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Top Functional Medicine Labs To Run Bi-Annually On Your Crohn's Patients

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Top Functional Medicine Labs To Run Bi-Annually On Your Crohn's Patients

Around half a million Americans have Crohn's disease, affecting both men and women, including children. It can often occur in people in their late teens, 20s, or early 30s, and I have seen this condition significantly impact some of my patients' daily lives. However, this chronic digestive condition can be effectively managed with comprehensive care and individualized treatments. Functional medicine labs can provide an advantage in part of the healing journey, enabling practitioners to personalize treatment protocols for their Crohn's patients. Think of these labs as helpful resources to improve health based on the specific needs of each individual.


What is Crohn's Disease?

Crohn's disease is a type of chronic inflammatory bowel condition affecting the gastrointestinal tract. It's also known as regional enteritis or ileitis. This condition can lead to symptoms like diarrhea, stomach cramps, feeling of fullness, fever, loss of appetite, weight loss, abnormal skin tags on the buttocks, anal fissures, anal fistulas, and rectal bleeding, with occasional flare-ups. Crohn's can occur at any age but affects more young people. There are four different forms of Crohn's based on which digestive tract sections are involved. Ileocolitis is inflammation in the small intestine and part of the large intestine (colon), the most common type. Ileitis is swelling and inflammation in the small intestine (ileum). Another type is gastroduodenal, which is inflammation and irritation in the stomach and the top of the small intestine (duodenum). The final form is Jejunoileitis consisting of patchy inflammation in the top half of the small intestine (jejunum).

The disease follows a pattern of flare-ups with severe symptoms and periods of remission with little or no symptoms, which can last for weeks to years, and it's difficult to predict when flare-ups will occur.

Why is it Important to Run Functional Medicine Labs Bi-Annually on Your Crohn's Patients?

Bi-annually testing for patients with Crohn's can positively influence the impact of this condition. Since this condition occurs mainly in younger individuals, these tests can provide the necessary information to guide them in treatment options that fit into their lifestyles and routines. Flares can also happen unexpectedly but can be significantly reduced with insights into the underlying factors leading to these flares. Early detection is also vital as Crohn's can lead to chronic inflammation, resulting in further negative consequences like abscesses, bowel obstructions, and colon cancer.

Regular testing is a helpful tool that identifies triggers for Crohn's and the periodic flares, allowing timely interventions to improve symptoms and reduce the risk of severe complications for patients living with this disorder.

What Causes Crohn's Disease?

Crohn's disease has an unknown cause and likely results from a combination of genetic and environmental factors, leading to chronic inflammation and increased intestinal permeability. It affects both genders equally, often developing between ages 15-30, and a family history of IBD increases the risk. 

Certain genes like NOD2, IL23R, and ATG16L1 are associated with Crohn's. Environmental factors like living in developed areas are linked to higher risk, while intestinal permeability during flares may contribute to the disease. 

Infections from pathogenic bacteria and viruses like Epstein Barr Virus (EBV) are associated with Crohn's, as well as dysbiosis in the gut microbiome. Smoking doubles the risk and worsens symptoms, and a Western diet high in fat and low in fiber is linked to increased risk. 

Complications of Crohn's disease include abscesses, anal fissures, bowel obstructions, colon cancer, fistulas, malnutrition, and ulcers.

Top Functional Medicine Labs to Run Bi-Annually on Your Crohn's Patients

It's essential to understand that the diagnosis of Crohn's disease is completed through colonoscopy or endoscopy. However, functional labs can be regularly run to help screen and monitor patients' progress. Here are some labs commonly used by functional medicine practitioners:

Comprehensive Stool Analysis

A thorough stool test can identify intestinal infections and signs of underlying inflammatory bowel disorders like Crohn's. It assesses the microbiome's health and detects imbalances that may affect digestion and absorption and cause inflammation in this disorder. The results of this stool panel can guide specific treatment options, such as personalized nutritional plans and supplements to rebalance the microbiome to improve gut inflammation. Retesting can evaluate treatment effectiveness and monitor intestinal inflammation.

Intestinal Permeability Testing

Leaky gut, also called intestinal permeability, is associated with many chronic inflammatory disorders like Crohn's disease. Leaky gut can lead to chronic gut inflammation, worsening symptoms in Crohn's patients. Therefore, it is crucial to stay on top of this inflammatory response through regular testing. Most people with Crohn's disease show signs of leaky gut. Recent studies suggest that even in symptom-free individuals, increased permeability is linked to a higher risk of developing the condition in the future. Functional practitioners often use zonulin measurements to assess intestinal permeability. This test is often done through serum samples to help measure zonulin levels, as well as antibodies to zonulin, actin, and lipopolysaccharide, which are all indicators of leaky gut to help manage symptoms related to intestinal permeability and reduce active disease flares.

