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I often get messages from people with Hashimoto’s and autoimmune disease that say “Thanks for your efforts, but I’ve already tried everything. I have cut out gluten, dairy and soy and still have Hashimoto’s. How can your book help me?” 

While changing your diet is a really important first step that will greatly help many of you, if you do not see a complete remission of your condition within 3-6 months, I encourage you to dig deeper. Changing my diet was a really important step in my healing journey, but it was just the beginning.
Dr. Alessio Fasano, world-renowned gastroenterologist, Celiac disease and autoimmunity expert, describes autoimmunity as a three-legged stool that needs three things to be present to manifest:

1.    The right genes

2.    The trigger

3.    Intestinal permeability

While we can’t change our genes, we can reverse the autoimmune condition by removing triggers and intestinal permeability. 

Dr. Fasano uses the example of Celiac disease to explain this phenomenon. Celiac disease is a unique autoimmune condition where gluten acts as both the trigger, and the cause of intestinal permeability! Once gluten is removed, the body is able to heal and regenerate itself.  

Infections have been implicated as triggers in many cases of autoimmunity, and identifying and removing infections may result in a complete remission of the autoimmune condition. 

Although we can’t always identify and even remove all of the triggers, such as Epstein Barr Virus (the virus that causes Mono), another option is to fix the intestinal permeability. This will also allow many individuals to put their condition into remission, as the “three legged stool” of autoimmunity will no longer be able to stand!

Based on my research over the last four years, I’d like to share with you six potential root causes of intestinal permeability. There are of course many additional root causes, but these six are a great place to start. 

Note: some of you may have more than one root cause, and I encourage you to dig!

Root Cause #1: Gluten Sensitivity

Gluten sensitivity and Celiac disease have been implicated in various autoimmune conditions ranging from Hashimoto’s, Graves’ disease and Rheumatoid Arthritis. Various tests can be done to determine if one has Celiac disease/gluten sensitivity, however the condition may not always show up on tests. Some individuals do not learn of their sensitivity until they remove gluten from their diets. 

Gluten sensitivity may be the sole root cause, or it may be one of a few root causes. Every person with an autoimmune thyroid condition should remove gluten from his/her diet. Even in those who do not have Celiac or gluten sensitivity, gluten causes intestinal permeability. 

If gluten was the sole root cause, the person should see a complete remission of thyroid antibodies and thyroid function may even return to normal within 3-6 months! If not, we may need to dig deeper… 

Treatment: Pretty straight forward… Testing for Celiac/gluten disease, and removing gluten from the diet

Root Cause #2: Gluten Sensitivity and Cross Reactive Proteins

In addition to gluten sensitivity, individuals with Hashimoto’s may also be reactive to multiple other proteins including grains like rice, quinoa, and corn. Some experts, like Dr. William Davis, author of Wheat Belly, claim that human beings did not evolve to eat  “grasses” like wheat, rice or corn. 

Other individuals may also react to dairy, eggs, nuts, seeds, nightshades...

There are specialised DNA labs that offer additional testing options for food sensitivities. 

Treatments of Choice: Testing, elimination diet, Paleo Diet, Autoimmune Paleo Diet, and in some cases a rotation diet may be beneficial. Working with a nutrition coach can be extremely beneficial in this respect. Supplements to help restore the gut lining may be beneficial as well. Systemic enzymes may prevent reactions to new foods, and reduce reactions to current foods. 

Root Cause #3: Glutamine/Zinc Depletion

Zinc and glutamine are among the two substances that are required for rebuilding intestinal lining. In times of stress, the body will pull these substances from our intestines and uses them for other things, such as production of adrenal hormones.  

In most cases, these substances become available to us through food, and things go back to normal after the stressful time is over, and the gut lining is rebuilt with new ingredients. 

This becomes an issue for those under prolonged stress, those with low stomach acid (which is needed to extract zinc from proteins), and those that follow a diet low in animal protein, including vegans and vegetarians, as glutamine is primarily found in animal protein (including eggs and dairy).

Some individuals who followed vegan/vegetarian diets and then introduced animal proteins back into their diets have been able to put their Hashimoto’s in remission. I believe this is because the glutamine and other ingredients allowed them to rebuild their gut lining. 

