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Basics of Immune Balancing for Hashimoto’s


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This article is part of a special report on Thyroid Disorders. To see the other articles in this series, click here.

In the first post in this series, we established that hypothyroidism is caused by an autoimmune disease (called Hashimoto’s) in the vast majority of cases. