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An Integrative Medicine Approach to Celiac Disease

Medically reviewed by 
An Integrative Medicine Approach to Celiac Disease

Celiac disease is a chronic autoimmune disease impacting the digestive and immune systems. It occurs due to interactions among a triad of factors: genetic susceptibility, environmental factors, and the state of the gut, including the balance of the microbiome and extent of intestinal permeability.

While often undiagnosed for years, celiac disease affects 1.4% of the world population and is becoming more common. A Functional Medicine approach to treating Celiac Disease will allow accurate and timely diagnosis to help prevent symptoms and intestinal injury.


What is Celiac Disease

Celiac disease is an autoimmune disease that occurs in genetically predisposed people. When someone with celiac disease eats gluten proteins, immune cells treat them as an invading danger and mount an attack. This results in inflammation and damage to the small intestine cells, making it difficult to absorb nutrients properly.

Celiac Disease Signs & Symptoms

Gastrointestinal Symptoms Associated with Celiac Disease

  • Diarrhea
  • Steatorrhea or fat in the stool due to an inability to properly digest it
  • Weight loss
  • Failure to thrive

Malabsorption of Nutrients Symptoms Associated with Celiac Disease

  • Iron-deficiency anemia
  • Mouth canker sores (aphthous stomatitis)
  • Chronic fatigue
  • Impaired growth
  • Itchy blistering skin rash (dermatitis herpetiformis)
  • Reduced bone density
  • Hormone imbalances and reproductive problems
  • Neurological symptoms
  • If left untreated, complications such as adenocarcinoma of the small intestine, liver damage, and non-Hodgkin’s lymphoma may result. In addition, patients have an increased risk for developing certain psychiatric and neurodevelopmental disorders, including autistic spectrum disorder, attention deficit hyperactivity disorder, depression, anxiety, and eating disorders.

Celiac Disease Possible Causes


Autoimmunity is triggered by gluten exposure in an individual with genetic susceptibility. Intestinal permeability or leaky gut also plays an important pathophysiological role in celiac disease.

Specific gene variants (haplotypes HLA-DQ2, HLA-DQ8, and non-HLA) impact the immune system’s response. When exposed to gluten, an imbalanced microbiome and leaky intestinal lining can develop autoantibodies that continue to damage the intestinal lining.


Gluten includes proteins that are present in grains like wheat, wheat berries, durum, emmer, semolina, spelt, farina, farro, graham, kamut, rye, and barley. Gliadin is one of the two main proteins in gluten and is responsible for most of the adverse health effects.

When exposed to Gliadin, antibodies against tissue transglutaminase-2 (t-TG2) are produced, and the immune system attacks the small intestine’s villi. This autoimmune attack destroys these finger-like projections of the cells lining the digestive tract (enterocytes), which are responsible for the absorption of nutrients and the release of enzymes.


Zonulin is a master regulator of intestinal permeability released in response to triggers. Evolutionarily, it is a defense to fight off offending microorganisms in the small intestine.

In addition to certain bacteria, Gliadin also causes the release of zonulin. Under these states, zonulin weakens the structure of intestinal epithelial tight junctions (the barrier gates between cells) resulting in permeability.resulting in permeability. This “leaky gut” allows for the passage of antigens such as macromolecules (fats, proteins, carbohydrates), toxins, food proteins, or other substances from the gut into the body. Once these invaders enter the bloodstream through the leaky gut, the body begins to attack them, causing many chronic inflammatory and autoimmune diseases, including celiac disease.

Endocrine Autoimmunity

There is a close relationship between celiac disease and endocrine autoimmunity, including Type 1 diabetes mellitus, autoimmune thyroid disease, and autoimmune hepatitis, which is largely explained by a shared common genetic background. Not everyone with these genes will develop symptoms of celiac disease, as exposure to gluten is required to instigate the autoimmune response.

Environmental Influences

The rise of celiac disease also has environmental influences. Non-genetic environmental exposures like breastfeeding and natural (vs. C-section) birth influence the microbiome positively. In contrast, exposures like gastrointestinal viral infections (especially during childhood) make an individual more susceptible to developing fully symptomatic disease.

Functional Medicine Labs to Test for Celiac Disease

Duodenum Biopsy

The classical gold standard for diagnosis has been small intestine (duodenum) biopsy to assess villi damage while gluten is being consumed. This allows for visual confirmation of the type of intestinal damage and inflammation, which is specific to celiac disease.

Celiac Antibodies Lab Test

Because of the invasive nature of the duodenum biopsy, risks involved, and the increasing accuracy of available blood testing, the current recommendation from the American College of Gastroenterology is to use tTG IgA as the first-line test for patients two years and older with suspected celiac disease.

Less invasive blood tests are available to check for antibodies to t-TG2, endomysial, and deamidated gliadin peptide. Looking at both immunoglobulin-A (IgA) and -G (IgG) antibodies against t-TG2 increases accuracy.

