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An Evidence-Based Nutrition Approach to Autoimmune IBD

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An Evidence-Based Nutrition Approach to Autoimmune IBD

Autoimmune disease impacts as much as 4.5% of the world's population and as many as 50 million Americans, with numbers continuing to rise. Research suggests significant concern for the increase in autoimmune disease prevalence and attributes this rise to changes in our environment, lifestyle, stress, and nutrition.

In particular, inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are increasing worldwide, with rates growing by as much as 46%. This article highlights the importance of nutritional interventions in IBD management.


What is Autoimmune IBD?

Autoimmune conditions result from a complex interaction of factors that lead to immune system dysfunction. Rather than protecting the body from unwanted intruders, the immune system becomes imbalanced and attacks the body's own tissues.

Digestive autoimmune conditions, known as inflammatory bowel disease (IBD), are chronic conditions that involve a dysregulated immune response in the gastrointestinal (GI) tract, leading to inflammation, pain, and tissue damage. The two types of IBD are Crohn's disease (CD) and ulcerative colitis (UC), each with distinct characteristics, symptoms, and patterns of inflammation.

Nutrition and dietary interventions are emerging as effective tools in managing health outcomes, decreasing symptoms, and improving quality of life. 

Signs and Symptoms of IBD 

IBD includes two distinct conditions.

Crohn's Disease

Crohn's disease (CD) primarily impacts the small intestine but can occur anywhere along the digestive tract. Symptoms may include:

  • Diarrhea
  • Blood loss
  • Abdominal pain
  • Abdominal distension
  • Weight loss

Ulcerative Colitis

Ulcerative colitis (UC) impacts the large intestine. Symptoms may include:

  • Diarrhea
  • Rectal bleeding
  • Lower abdominal pain
  • Severe dehydration
  • Weight loss 

Root Cause of IBD 

There are over 80 recognized autoimmune diseases, with research supporting disease development as a combination of risk factors, including environment, lifestyle, infectious disease, genetic predisposition, and nutrition.

In CD and UC, the body's immune system misfires. This misguided immune response involves inflammatory immune mediators mistakenly attacking the GI tract, leading to inflammation and disruptive symptoms. These disruptions and additional risk factors increase the chance of developing IBD. 

Understanding the factors contributing to IBD's development and progression can help develop personalized, evidence-based solutions.


  • Genetic predisposition: Individuals with a familial predisposition to tight junction dysfunction and altered intestinal permeability may be at a higher risk for the development of IBD.
  • Family history: A family history of IBD represents a shared genetic and environmental pattern that may contribute to an increased risk of disease development. 
  • Epigenetic expression: Epigenetic factors, such as methylation, influence genetic expression and the biomarkers associated with IBD.


  • Infectious disease can trigger autoimmunity through molecular mimicry, the autoimmune bystander effect, or antigen-specific mechanisms.
  • Antibiotic use can lead to changes in the microbiome, such as decreased microbiome diversity, which has been linked to the development of IBD
  • Exposure to toxins can contribute to GI tract damage and inflammation, which influences intestinal permeability and immune dysregulation.


  • Nutrition: Up to 80% of the immune system is in the gut. Problematic dietary habits and imbalanced nutrition can increase intestinal permeability, inflammation, immune system dysregulation, and decrease microbiome diversity.
  • Physical inactivity: A sedentary lifestyle can promote inflammation, exacerbating comorbidities and other underlying factors.
  • Stress and sleep: Excessive or chronic stress and poor sleep can increase the body's demands, leading to inflammation and immune system imbalances.

Diagnosing IBD

An IBD diagnosis is made by a qualified practitioner and may entail the following:

  1. A comprehensive patient history and physical exam.
  2. Initial testing may include:some text
    •  Blood tests to identify specific antibodies and inflammatory markers that can help diagnose and distinguish CD from UC.
    • Stool tests to identify inflammatory markers and underlying imbalances.
  3. Diagnostic imaging may be used to assess the location and severity of the condition:some text
    • Endoscopy (for CD)
    • Colonoscopy (for UC)
  4. Additional imaging may be ordered by the physician as needed: some text
    • Contrast radiography
    • Magnetic resonance imaging (MRI)
    • Computed tomography (CT)

Functional Medicine Labs for IBD

Functional medicine labs are a comprehensive tool for identifying underlying imbalances and inflammatory markers in IBD patients. They can help inform treatment interventions that conventional labs may overlook.

Comprehensive Stool Analysis

A Comprehensive Stool Analysis can assess microbiome balance and inflammatory markers, providing insights into potential dysbiosis and intestinal permeability that may warrant intervention for improving overall gut health. Some examples include: 

Food Sensitivity Testing

Food Sensitivity Tests evaluate the immune response to different types of food that may contribute to GI damage, inflammation, and autoimmune disease severity, helping to direct personalized nutrition interventions. Some examples include:

Autoimmune Testing

Autoimmune tests measure the presence of specific antibodies that help to differentiate Crohn’s and ulcerative colitis. 

While anti-saccharomyces cerevisiae antibodies (ASCA) may indicate CD, perinuclear anti-neutrophil cytoplasmic antibodies (pANCA) can indicate UC. Some examples offered by Rupa Health include:

Additional testing may be helpful to look for non-specific inflammatory markers, like C-reactive protein (CRP), or common micronutrient deficiencies due to a damaged GI tract and nutrient absorption issues. 


Conventional Treatment Modalities for IBD

Conventional treatment options for IBD include medications aimed at suppressing immune activity or reducing inflammation, such as immunosuppressant medications, steroids, and other biologics. 

While these treatments can relieve symptoms, they often have adverse side effects and do not address the root cause. In advanced stages, surgical intervention may be required to manage progressed disease states. 