Solutions for this root cause: Glutamine supplements , zinc supplements , bone broths, gelatin, well-cooked meats, Betaine HCL(digestive enzymes to extract zinc from food), and any of the nutrient dense diets.

Note: Other nutrients like Vitamin D are also required for proper gut barrier function. Most of these interventions and supplements will help for just about everyone with Hashimoto’s.  

Root Cause #4: Parasite

You may think that parasites are only present in malnourished third world countries. Not so. Depending on the sources, 30-70% of Americans may be infected with parasites.  Current detection methods miss many parasites, and honestly, how many of you have been routinely tested for parasites?

A parasite found in the intestines can cause a tremendous amount of damage and has the ability to cause intestinal permeability, food sensitivities and autoimmune disease. If you are someone who developed your condition after a period of intense stress, I urge you to get tested, as stress makes us more susceptible to parasites. 

Unfortunately diets are a short-term fix. People with parasites have multiple food sensitivities, that don’t go away no matter what they eat or don’t eat. A person may feel better initially after removing sensitizing foods, only to start feeling worse once new foods become reactive. You can be on the perfect diet, and take loads of supplements, but if you have a parasite, it doesn’t matter; you will not be able to fully recover. 

There are many different types of parasites, including worms, amoebas and protozoa. Different treatments work for different parasites, thus while general parasite cleanses can sometimes help, I prefer to figure out the specific type of parasite through advanced testing.  For parasites in autoimmune disease, I take the approach “guilty until proven innocent”, as I have seen many people with 5-10 negative tests for parasites finally come up positive on one of the above mentioned tests. 

Temporary Fix: probiotics, low carbohydrate diets and diets such as the Autoimmune Paleo Diet will make it easier for us to tolerate the parasite symptomatically, but will not result in elimination of the parasite or the autoimmune condition.

Solution: antiparasitic herbs tailored to the parasite, specific antiparasitic medications, certain supplements, the probiotic S Boulardii and low carbohydrate diets will help as well.

Root Cause #5 Small Intestinal Bacterial Overgrowth (SIBO)

SIBO is an overgrowth of bacterial in the small bowel, or small intestine. This overgrowth can be caused by antibiotic overuse and starchy foods, among others. The SIBO results in intestinal permeability as the body tries to get rid of the excess bacteria.  

Testing: Basic breath testing for SIBO can be self ordered by patients, gastroenterologists and major Academic Treatment Centers will have access to advanced diagnostic tests. 

Treatment options: antibiotics, antimicrobial herbs, elemental diet and diets like the Specific Carbohydrate Diet, Low FODMAPS diet and GAPS diet are the treatments of choice for SIBO. 

Root Cause #6 Fungal Infections

The fungus Candida can cause intestinal permeability and has been implicated in autoimmune disease and food sensitivities. Liz Schau, holistic nutritionist was kind enough to share her Hashimoto’s remission story after overcoming Candida. You can read her story . Liz's Root Cause

Liz never felt healthy as a child. Something was always off. She constantly had sore throats, ear infections and battled with her mood. She was always on antibiotics. She was the kid that often missed field trips due to a stomach ache or some other ailment.

Things took a turn for the worse when Liz got to college, she began dealing with extreme fatigue, gained weight and dealt with a persistent sore throat on a daily basis.  During her third year in college she remembers being so exhausted she would sleep through the night, wake up at ten, eat and then go back to sleep again. 

After breaking up with a boyfriend, she gained 60 lbs during a seven month time period. At this point her period had stopped and she developed palpitations and had frequent urinary symptoms. This led her to seek care at her university’s clinic, where she was finally diagnosed with hypothyroidism in the summer of 2007. She was given Synthroid and told that everything would be back to normal within two months. 

Unfortunately, as for many of us, the normal never came. After college, Liz moved to New York and was frustrated that the medications were not helping. She continued to get worse and continued to seek medical care. 

Finally a diagnosis...

