Posted on: February 27, 2018 at 3:59 pm
Last updated: September 26, 2018 at 10:07 am

Hashimoto’s thyroiditis is an autoimmune condition of the thyroid gland, affecting an estimated 75-90% of people suffering from hypothyroidism or lowered thyroid gland function.

While the diagnosis of hashimoto’s may make you think that this is a thyroid-specific condition, it’s important to note that the condition is one of the immune system, attacking the thyroid. We should actually be looking at immune function and why the issue occurred in the first place. So let’s dive deeper into the root cause of this condition – hyperactivation of the immune system.

Seventy to eighty percent of your immune system is actually located in your gut lining, where most bacteria, viruses, fungi and parasites could potentially enter the body. The immune cells and antibodies they produce, protect us from opportunistic microbes that want to invade our body and use our nutrients.

Sometimes our diet can cause major issues in the gut lining, leading to immune system activation. Certain foods can actually break down the proteins that link adjacent cells together, causing holes to form between cells. This phenomenon is called intestinal hyperpermeability, or leaky gut.



There are some foods that can cause this phenomenon quite commonly, including:

  • Wheat Gluten
  • Barley Gluten
  • Rye Gluten
  • Spelt Gluten
  • Cow’s milk dairy
  • Unsprouted grains (like brown rice)
  • Refined sugars and artificial sweeteners
  • Refined vegetable oils (sunflower, safflower, soybean and canola oils)
  • Nightshade vegetables

Dietary choices like the options listed here are common causes of leaky gut, but they are not the only cause of this syndrome.

Bacteria are present in our digestive tract, with particularly high numbers in the large intestine, to help us break down foods that contain fiber – essentially what we cannot break down on our own. If we eat foods on a standard American diet, these bacteria become depleted of their nutrient sources and will become agitated. Occasionally they will attempt to enter the small intestine and get the nutrients that they are missing.

If this happens, a specific type of bacteria called gram-negative bacteria will continue to create an endotoxin known as Lipopolysaccharide (LPS for short) which is also very strong at breaking down the proteins between adjacent cells, leading to leaky gut. Dietary and bacterial leaky gut are the sources of immune system hyperactivation in the gut.

Once the immune system is activated, a process called molecular mimicry occurs in which the proteins of gluten, dairy and LPS actually mimic components that look similar to proteins on the surface of the thyroid gland. Over time, the immune system becomes so active that it cannot tell the difference between the dietary or bacterial proteins, and our thyroid proteins, so it begins to attack the thyroid gland. This is called Hashimoto’s thyroiditis.

Your physician can actually test for these antibodies with basic blood work – ask them to look for TPO and TGB antibodies.

Step 1:


The first step in overcoming this condition, is to change your diet. Cut out any foods that could be offending the gut lining, and start with the ones on the list above.

Step 2:

Get testing done to see if there are microbes living in your gut, that should not be there. Speak to a functional medicine practitioner about getting the right testing. I recommend having a Urinary Organic Acid test (by Genova Diagnostics) to tell you about nutrient deficiencies as well as a DNA stool analysis (from Diagnostic Solutions Lab) to determine exactly what is happening in the gut.

Step 3:

Add supplements to help support the thyroid, immune system and gut. The best supplements I recommend are:

  • Selenium-Selenium is an important co-factor as it allows us to produce active thyroid hormone (T3) from inactive thyroid hormone (T4)
  • Magnesium- Magnesium supports the adrenal glands and allows you to sleep more calmly. Sleep is important in body recovery as we produce and secrete growth hormone between 10pm and 2am while we are sleeping. This is our main recovery hormone. Choose either Magnesium citrate, or if you are having loose stools due to the citrate form, choose Magnesium bisglycinate.
  • Probiotics- I prefer to use spore-based probiotics as they are derived in nature and do not need to be stored in a refrigerator. They tend to plug all the holes in the gut and produce a more broad-spectrum of gut flora. I personally use MegaSpore Biotic.
  • B-vitamins- B-vitamins are essential in the production of energy in the Mitochondria, specifically what the thyroid hormones effect in each cell. A high quality, B-complex is a great option for this supplementation as it helps to boost your energy and gives you the right co-factors necessary for the citric acid cycle
  • Vitamin D- If you live in a colder climate, vitamin D is commonly extremely deficient. Supplementing with Vitamin D drops and getting out into the sun as much as possible is highly effective in improving immune system balance.

It’s important to remember, that dietary and lifestyle strategies are the most important changes that you can make. Supplements and nutrient additions are exactly that – supplementary. Focus on making the dietary and lifestyle changes first as they are necessary for supplements to be as effective as you want them to be.

If you are interested in speaking with me, Dr. Navaz Habib, directly, you may book a complimentary 15-minute phone call by going to, during which I will listen to your story and tell you about the programs we offer to our amazing patients at the Living Proof Institute. We have supported thousands of patients on their journey to overcoming their challenges and optimizing their health.

This great post was written by Dr. Navaz Habib. We encourage you to go check out his website and follow him on Facebook and Twitter.


Dr. Navaz Habib
Dr. Habib is a Chiropractor, Functional Medicine Practitioner and Acupuncture Provider based out of the Greater Toronto Area. He consults with patients world-wide in regards to autoimmune, brain, gut and hormone health conditions. His goal is to find the root cause of the biochemical, physiologic, genetic, environmental and lifestyle factors contributing to his patients symptoms. Virtual consultations are available world-wide and on location in Toronto.

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