The best foods for gut health, backed by science

By Charlie Williams
Published October 28, 2020

Key Takeaways

Scientists and the public have long been fascinated by the human gut microbiome—and with a name like that, why wouldn’t they be? It sounds like the stuff of science fiction. In fact, the microbiome refers to something much more down-to-earth: the estimated 100 trillion microbes—including bacteria, fungi, and viruses—which are primarily found in the gut, but also on our skin and other parts of the body. 

The gut has been under a microscope in the science world for more than a century, but in the past two decades, there’s been a virtual explosion of research and mainstream interest in the microbiome. We’ve learned that these microbes, or “gut microbiota,” play a leading role in many of the body’s essential functions, including metabolism, immune defense, nutrition, and behavior. In fact, these days, the microbiome is often considered a supporting organ.  

While our DNA, the environment, and medication use are all factors in determining the kinds of microbiota in our gut, current research suggests that diet is one of the main drivers—for better or worse—in shaping the diversity of gut microbiota across our lifetime. With that in mind, here are the best foods for gut health, backed by science.

Fruits, vegetables, and legumes

Besides being tasty and generally good for your health, fruits, vegetables, and legumes work wonders on the gut microbiome. In a study published in the journal Anaerobe, scientists found that participants who ate two apples a day for 2 weeks had healthier intestinal environments as measured by increases in bifidobacteria, a genus of bacteria believed to exert positive health benefits on their host. The improvements came thanks to apple pectin, a complex carbohydrate and soluble fiber found in apple peels. Pectin is also found in the plant cells of citrus fruits, other fruits, and in vegetables, including carrots, peas, potatoes, green beans, and parsnips. 

Similar results were found in another study, where participants who drank a wild blueberry beverage for 6 weeks experienced significant increases in bifidobacteria, compared to those who drank a placebo. Researchers pointed to the fruit’s plentiful polyphenols as the key driver of improved gut health. Polyphenols have also been shown to defend against harmful pathogens and oxidation, and can be found in other berries, grapes, apples, pears, and cherries, as well as tea, coffee, cereals, dry legumes, and chocolate.

In addition to fruits, many legumes, beans and other vegetables contain high amounts of fiber, which stimulates the growth of beneficial gut bacteria, including bifidobacteria. Good high-fiber choices include chickpeas, lentils, beans (kidney, pinto, and white beans), artichokes, broccoli, green peas, and more. 

Fermented foods

One of the first scientific allusions to the microbiome came on behalf of Eli Metchnikoff, a Russian scientist of the Pasteur Institute in Paris who, in the early 1900s, believed that rural Bulgarian peasants, who lived in poverty and in harsh climates, lived longer than wealthier Europeans because they ate fermented milk products containing lactic acid bacteria. He was the first scientist to suggest that it was possible to modify the gut microbiome by replacing bad bacteria with good ones. It was a novel enough hypothesis to earn him the Nobel Prize in 1908.

Indeed, fermented milk products like yogurt have been found to help increase the amount of lactobacilli—a type of bacteria that scientists agree brings balance to the gut—and decrease the amount of Enterobacteriaceae, which has well-documented downsides, including being the culprit behind many healthcare-associated infections.

Fermented foods are considered probiotic foods, which contain beneficial live microbiota that may further alter the gut microbiome. These include foods like yogurt with live active cultures, kefir, pickled vegetables, kombucha tea, kimchi, miso, tempeh, and sauerkraut.

But beware of the potential pitfalls in this food category. For starters, many yogurts have tons of sugar, the downsides of which counteract benefits to the microbiome. The same goes for wine, which is indeed rich in polyphenols, but of course, rich in alcohol, too. Kombucha, for its part, exists in a scientific gray area and can’t be definitively tied to net health benefits without more research.

Whole grains

It’s possible that the wide range of health benefits linked to whole grains are due in large part to the fact that they’re prebiotic, a name for nondigestible foods that promote beneficial microbiota growth. 

In one randomized control trial, researchers followed 31 participants who consumed 48 g of breakfast cereals daily for 3 weeks. Participants were split into two groups—one that ate whole grain cereal and one that ate wheat bran cereal. They found that the number of fecal bifidobacterial and lactobacilli were significantly higher upon ingestion of the whole grain cereal compared with wheat bran cereal. 

Another study found that beta-glucan, a non-digestible carb common in whole grains, can positively modulate gut microbiota. Results revealed that beta-glucan supplementation increased Bacteroides and Prevotella abundances but decreased Dorea. Changes in the levels of these three bacteria correlated with improvement in cardiovascular disease risk factors, including body mass index, waist circumference, blood pressure, and triglyceride levels. 

Additional tips for a healthy gut

Encourage breastfeeding. Breastfeeding helps shape the gut microbiota in early life in ways that can lead to the prevention of allergies.

Mix it up. A healthy gut microbiome is dependent on a diverse diet, so be sure to eat a wide variety of foods, rather than relying too heavily on a single food group for nutrition.

Limit antibiotic use. Take antibiotics only when necessary, as they kill many bad as well as good bacteria in the gut microbiome—possibly contributing to weight gain and antibiotic resistance.

Take a probiotic supplement. Probiotics are live bacteria that can help restore gut health by “reseeding” it with healthy microbes.

Avoid artificial sweeteners. While artificial sweeteners can help people lose weight, studies have shown that they can induce glucose intolerance by causing alterations in the gut microbiota.

The bottom line

As more data rolls in, it becomes increasingly clear that the gut microbiome plays a huge part in determining our health. The good news is that even though the tiny bacteria, fungi, and viruses living inside our bellies might feel like they’re out of our control, we can take positive steps to ensure they stay healthy and keep us healthy, too. 

Want to ensure your microbiome is the healthiest it can be? Follow the tips above and keep an eye out for new studies—more are sure to come.

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