Finally, a doctor at a NY walk-in clinic tested her thyroid antibodies, and the antibodies were in the 500 range (normal is
Liz was up to 175 mcg of Synthroid, but never felt well. She kept getting worse and worse. She felt fat, depressed, tired and bloated. She experienced hives, recurrent infections, and menstrual irregularities. She felt like she was not going to be able to go on. 

Taking charge of her own health...

However, feeling unwell was a blessing in disguise for Liz, as it led her to find the root cause of her condition, allowing her to treat it and put her Hashimoto’s into remission. 

Like many of us, she started to “Google” her many symptoms and stumbled upon Candidiasis. She ran out and bought the Yeast Connection by Dr. Crook. This book explained that Hashimoto’s can be caused by Candida. 

A light-bulb went out in her head, and she knew this was it, and that she was going to be able to get herself well if she worked hard enough. So she took charge of her own health…she started a basic anti-yeast diet avoiding mushrooms, vinegar, processed foods and yeast-leavened breads. 

She was amazed to see that her thyroid numbers improved dramatically after being on an anti-yeast diet for four months. She continued on the diet until she learned about the gluten/autoimmune connection. She then discovered that she was also reacting to dairy. 

Over the course of 1.5-2 years, Liz dabbled in different diets, including a Candida diet, grain free diet, raw foods diet, paleo/primal diet , and the Body Ecology Diet. She found that some of the diets agreed with her and made her better, but that the raw food diet did not. 

She started taking probiotics and raw fermented foods to add beneficial bacteria back to her body. 

Her TSH began to normalize, and her antibodies disappeared. It had been a “spontaneous remission” according to her doctor. Under the supervision of her doctor, Liz was able to wean off her thyroid medications in August 2009. She wasn't on a a low dose of medications either, she was up to 175mg of Synthroid per day! Her thyroid was able to regenerate after the triggers were removed!

“The doctor was not interested in the diet I was following, or in any of the reasons why I thought I was getting better. He said ‘Don’t tell me about your diet’. However, I believe that healing my gut was the key. The yeast overgrowth and food sensitivities were the real issue”. Liz says.

Now that she has healed her gut,  she has been able to introduce a lot more foods, including properly prepared grains, fermented foods, real fats and dairy. She is a proponent of the Weston A. Price foundation and of using healing and native foods.

She continues to monitor her thyroid, and has had a normal TSH during her last pregnancy and her last antibody test (which was done in December 2012) showed that her antibodies were still below 10. She believes that Candida will always be an issue for her, but knows what she needs to do to control it. 

Testing: Gut testing such as the GI Effects profile may help determine if there is an overgrowth of Candida in the bowels. 

Treatment:  Probiotics, anti-fungal herbs and medications, anti-candida diets  .

So what’s your root cause? 

I encourage you to Dig at it! It’s not always the same for each person, and I wrote my book to help you figure that out!  I cover each of the above mentioned root causes in great detail and provide much  more information on many additional root causes, and how to find yours. 

Izabella Wentz, PharmD


1.    Sategna-Guidetti C, Volta U, Ciacci C, Usai P, Carlino A, De Franceschi L, Camera A, Pelli A, Brossa C. Prevalence of thyroid disorders in untreated adult celiac disease patients and effect of gluten withdrawal: an Italian multicenter study. Am J Gastroenterol. 2001 Mar;96(3):751-7. 


 Read further with the Root Cause by Izabelle Wentz


Kindest Regards

David Arthur,Clinical Pharmacist B.Pharm(Wits); ABAAHP Diplomate

(American Board of Anti-Aging Healthcare Practitioners)

FAARFM – Advanced Fellow in Antiaging, Regenerative and Functional Medicine Integrative Medical Centre  Anti-Aging & Preventive Medicine Specialists 

NUGO (European Nutrigenomics Organization): Full Certification in Polymorphism Responsiveness to diet, Molecular Nutrition and Genomics, Proteomics



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“The advice contained here is for information purposes only.  It is not intended as a substitute for advice from your doctor or other health care professional.  You should consult with a healthcare professional before starting any diet, exercise or supplementation program, before taking any medication, or if you have, or suspect you might have, a health problem.  You should not stop taking any medication without first consulting your doctor.”