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Healing Crohn’s Disease With Functional Medicine

Dr Auto Immune
October 18, 2022

Digestive issues are becoming more and more common! From bloating to IBS to SIBO and Candida overgrowth, there’s no shortage of people walking into my office hoping for a solution to their GI issues.

Today, I’m going to dive into one of the more serious GI issues I see among my patients — Crohn’s disease.

Many people with Crohn’s feel hopeless and like there’s no more that can be done. But I’m here to tell you that no matter what you’ve heard, there are steps you can take to improve your digestion and see improvements in your symptoms. Keep reading for everything you need to know.

What is Crohn’s Disease?

Like ulcerative colitis, Crohn’s disease is an inflammatory bowel disease. As of 2015, about 1.3% of the United States population had inflammatory bowel disease (IBD).

IBD is different from IBS in that it is characterized as an autoimmune disease, meaning the underlying cause of Crohn’s is an immune system malfunction that causes the immune system to attack the body’s own tissues.

In the case of Crohn’s, the body attacks the intestinal lining, leading to localized inflammation.

What Are the Symptoms of Crohn’s Disease?

The inflammation caused by Crohn’s can lead to a host of symptoms, including:

  • Diarrhea
  • Bloating
  • Abdominal pain
  • Rectal bleeding and pain
  • Unintended weight loss
  • Loss of appetite
  • Nutrient deficiencies
  • Fatigue
  • Low mood or depression
  • Brittle nails
  • Hair loss
  • Nausea and vomiting

To be diagnosed with Crohn’s disease, these symptoms would have to be moderate to severe, and chronic.

In order to officially make a Crohn’s disease diagnosis, a doctor will also do laboratory tests to check your inflammation levels, signs of nutrient deficiencies such as anemia, and infections as well as X-rays, CT scans, a colonoscopy, and an endoscopy.

What Does a Functional Medicine Crohn’s Diet Plan Look Like?

If you’ve been diagnosed with Crohn’s disease, you may have already noticed that certain foods seem to trigger your symptoms and other foods seem to be “safe.” And while every person’s trigger foods are slightly different, almost all Crohn’s patients can benefit from reducing their intake of:

  • Lectin-containing foods like beans and legumes
  • Nuts and seeds
  • Gluten-containing grains
  • Dairy
  • Processed foods
  • Raw vegetables
  • Caffeine
  • Sorbitol, xylitol, or other sugar alcohols
  • Alcohol
  • Spicy foods
  • Raw fruits

You may be reading the list above and feel a little bummed out. Does this mean you can’t enjoy your morning cappuccino or popcorn at the movies? Dr. Ian Hollaman, aka Dr. Autoimmune recommends reducing these foods as much as possible, especially in the first few months, but you may be able to be more flexible once your symptoms have improved.

The good news is that there are a ton of delicious foods that can actually benefit your gut health, such as:

  • Organic meats
  • Fatty fish
  • Cooked vegetables
  • Dark leafy greens
  • Fruits and vegetables

As a general rule, it’s been noticed that people with Crohn’s seem to benefit from eating cooked foods, which means soups, stews, and stir fry are your new best friends.

Crohn’s can have serious consequences and should not be ignored. That being said, if your doctor does not seem open to dietary or lifestyle changes, or tells you they won’t make a difference, that is a red flag that you may want to find another physician to manage your care. Why? Because study after study has shown that lifestyle factors DO matter when it comes to Crohn’s and all inflammatory bowel diseases for that matter.

Non-Food Lifestyle Choices That Can Improve Symptoms.

Even though Crohn’s is a gut-centric disease, there are other non-food lifestyle choices that seem to be able to improve symptoms. If you have Crohn’s, I recommend exploring the following:

1. Avoid smoking-

Tobacco products have been linked to the development of Crohn’s and an increased number of flare-ups.

2. Manage stress-

Stress is not necessarily a cause of Crohn’s but it can definitely trigger flare-ups and worsen symptoms. I recommend yoga, meditation, or gratitude practices as a way to manage daily stress.

3. Take fish oil-

Fish oil may help reduce the underlying inflammation present in Crohn’s disease. In fact, one study showed that patients taking fish oil were twice as likely to remain in remission compared to patients not taking fish oil.

4. Try acupuncture-

Another great option is the traditional Chinese medicine modality acupuncture. While the research isn’t conclusive, several clinical trials have shown promising results that acupuncture could be helpful for inflammatory bowel disease.

How Functional Medicine Can Help Heal Crohn’s Disease

Many patients with Crohn’s disease report feeling frustrated with conventional medical protocols. Patients overwhelmed with drug risks and side effects want an alternative approach. Functional medicine practitioners like Dr. Ian Hollaman (aka Dr. Autoimmune) is an expert in alternative therapies- He has found that when he helps clients with Crohn’s disease change their lifestyle, he can help them change the severity of their disease.

He then customizes a program that utilizes diagnostic tests, protocols, and procedures to help identify autoimmune triggers caused by Crohn’s disease which may be contributing to the client’s symptoms.

He then uses additional protocols to help the body deal with the identified stressors.

How Is Crohn’s Disease Diagnosed?

