• Experts believe that Crohn’s disease results from an abnormal immune response to gut bacteria in people with a genetic predisposition to the condition.
  • Researchers are studying a variety of treatments to promote a healthy balance of gut bacteria. The treatments include probiotic supplements, fecal microbiota transplantation (FMT), and exclusion diets.
  • More research is necessary to understand the potential benefits and risks of different treatment approaches.

Crohn’s disease is a type of inflammatory bowel disease (IBD) that involves chronic inflammation in the digestive tract. It causes symptoms such as abdominal pain, cramping, diarrhea, weight loss, and fever. People with Crohn’s disease typically experience periods of remission, during which the disease is inactive, alternating with periods of relapse, when the symptoms return or worsen.

Experts do not know exactly what causes Crohn’s disease, but they believe that it results from an abnormal immune response to gut bacteria in people with a genetic predisposition to the condition. Researchers are studying a variety of strategies to promote healthy gut bacteria in people with Crohn’s disease.

“Although we’re still in the early stages, it’s really exciting that the first microbiome therapeutics are starting to make their way into real life,” Dr. Arun Swaminath, the chief of gastroenterology at Northwell Health’s Lenox Hill Hospital in New York City, told Medical News Today.

Here, we explore the role that bacteria may play in the development and treatment of Crohn’s disease.

Trillions of bacteria and other microbes live in the human digestive tract. Collectively, these microbes and the substances they produce make up the microbiome.

Although some bacteria cause disease, many play important roles in human health. So-called “friendly” bacteria help digest foods, synthesize nutrients, and regulate the immune system.

Dysbiosis is the term for an abnormal balance of microbes in the body, and it may contribute to certain health conditions, including Crohn’s disease and other types of IBD.

“In general, the gut bacteria in people with Crohn’s disease are less diverse, and there are changes in the abundance of specific species,” Dr. Kerri Glassner, a gastroenterology specialist at Houston Methodist in Texas, told MNT.

Research suggests that people with active IBD tend to have lower levels of friendly intestinal bacteria, such as Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii. Studies have also shown that these individuals have low levels of certain protective metabolites. Friendly bacteria produce these compounds when they break down food.

People with IBD also tend to have more potentially pathogenic bacteria in their gut than people without IBD. These include a type of bacteria known as adherent-invasive Escherichia coli (AIEC).

According to a 2021 study in Cell Host & Microbe, AIEC produces a metabolite that triggers inflammation when it interacts with immune cells in the lining of the intestine. A 2022 study found that inflammation creates an environment conducive to the growth of AIEC.

If dysbiosis plays a role in Crohn’s disease, changing the composition of the microbiome might help treat the condition. Scientists are studying a variety of treatments to reduce disease-causing microbes and promote the growth of friendly bacteria in people with Crohn’s disease.

These treatments include:

  • antibiotics
  • probiotics
  • FMT
  • dietary changes

Some of these treatments are widely available. Others are only available in clinical trials.


Antibiotics are a class of medication that kills bacteria.

Doctors often prescribe antibiotics to people who undergo surgery for Crohn’s disease and those who develop infections or certain complications, such as abscesses.

Some studies have also examined the use of antibiotics to induce remission in Crohn’s disease. When researchers reviewed the evidence, they found that the benefits of antibiotics for treating active Crohn’s disease are likely modest. The authors conclude that more research on this treatment approach is necessary.

Exposure to antibiotics can cause some bacteria to become resistant to this treatment.

Antibiotics can also kill friendly bacteria along with harmful bacteria, which may contribute to dysbiosis. “They can wipe out all different types of bacteria, so you’re not just getting rid of the ‘bad’ ones,” said Dr. Swaminath.


Probiotics are live bacteria and other microorganisms that provide health benefits. They are present in certain foods and available as dietary supplements. Companies sometimes sell probiotics in combination with prebiotics, which are types of fiber upon which bacteria feed.

A 2020 Cochrane review reports on a small randomized controlled trial that compared probiotics with a placebo for inducing remission in Crohn’s disease. It found that probiotics were no more effective than a placebo for inducing remission.

A 2020 review from the American Gastroenterological Association also found a lack of evidence to support the benefits of probiotics for inducing or maintaining remission in Crohn’s disease.

Efforts to develop and identify effective probiotic treatments for Crohn’s disease continue.

For example, scientists have specifically designed two proprietary blends of bacterial strains called GUT-103 and GUT-108 to treat dysbiosis in IBD. In a 2021 animal study, mice with inflammation of the colon had more friendly bacteria, fewer disease-causing bacteria, and reduced inflammation after receiving these probiotic products. Researchers must conduct clinical trials to learn how these products affect the microbiome in humans.

It is possible that some people with Crohn’s disease may benefit more than others from certain probiotics or other treatments. “In the future, I think we will see more studies evaluating the specific microbiome changes in each individual patient with IBD, allowing us to better personalize therapy,” said Dr. Glassner.

Probiotic supplements are subject to less strict regulations than pharmaceutical drugs in the United States. A company may describe a product as “probiotic” even if it has no proven health benefits. Companies do not always label the specific microbial strains that probiotic supplements contain.

Fecal microbiota transplantation

In FMT, doctors collect stool from a number of healthy donors. Healthcare professionals then pool these specimens together and transplant them into other people’s digestive systems.

