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Crohn’s Disease And The Gut Microbiota

5 mins read Apr 15, 2023

The link between Crohn’s disease and the gut microbiota shows that loss of beneficial bacteria and growth of harmful species may drive inflammation. Fiber, prebiotics, probiotics, and diets like SCD or low-FODMAP can help restore balance and relieve symptoms.

Written BySena Gok, M.D.
Reviewed ByChidozie Ojobor, Ph.D.

What is Crohn's Disease?

Inflammatory bowel disease (IBD) is a condition that can affect any part of the digestive tract, leading to symptoms such as abdominal pain, diarrhea, and weight loss. Crohn’s disease is one of the two main types of IBD, and it is more common in developed countries like the United States and Europe. About 1 million Americans are estimated to be affected by IBD’s like Crohn’s, but it’s not just the US — it can impact over 2 million people in North America, 3.2 million in Europe, and millions more worldwide. During flares, people with Crohn’s disease may experience a range of symptoms, such as abdominal cramping, fatigue, and a loss of appetite, which can be debilitating and impact daily activities such as work, school, and social interactions. Beyond the impact on health, Crohn’s disease also carries a significant financial burden. Estimates range from $14.9–15.5 billion annually, underscoring the importance of early diagnosis and effective treatment.

Discovered by Dr. Burrill B. Crohn and colleagues in 1932, Crohn’s disease has been extensively studied and treated since then. However, despite significant progress in understanding the condition and its therapeutic options, the root cause of the disease remains uncertain, and only symptom control is available as of now. That said, there are factors that are known to exacerbate symptoms of Crohn’s disease, therefore addressing them would help to manage the condition better.

Gut Microbiome and Inflammation Connection

Studies have established that gut bacteria composition and diversity are associated with the development of Crohn’s disease. An imbalance in the relative gut bacterial community, known as dysbiosis, is a characteristic feature in patients suffering from this inflammatory bowel disease. For example, the abundance of beneficial bacteria such as Eubacterium rectale and Roseburia intestinalis were significantly reduced in Crohn’s disease patients compared to their healthy controls, whereas a significant increase in harmful bacteria such as Bacteriodes fragilis was also observed.

Moreover, the gut microbiota is of particular interest in Crohn’s disease because of its connection to genes that regulate the immune response. The immune system in the gut protects the body from harmful bacteria but also tolerates the beneficial microorganisms in the gut. This balance is influenced by the interaction of microbes with the intestinal cells, specifically dendritic cells, which are immune cells in the gut. Typically, some individuals with Crohn’s disease harbor genetic mutations that could cause an abnormal immune response within the gut ecosystem, leading to an inflammatory state that does not favor beneficial bacteria in the gut. Studies have found that patients with Crohn’s disease have higher levels of certain harmful bacteria, like E. coli and Campylobacter, and lower levels of beneficial bacteria, such as Faecalibacterium prausnitzii which are known to produce short-chain fatty acids with anti-inflammatory effects.

Crohn's Disease Symptoms

Crohn’s disease can cause a variety of symptoms that may differ in severity from person to person. Common signs include:

  • Chronic diarrhea
  • Fever
  • Fatigue and weakness
  • Abdominal pain and cramping
  • Blood in the stool
  • Mouth ulcers
  • Loss of appetite and unintended weight loss
  • Pain or drainage around the anus due to the formation of a fistula, which is an abnormal connection between the intestine and the skin

This condition can impact any section of the digestive tract, from the mouth to the anus, though it most commonly affects the terminal part of the small intestine (ileum). The inflammation may appear in isolated patches or extend continuously along the intestinal lining. In some individuals, the disease is limited to the colon (large intestine).

The symptoms of Crohn’s disease can develop gradually but may also appear suddenly without warning. Many individuals experience periods of remission, during which symptoms significantly improve or disappear, followed by flare-ups where the disease becomes active again.

Additional Symptoms in Severe Cases

In more severe cases, Crohn’s disease can lead to complications that extend beyond the digestive system, affecting various organs and bodily functions. Inflammation may occur in the skin, eyes, or joints, leading to conditions such as erythema nodosum, uveitis, or arthritis. The liver and bile ducts can also become inflamed, potentially resulting in primary sclerosing cholangitis, a progressive condition that affects bile flow. Additionally, individuals with Crohn’s disease may develop kidney stones due to disruptions in calcium and oxalate absorption. Chronic blood loss or impaired nutrient absorption can lead to iron deficiency anemia, causing fatigue and weakness. In children, prolonged inflammation and malnutrition may result in delayed growth and puberty, highlighting the importance of early diagnosis and effective disease management.

Crohn's Disease Treatment Options

Current ways of managing symptoms of Crohn’s disease include medication intake, surgery, and dietary changes. Adding fiber and prebiotics to one’s diet can help restore balance to one’s microbiome, while probiotics may help shape the microbiome. It is important to note, however, that probiotics have limited effectiveness in patients with Crohn’s disease, who often have reduced bacterial diversity. This can potentially be improved by using bacterial combinations or adjusting the diet. Different diets, such as the SCD (Specific Carbohydrate Diet) and low FODMAP (Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols), have been found to improve symptoms and quality of life in some Crohn’s patients. The SCD diet restricts complex carbohydrates, grains, and dairy products, while the low FODMAP diet avoids specific carbohydrates in some fruits, vegetables, and grains. For some people, a primarily vegetarian diet has also been shown to prevent relapses and maintain symptom-free periods without drugs.

Each person with Crohn’s disease may require a different diet to manage their symptoms. If you or someone you know has Crohn’s disease, seeking proper care and treatment is essential to reduce its impact on daily life. Consultation with a healthcare professional is recommended to receive personalized dietary recommendations and develop a treatment plan that suits individual needs. With proper support, managing Crohn’s disease and taking control of your health and well-being is possible.


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