Diagnosing Crohn’s disease may often prove to be a complicated task, given the complexity of symptoms, the varying degree of their severity, and the fact that the signs may not manifest the same way for all patients. It is likely that several different types of tests are needed, after considering your symptoms, their frequency, and seriousness.

Functional Medicine Labs to Test for Crohn’s Disease

Functional medicine testing can assess the extent of inflammation in the intestines and the rest of the body along with nutrient deficiencies, anemia, and infections and help identify underlying contributing factors.


The Celiac, IBS, and Crohn’s Assay (CICA) measure genetic risk markers and antibodies directed against yeast in the gut (Anti-Saccharomyces Cerevisiae Antibody (ASCA), which is an indicator for the presence and severity of Crohn’s.


Fecal calprotectin is a marker of mucosal inflammation in IBD and can be used to monitor disease activity.

Comprehensive Stool Test

The GI-MAP assesses relative amounts of healthy and unbalanced gut bacteria, inflammation and leaky gut markers, parasites, and yeast overgrowth. Individuals with Crohn’s frequently have an overgrowth of Candida and Malassezia yeasts that join harmful bacteria to create biofilms that are difficult for the immune system to get rid of. This can trigger autoimmunity and perpetuate the cycle of inflammation, so detecting and healing gut infections and imbalances is important.

Micronutrient Testing

Crohn’s causes nutrient deficiencies that result in further immune system dysregulation and impaired healing. The damaged intestines cannot effectively absorb nutrients, leading to deficiencies in iron, vitamin B12, folate, vitamin D, magnesium, and other nutrients.

The functional status of nutrients within the cell can be assessed with a micronutrient panel to target any deficiencies.

Other Labs

Other basic labs to assess contributing factors and complications include

  • complete blood count (CBC) to detect infection and anemia
  • inflammation markers such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) to assess inflammation throughout the body, and
  • liver function tests to screen for liver and bile duct problems.

After careful consideration, a highly trained integrative functional medicine practitioner can determine the presence of Crohn’s disease, its location in the digestive tract, and its state of progression.

If you’re an individual suffering from chronic inflammatory bowel disease, it is imperative to develop a close, trusting, and reliable relationship with your integrative functional medicine practitioner to avoid the worsening of your condition and even to restore the standard functions of the digestive system.

Why is it Important to Work With an Integrative Functional Medicine Practitioner?

An integrative functional medicine practitioner will examine all areas of your life when creating a plan for managing your Crohn’s disease symptoms.

With the help of various scientifically proven allopathic and complementary medicinal methods this disorder may become entirely manageable, remaining in remission for extended periods of time. The goal of care therefore, will always be:

  • to control the inflammatory processes, most often with the help of anti-inflammatories
  • to balance the immune system- by aiding its health with proper nutrition
  • to correct any nutritional deficiencies developed by creating a proper diet protocol and adding appropriate supplementation
  • to relieve all bothersome symptoms, usually with the help of natural therapies, herbal remedies, stress relief, and other alternative approaches

Functional Medicine Care for Crohn’s Disease

A functional medicine approach to Crohn’s disease addresses underlying factors to balance the immune system, calm inflammation, and avoid the progression of the disease to avoid complications.

Lifestyle Changes You Can Make


Diet strongly influences the gut microenvironment, impacting microbial composition, function, gut barrier, and immunity.

The composition of the gut microbiota can change in response to diet. So like we mentioned above, an individualized nutrient-rich, anti-inflammatory diet can help balance inflammation to avoid flares and further irritation to the gastrointestinal tract while optimizing nutrients.

Support the Microbiome

A properly balanced gut microbiome is crucial for balanced immune function. A diet rich in unprocessed whole foods that incorporates probiotic-rich foods like miso, kimchi, and sauerkraut combined with prebiotic-rich foods like leeks, artichokes, garlic, and beans that nourish healthy bacteria is critical for repairing the intestinal lining and reducing symptoms.

In addition to diet, probiotic supplements like Lactobacillus and Bifidobacterium have been shown to improve Crohn’s.

Manage Stress

Stress increases cortisol and inflammation in the gut via the “brain-gut axis,” triggering flare-ups. Therefore, stress management practices like yoga, meditation, breathwork, or gratitude practices and addressing emotions and trauma are helpful.


Exercise decreases the expression of inflammatory substances and encourages repair of the damaged intestines.

Fecal Microbiota Transplantation (FMT)

FMT is an emerging experimental treatment strategy for Crohn’s.

Dr. Ian Hollaman aka Dr. Autoimmune

Dr. Ian Hollaman, aka Dr. Autoimmune, along with his team, is one of the top functional medicine telehealth providers in the world! We offer webcam health consultations for people suffering from autoimmune diseases.

At Dr. Autoimmune, we use a functional medicine approach to identify the root cause of your condition and develop a custom plan using diet, supplementation, and lifestyle change to help you reach your health goals.

With an 85% success rate, we are confident that we can get you the results you are looking for.

If you’re ready for your life to change click here or just click the “Start Your Journey” button below.

We are the autoimmune wellness specialists that Boulder, CO. residents trust!

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