Specialty testing while eating gluten can detect antibodies to gluten proteins. Some options include Elisa LRA Gluten Panel (IgG, IgM, IgA), and Genova Diagnostics Celiac and Gluten Sensitivity (IgG & IgA).

Zonulin Lab Test

The leaky gut marker zonulin can also be evaluated.

Comprehensive Stool Test

Several studies have reported different types of imbalances in the microbiome in people with celiac disease, suggesting that the composition of gut bacteria may influence which types of symptoms patients display and help explain why different people have different manifestations of disease (headaches and GI symptoms vs. joint pain and GI symptoms are two examples).

Further, research suggests that some patients’ persistent symptoms even when following a long-term gluten-free diet may be due to less bacterial diversity in the gut (fewer different types of bacteria) and an imbalance in certain types of bacteria.

A Comprehensive Stool Test measures amounts of healthy and unbalanced gut bacteria (dysbiosis), inflammatory markers, leaky gut, parasites, and yeast to assess the state of the gut and guide treatment aimed at restoring balance.

Testing for Micronutrient Deficiencies

Due to intestinal damage, patients often have micronutrient deficiencies impacting B9, B6, B12, iron, zinc, calcium, copper, fat-soluble vitamins (A, D, E, K), and fiber. SpectraCell's Micronutrient Panel assesses the functional status of nutrients within cells.

Food Sensitivities Test

Increased intestinal permeability contributes to food sensitivities and cross-reactivity. These can be identified with ELISA testing or Cyrex’s Array 4 to test for gluten-associated cross-reactive foods and food sensitivities using IgA and IgG antibodies.

Functional Medicine Treatment for Celiac Disease

Treating celiac disease and preventing damage to the intestinal lining requires an individualized multifactorial approach that acknowledges the factors that lead to this autoimmune disease— intestinal permeability, genetics, and environmental factors. Research also suggests lifestyle and environmental approaches help prevent complications.

Gluten Free Diet

The primary treatment to prevent symptoms and advanced complications of celiac disease is a life-long, strict gluten-free diet along with the removal of any cross-reactive foods or food sensitivities.

Avoiding gluten from food, medicines, and other substances can ease symptoms, improve quality of life, and prevent complications.

Sticking with whole foods is most effective at reducing inflammation because many processed gluten-free replacements contain large amounts of refined carbohydrates and sugar and trace amounts of gluten. They can also be made from ingredients like rice which is high in arsenic. Nutrient-dense fresh foods also help replenish vitamins and minerals to restore malnourished cells. Some whole food gluten-free alternatives include millet, buckwheat, quinoa, brown rice, and amaranth.

Balancing the Microbiome and Heal the Gut

Eliminating gluten and replacing it with a nutritious, balanced diet begins to help heal the gut. Additional measures can ensure the small intestine returns to proper functioning. For example, restoring equilibrium in the gut microbiota is critical for repairing the mucosal barrier and stopping autoimmunity. This may be accomplished through an individualized balanced whole foods diet incorporating pre- and probiotic-rich foods as tolerated. Fermented foods like kimchi and sauerkraut contain naturally-occurring probiotics that enhance the microbiome, while prebiotic-rich foods like artichokes, garlic, and beans can nourish healthy bacteria.


Probiotic supplements tailored to individual needs and digestive enzymes can also help restore gut health and proper digestion and absorption of nutrients. Some probiotics that help celiac patients include Bifidobacterium infantis, Bifidobacterium longum, Bifidobacterium breve, Lactobacillus casei, and Lactobacillus plantarum. In addition, the amino acid L-glutamine can strengthen the intestinal barrier.

Emerging Treatments

Other treatments under study target mistakenly ingested gluten to prevent damage and inflammation. These include gluten-specific enzymes (proteases) that target gluten and degrade it into small fragments in the stomach before they pass into the duodenum and certain types of probiotics to improve gastrointestinal symptoms. For example, Lactobacillus rhamnosus GG inhibits Gliadin from altering intestinal permeability.

In addition, larazotide acetate is under study for preventing symptoms of celiac disease. This medication is a zonulin antagonist which blocks the disassembly of tight junctions in the intestines, thereby limiting gluten crossing a permeable intestinal mucosal barrier where it can lead to autoimmunity.  


Celiac disease manifests with intestinal and extraintestinal symptoms such as diarrhea, malnutrition, and chronic fatigue. Since this autoimmune condition results when a person with susceptible genetics develops intestinal permeability and is exposed to proteins in gluten, tests that measure the immune system’s reaction to gluten can help with diagnosis.

Functional Medicine lab test measuring tissue transglutaminase autoantibodies, anti-gliadin antibodies, and food sensitivities can help personalize an approach that reduces inflammation and stops the autoimmune response to gluten that damages the intestinal lining and results in symptoms.

A healthy gluten-free diet filled with a variety of nutrient-dense whole foods and probiotics personalized to the needs of each individual helps reduce symptoms, repair the gut, replenish nutrients, and prevent complications. Dietary and lifestyle approaches that address increased intestinal permeability and rebalance the gut microbiota support healing.

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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