity in food choices remain key to maintaining a balanced and healthy lifestyle.