11 Diseases That Can Start with Your Gut Bacteria

Updated: Mar. 16, 2021

Trillions of microscopic organisms make up your microbiome, and scientists are beginning to pin down the ways that these bugs can help or hurt your health

C. difficile Infection

Young man having painful stomachache on bedroom at home.neotemlpars/ShutterstockThe classic example of a disease that originates in the gut microbiome is infection by C. difficile, a bacteria that causes diarrhea, stomach cramps, fever, and in severe cases, kidney failure. It often develops in people who have taken heavy-duty antibiotics that killed off the normal bacteria in their digestive tract, says Purna Kashyap, MBBS, a gastroenterologist who is co-director of the Microbiome Program at the Mayo Clinic’s Center for Individualized Medicine. “If you disrupt the microbiome [the bacterial environment in the digestive tract] by giving it an insult like antibiotics or hospitalization, the bacteria start getting scattered and you lose some of them,” he says. When you lose that bacterial diversity, you have a weak spot that other bacteria can take advantage of, he points out. “That’s exactly what these opportunistic pathogens like C. difficile do.”

Doctors had been treating the infection with yet more antibiotics, but in recent years fecal transplants have become the forward-thinking treatment—where stool from healthy donors is transplanted into the colons of C. difficile patients—with a 90 percent success rate, according to the Mayo Clinic. “We can fill up all of these empty areas in the gut where the bacteria was taking advantage, creating an environment of competition because C. difficile cannot compete with a healthy microbiome,” Kashyap says.

Colon cancer

Scientists have found that toxins produced by two types of bacteria—E. coli and B. fragilis—combine in the colon to damage DNA, according to the New York Times. In a 2018 paper published in the journal Science, the researchers suggest that the discovery could, in the near future, lead to a test that would identify patients who should be monitored closely for colon cancer; plus, their findings could lead to the development of a vaccine that protects against colon cancer.

Kashyap expects to see a greater emphasis on understanding all patients’ microbiomes in coming years, so health care providers will be able to identify problems and possibly anticipate illnesses. “It could become one of the things we’ll monitor in an individual,” he says. Don’t miss these 7 signs that your gut might be unhealthy.

Irritable bowel syndrome (IBS)

This chronic digestive problem can cause extreme abdominal discomfort as well as diarrhea or constipation. Unfortunately, researchers aren’t certain what causes it, and there are few successful treatments beyond avoiding trigger foods and stress. But Kashyap says that the microbiome plays a role in how fast the gut moves digested material along, which is a primary component of irritable bowel syndrome (IBS). The problem lies in determining which bacteria contribute to the problem. “We’re now starting to look beyond just figuring out the composition” of the microbiome, he says. “We’re beginning to look at what bacteria are doing, so we can decide whether what they’re doing can lead to a disease or can perpetuate a disease.”

What might help some? Fasting. In this study, researchers looked at fifty-eight patients with IBS and divided them into two groups. One group was given prescription meds and psychotherapy to reduce IBS symptoms, while the other group fasted for 10 days, drinking only water. The fasting group reported improvement in 7 of 10 symptoms.

Inflammatory bowel disease

The two most common types of inflammatory bowel disease (IBD) are Crohn’s disease and ulcerative colitis, and they’re serious trouble for patients. This chronic inflammation in the digestive tract can become life-threatening during severe flare-ups. There’s a genetic component to IBD, though doctors can’t explain the origin of most cases. Kashyap says the microbiome is a player: “We have found that people with IBD have a very different microbial composition.” The bacteria in their guts “might be producing substances which are promoting inflammation; they might be interacting with the immune system to trigger inflammation—there are multiple different ways in which the microbes might be affecting the host.”

Researchers have tried treating patients with fecal transplants, but so far the procedure has been less successful for IBD than for C. difficile. Still, Kashyap is optimistic, saying that the focus now is on how to tailor transplants to treat the inflammation. He speculates that doctors may need to focus on the types of bacteria involved. “The donor may be important in patients with IBD, or maybe we have to give it multiple times or use a different formulation,” he says.

