Medically reviewed by Jenny Blair, MD 

There are differences between the microorganisms in the gastrointestinal system of healthy people and those with IBD. Eating fermented foods may alter your gastrointestinal microorganisms (your microbiota) in beneficial ways. Here’s what you need to know.

What Do Bacteria Have to Do with It?

The bacteria in our gut are really important for our health, says Robin Rothstein, MD, professor of clinical medicine at the Lewis Katz School of Medicine at Temple University (LKSOM) and co-medical director of the Inflammatory Bowel Disease Program at LKSOM in Philadelphia.

However, she says, certain eating patterns, such as a diet high in processed foods or sugar, may select out some beneficial bacteria and allow the number of bad microbes to increase. In other words, even for people who don’t have IBD, eating the right foods may ensure a good balance of microorganisms in our gut.

Studies with people with IBD find an imbalance in the gut microbiota, called dysbiosis, explains Kelly Issokson, MS, RD, CNSC, a registered dietitian in the Nutrition and Integrative IBD Program at Cedars-Sinai. Some experts think there may be an association between diet, gut microbes, and IBD.

In Japan, for example, the incidence of IBD has grown rapidly over the last 30 years as residents have abandoned their traditional diet, which tends to be high in fiber and fermented foods and low in fat, in favor of the typical western diet of high saturated fat, red meat, and processed foods.

Japan isn’t alone. “The incidence of IBD is growing as societies become more urbanized, as we retreat from farms [where we’re exposed to dirt and animals] to move into cities,” Dr. Rothstein says. “It may have to do with our microbiota.”

fermented foods and their possible benefits for IBD patientsFermented Foods May Help

Fermented foods have a range of microorganisms that are beneficial to our intestine and help us digest foods, Issokson says. One way they do this is by converting dietary fiber, which is fermented by microbes in the colon, into short-chain fatty acids (SCFA). SCFAs may be important in preventing and treating bowel disorders. One of these important SCFAs is butyrate. Butyrate provides energy for the cells that line the colon. It has anti-inflammatory factors and is good for gastrointestinal health.

Unfortunately, patients with IBD often limit their fiber intake, especially during a flare. Low-fiber diets can lead to an undernourished microbiota and subsequent chronic inflammation. Gradually adding fermented foods may make it possible to include more dietary fiber (except in the case of intestinal obstruction), which in turn can change the makeup of the gut microbiota.

“I typically recommend IBD patients eat foods like yogurt, kefir (a drinkable yogurt), kimchi, miso, or natto (fermented soybeans),” Issokson says. “These foods have beneficial probiotics [healthy bacteria] that can hopefully help balance the dysbiosis and help reduce gastrointestinal symptoms, such as gas, bloating, and discomfort.”

Fermented foods may also be helpful if you have a dangerous infection. “I will absolutely recommend fermented foods if a patient has a C. diff infection,” says Anne Tuskey, MD, a gastroenterologist and associate professor at University of Virginia Health System. C. diff (Clostridium difficile or C. difficile) refers to a bacterial infection of the colon that causes gastrointestinal symptoms, especially diarrhea.

“We are seeing a rise in community-acquired C. diff in the general population and a tremendous increase in people with IBD [especially colitis],” Dr. Tuskey says. “It’s one of the first things I check for when a patient presents to the clinic with a flare.”

Unfortunately, Dr. Tuskey says, she’s diagnosing IBD patients with C. diff about every other week, and she suspects this increased incidence may be due to dysbiosis in the gut. The science isn’t yet clear or conclusive on the role of probiotics in reducing the risk of C. diff infection. However, Dr. Tuskey will recommend foods such as kefir or yogurt to IBD patients with C. diff to try to restore the balance of good bacteria.

Dr. Tuskey is quick to add that the shortage of data on the benefits of fermented foods and IBD is due to the scarcity of studies on the subject. She believes this will change as we learn more about our microbiota. “Stay tuned,” she says. “I believe we are just the tip of the iceberg with our microbiome.”

In the meantime, talk to your gastroenterologist or a registered dietitian if you want to try adding fermented foods to your diet.


Kathleen Hall covers consumer health topics and is a member of the Association of Health Care Journalists. Her work has appeared at Sharecare, U.S. News & World Report and Everyday Health, among others.

Jenny Blair is a writer and journalist covering science, medicine, and the humanities. She earned her MD at Yale University, then completed a residency in emergency medicine at the University of Chicago. After several years in practice, she transitioned to working with words and ideas full-time. Jenny has contributed to Discover, New Scientist, Washington Spectator, and Medtech Insight, among other publications. She lives in New York City.

Oshi is a tracking tool and content resource. It does not render medical advice or services, and it is not intended to diagnose, treat, cure, or prevent any disease. You should always review this information with your healthcare professionals.