Nutrition Approaches for Managing IBD

Research shows that evidence-based nutrition interventions can improve quality of life, reduce disease biomarkers, decrease inflammation, and minimize symptoms for IBD patients.

Dietary Modifications

Nutrition dramatically impacts the health of the intricate gut-immune connection. Removing food triggers that affect immune system function can reduce inflammation, balance the microbiome, and positively impact GI function. 

Foods to prioritize include: 

  • Whole foods: Research suggests that incorporating more than 30 types of whole, unprocessed plants per week can lead to a more diverse microbial community and metabolites with wide-ranging health implications.
  • Nutrient-dense foods: Foods rich in micronutrients, such as vitamins, minerals, and polyphenols, can help modulate immune function and reduce inflammation. 

Foods to limit include:

  • Inflammatory foods: Studies indicate that diets rich in inflammatory foods, such as those in the standard American diet (SAD), contribute to the negative modification of the microbiome. This extends to foods cooked in inflammatory oils (high in Omega-6) or shelf-stable foods that contain stabilizers and preservatives. 
  • Ultra-processed foods: Heavily processed foods include additives, emulsifiers, pollutants (such as pesticides), heavy metals, dyes, and preservatives that may trigger IBD.
  • Simple carbohydrates and refined sugars: These foods have been stripped of their nutrients, leading to poor metabolic health and inflammation. 

Therapeutic Diets 

There are a range of therapeutic diets that offer helpful guidelines for individuals with IBD. Functional nutritionists can modify nutrition interventions based on the patient's test results, symptoms, and food sensitivities. Examples of these specialized diets include:

  • Autoimmune Paleo Diet (AIP): This diet limits inflammatory and immune triggers by prioritizing nutrient-dense foods and eliminating foods commonly associated with inflammation, such as grains, legumes, refined sugar, dairy, and processed foods.
  • Low FODMAP: This diet removes fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs), which are short-chain carbohydrates that easily ferment in the intestine and can be difficult to digest in damaged GI systems.
  • Anti-inflammatory Diet: Beneficial for GI and immune health, this diet incorporates whole, anti-inflammatory foods rich in polyphenols and antioxidants.
  • Mediterranean Diet: Based on traditional diets from the Mediterranean region, this diet includes fruits and vegetables, unprocessed whole grains, high-quality animal protein, and healthy fats like olive oil.
  • Elimination Diet: For more advanced cases of IBD, elimination diets involve removing problematic foods for a period of time, tracking symptoms, and careful reintroduction under the guidance of a qualified nutrition professional.

Personalized Nutrition

Personalized dietary interventions are the most effective at addressing functional symptoms and navigating triggers that are specific to the individual

It may be helpful to start within the parameters of a common therapeutic diet for IBD and work with a qualified nutritionist to make personalized adjustments, accounting for individualized test results, presenting symptoms, food sensitivities, preferences, cultural considerations, socioeconomic factors, and food access.

Nutritional Supplements

Nutrient deficiencies are common in IBD due to the impact of the disease on the microbiome and integrity of the GI tract, which can lead to malabsorption. Personalized recommendations can be made on a case-by-case basis by reviewing functional labs, tracking symptoms, and follow-up care with a qualified provider. Common nutrient deficiencies include: 

  • B Vitamins, including B6, B9 (folate), and B12, have been shown to support methylation and modulate the inflammatory response. 
  • Vitamin D can help regulate an imbalanced immune response, support a healthy microbiome, and reduce IBD severity.
  • Iron is a multipurpose mineral that impacts many functions, such as transporting oxygen in the blood and supporting cognitive health. Based on symptoms and disease severity, levels may be tested to assess for iron deficiency anemia.
  • Omega-3 (EPA/DHA), known for its anti-inflammatory properties, can help balance the inflammatory response and repair damaged GI tissue. 
  • Zinc carnosine has been shown to help repair damaged GI tissues, enhance gut mucosal integrity, and improve the strength of the intestinal barrier. 
  • Phytonutrient-rich plants contain anti-inflammatory compounds, like polyphenols, that support GI and microbial health. Examples include ginger, green tea, and curcumin.

Prioritize Gut Health 

Immune-modulating foods and lifestyle practices can help to heal the gut lining and support microbial diversity. Foods and lifestyle interventions that support a healthy gut include:

  • Fermented foods have been shown to reduce inflammation, increase microbial diversity, and modulate the immune response. Examples include kimchi, sauerkraut, kefir, and natural yogurts.
  • Plant-based fiber helps support the microbiome’s function and diversity, improving GI health and immune resilience.
  • Probiotics help balance microbial health, metabolites, and the immune response and may decrease IBD symptoms.
  • Exercise supports an anti-inflammatory response that helps maintain GI and microbial balance.

Additional Considerations

Autoimmune conditions are influenced by various factors, and symptoms can differ from patient to patient. Working with a qualified professional for personalized interventions can help patients navigate the complexities of their diagnosis. 

Tracking, regular check-ins, testing, and retesting can help define interventions that fit into patients' lives and align with their specific needs.


Key Takeaways

  • Inflammatory Bowel Disease (IBD) is an autoimmune condition characterized by a dysregulated immune response in the gastrointestinal (GI) tract. This response leads to inflammation, pain, tissue damage, and various symptoms.
  • Crohn's disease (CD) and ulcerative colitis (UC) are two types of IBD, each with distinct characteristics, symptoms, and patterns of inflammation. 
  • Functional Lab testing is an important tool for identifying underlying imbalances and inflammatory markers in IBD patients, which can help direct individualized nutritional interventions.
  • Dietary interventions and therapeutic diets prescribed by qualified nutritionists can reduce symptoms and improve quality of life. 
  • Personalized Nutrition interventions are the most effective method for addressing functional symptoms and navigating triggers that are specific to the individual.
The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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