Learn what differentiates ulcerative colitis vs. Crohn’s disease.

Multiple sclerosis

Man in wheelchair at home or in office.Halfpoint/ShutterstockYou might be getting the idea that gut bacteria can impact more than just your gut health. Researchers are finding evidence that the microbiome might promote an inappropriate immune response in other parts of the body. Multiple sclerosis (MS), a disease that causes tremors, fatigue, cognitive problems, and other symptoms, occurs when the immune system attacks the myelin coating on neurons. A 2017 study found that two types of bacteria are more common in MS patients, and the strains can cause cellular changes in healthy blood, increasing the likelihood of a dangerous autoimmune response, according to STAT News.

Check out these 50 great foods for gut health.

Rheumatoid arthritis

Another autoimmune disease, rheumatoid arthritis (RA) is a condition in which the immune system attacks primarily the joints, but also the skin, eyes, lungs, heart, and blood vessels. A recent pair of studies shed light on the possible role of the microbiome. The first study revealed that RA patients are more likely than healthy people to have several rare species of bacteria in their guts. In the second study, researchers transplanted a healthy strain of bacteria into mice with RA, and their symptoms improved. While the researchers aren’t sure why this approach works, they do believe the microbiome can stimulate the immune system to attack the body.


One of the most common immune problems are allergies—reactions to pollen, food, and other substances that lead to breathing trouble, hives, rashes, and other symptoms. Some researcher propose a “hygiene hypothesis“: Because most modern children grow up in extremely clean conditions, primarily indoors, they aren’t exposed to a variety of bacteria strains; when they do finally run into these micro-organisms, their immune systems overreact. But more recent research suggest it’s likely more complex than that and has to do with the interaction of the microbiome with microbes found in the environment. “Lifestyle, environmental exposure, urbanization, diet, and antibiotic use have a profound effects on the human microbiome, leading to failure of immunotolerance and increased risk of allergic disease,” suggests this paper.

Read about how a healthy gut can promote longevity.


Soft Focus of Weight Scale.eakasarn/ShutterstockBecause researchers consider obesity a metabolic disease, they’re looking at how the microbiome may promote weight gain. “The most obvious is the way we digest food,” Kashyap says. Some strains of bacteria glean more calories from food than other types. He says that the extra energy probably isn’t a large contributor to obesity, but there are other factors—some bacteria in the gastrointestinal tract can trigger the release of hormones that increase hunger. “We have to think about the bacteria as a component of the body which can contribute,” he says.


In patients with diabetes, the body has trouble processing blood sugar. Researchers know that when diabetics eat plenty of fiber, their health improves. Now, a study from earlier this year suggests that dietary fiber helps by nourishing gut bacteria that help influence insulin—the hormone that processes blood sugar—according to STAT News.

Even for people without diabetes, a fiber-rich diet is important for promoting the growth of healthy gut bacteria. “In more than 10 years of research, the only thing I constantly tell people is to eat dietary fiber,” Kashyap says. “And that means fiber from your food—that’s what keeps your microbiome diverse.” Here is the real reason fiber is such a big deal—and four things that happen when you eat more of it.

Heart disease

This catch-all term—heart (or cardiovascular) disease—can mean your arteries have been blocked by plaque, hardened by calcium, or narrowed by inflammation; the end result can be heart attacks or strokes. In recent years, researchers have been focusing on ways the microbiome might influence heart disease: Now it looks as though certain bacteria can create chemicals that interfere with the body’s ability to break down cholesterol, according to the Atlantic.

Mental illness

Some of the chemicals that gut bacteria produce act as neurotransmitters, Kashyap says, which means they can pass messages through your nervous system. They can produce substances interact with the brain to increase anxiety or other mental disorders.

In mouse studies, researchers have been able to treat behavior like depression, anxiety, and even autism, according to Scientific American, by introducing healthier strains of bacteria. They’re hoping to develop similar treatments for humans. Read about how your gut health can affect anxiety.