In its 2021 guidelines, the American College of Gastroenterology recommends FMT as a treatment for Clostridioides difficile infection that does not resolve with antibiotic treatment. C. difficile infection can cause severe diarrhea and other gastrointestinal symptoms.

A 2021 study in Gut Microbes reports that people with IBD have an increased risk of C. difficile infection. After trialing the use of FMT in 18 participants, the researchers found that it was safe and effective for treating recurrent C. difficile in people with IBD.

Some research suggests that FMT may also have benefits for treating IBD itself. When the researchers combined the results of six controlled trials, they found that 37% of participants experienced remission from IBD following FMT. Roughly 29% of people who received FMT experienced adverse events, which were mostly mild. These resolved within 24 hours of the transplant and included diarrhea, abdominal pain, nausea, flatulence, and fever.

“What they’ve shown is there are some people who do respond to stool transplants, and it’s worth figuring out why those people got better,” said Dr. Swaminath. “It’s not clear whether there’s something about the donor stool that went to those patients that was maybe better. We’re only starting to understand it.”

More research is necessary to identify the ideal traits of stool donors.

FMT remains an experimental treatment for Crohn’s disease, and it is not widely available outside of clinical trials. The Food and Drug Administration (FDA) warns that without proper testing of donor stool, FMT can cause potentially life threatening infections.

Dietary changes

Diet plays a key role in shaping the gut microbiome. Certain dietary changes may help promote the growth of friendly bacteria. More research is necessary to learn how specific diets affect the microbiome and disease activity in people with Crohn’s disease.

“A lot of people feel like if they can improve their gut health by improving their diets, they’ll be better off. I think on a macro level, that’s probably true. But it’s hard to show that in patients who’ve already got Crohn’s disease,” said Dr. Swaminath.

Exclusive enteral nutrition (EEN) is a liquid formula-based diet that can help induce and maintain remission in children with Crohn’s disease. According to a 2019 review in European Medical Journal: Gastroenterology, anti-inflammatory effects and changes in intestinal microbes might help account for the benefits of EEN.

A 2021 study of children with Crohn’s disease found that both EEN and a Crohn’s disease exclusion diet (CDED) may help induce remission. By the third week, 85% of children on EEN and 82% of children on CDED had a rapid response or achieved remission from Crohn’s disease. The CDED involves avoiding certain foods, such as dairy, gluten, and emulsifiers.

Some research has also linked the specific carbohydrate diet (SCD) and the autoimmune diet to reduced disease activity in Crohn’s disease. However, the authors note that there was insufficient evidence to recommend either diet. They add that the SCD is so restrictive that it is difficult to follow.

A 2021 study found that the Mediterranean diet provided similar benefits as the SCD for reducing the symptoms of Crohn’s disease.

These three diets differ in the foods they restrict, but they are all low in processed foods. As the Mediterranean diet is less restrictive, it may be easier to stick to in the long term.

“Based on the data we have, patients with Crohn’s disease benefit from a Mediterranean-type diet, low in processed foods and sugar,” said Dr. Glassner.

Before adjusting their diet to manage Crohn’s disease, people should speak with a doctor or dietitian who can help them learn how to meet their nutritional needs safely.

Research on microbiome-targeted treatments for Crohn’s disease is ongoing. Some experimental treatments are only available in the context of clinical trials.

Scientists use clinical trials to research medical interventions in humans. Taking part in clinical trials gives people the opportunity to receive experimental treatments, which may have benefits. However, these treatments may also pose risks that scientists do not yet clearly understand.

Before signing up for a clinical trial, people should speak with a doctor about the potential benefits and risks. They can also speak with the researchers running the trial to learn more about it.

To find clinical trials that are recruiting participants with Crohn’s disease, a person can search for the condition in the ClinicalTrials.gov database.

Ongoing research may lead to the development and approval of new treatments that effectively alter the microbiome in people with Crohn’s disease. In the meantime, various treatments are already available to treat Crohn’s disease.

A doctor may prescribe one or more of the following medications to reduce inflammation in people with Crohn’s disease:

  • aminosalicylates, such as:
    • balsalazide
    • mesalamine
    • olsalazine
    • sulfasalazine
  • corticosteroids, such as:
    • methylprednisolone
    • prednisone
  • immunomodulators, such as:
    • 6-mercaptopurine
    • azathioprine
    • cyclosporine
    • tacrolimus
  • anti-tumor necrosis factor-alpha therapies (anti-TNF-α), such as:
    • adalimumab
    • certolizumab
    • infliximab
  • anti-integrin therapies, such as:
    • natalizumab
    • vedolizumab
  • anti-interleukin-12/23 therapy, including:
    • ustekinumab

A doctor may also prescribe other treatments to help manage the symptoms or complications of Crohn’s disease. These include medication and surgery.

Although scientists do not know the exact cause of Crohn’s disease, they believe that gut bacteria play a role.

It is possible that promoting a healthy balance of gut bacteria in people with Crohn’s disease may reduce inflammation and symptoms of the condition. Research on probiotic supplements, FMT, exclusion diets, and other treatments that target the microbiome is ongoing.

A person can speak with a doctor to learn more about the role of the microbiome in Crohn’s disease and the potential benefits and risks of different treatment approaches. A doctor may prescribe medication, surgery, or other treatments to manage Crohn’s disease. In some cases, they might advise a person to take part in a clinical trial.