Food Sensitivity Testing

Evidence reveals that many patients report food reactions with chronic inflammatory bowel disease. Food sensitivity symptoms can be challenging to pinpoint as they may appear hours or days after eating specific foods. The food sensitivity panel checks antibodies in more than 180 different foods and is done through a finger prick or small blood sample. Regular testing for food sensitivities can be valuable for Crohn's patients to track reactions and associated symptoms, enabling them to personalize a dietary plan that supports gut healing by eliminating problematic foods.

Nutritional Deficiency Testing

More than half of patients with IBD experience micronutrient deficiencies, with iron, B12, vitamin D, vitamin K, folic acid, selenium, zinc, vitamin B6, and vitamin B1 being the most common. Deficiencies are more prevalent in Crohn's disease compared to ulcerative colitis, and they are more frequent during active disease than during remission.

A micronutrient panel can help healthcare providers detect deficiencies and nutrient imbalances associated with Crohn's. The test uses a serum sample to assess 40 different vitamins and minerals that may be lacking. It is recommended for individuals with inflammatory digestive conditions and should be done twice a year to evaluate absorption and adjust nutritional plans based on the results.

Inflammatory Markers

Since this is an inflammatory condition, assessing for baseline inflammation levels is vital in managing Crohn's. Retesting these levels after getting a baseline measurement and completing treatment interventions can monitor the effectiveness of those treatments. Inflammation markers like C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) are used to evaluate overall inflammation in the body. On the other hand, calprotectin indicates the presence of white blood cells and inflammation, making it helpful in assessing disease severity and treatment response. Lactoferrin is another marker of intestinal inflammation and white blood cell activity, often elevated during IBD flares. Practitioners can use these inflammatory markers for continued optimization of their treatment protocols for Crohn's patients.

Genetic Testing

Genetic testing doesn't need to be completed multiple times. However, the CICA Genetics test examines genetic markers associated with inflammatory digestive disorders like Crohn's disease. It provides insight into a patient's genetic risk for this condition by evaluating the markers NOD2 and ATG16L1. The presence of these markers indicates an increased risk for the development of Crohn's, which can enable practitioners to reduce these risk factors.



Crohn's disease flare-ups can be unpredictable and disrupt a person's daily routine. The functional medicine approach to Crohn's Disease considers various factors like genetics, altered microbiome, environmental exposures, and a leaky gut. These imbalances trigger excess inflammation in the digestive tract, which can exacerbate symptoms of Crohn's or increase the risk of flares. With the appropriate treatment and lifestyle adjustments which are made more personalized through regular functional medicine labs, patients with this condition can manage symptoms, prevent complications, and lead an active life.

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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Lab Tests in This Article

  1. Clinic, C. (2020). Crohn's Disease: Symptoms, Causes, Management & Treatment - Cleveland Clinic. Retrieved July 30, 2023, from Cleveland Clinic website:
  2. ‌(2023, March 17). Retrieved July 30, 2023, from Rupa Health website:
  3. Causes of Crohn's Disease. (2019). Retrieved July 31, 2023, from Crohn's & Colitis Foundation website:
  4. Ranasinghe IR, Hsu R. Crohn Disease. [Updated 2023 Feb 20]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from:
  5. Turpin, W., Lee, S.-H., Antonio, J., Madsen, K., Meddings, J. B., Larbi Bedrani, … Bernstein, C. N. (2020). Increased Intestinal Permeability Is Associated With Later Development of Crohn's Disease. 159(6), 2092-2100.e5.
  6. Carrière, J., Darfeuille-Michaud, A., & Nguyen, H. T. (2014). Infectious etiopathogenesis of Crohn's disease. World journal of gastroenterology, 20(34), 12102–12117.
  7. ‌Toxin-producing Yeast Strains in Gut Fuel IBD. (2022). Retrieved July 31, 2023, from WCM Newsroom website:
  8. ‌Weisshof, R., & Chermesh, I. (2015). Micronutrient deficiencies in inflammatory bowel disease. Current opinion in clinical nutrition and metabolic care, 18(6), 576–581.
  9. Ballegaard, M., Bjergstrøm, A., Brøndum, S., Hylander, E., Jensen, L., & Ladefoged, K. (1997). Self-reported food intolerance in chronic inflammatory bowel disease. Scandinavian journal of gastroenterology, 32(6), 569–571.
  10. Campos, M. (2017, September 22). Leaky gut: What is it, and what does it mean for you? - Harvard Health. Retrieved August 1, 2023, from Harvard Health website:
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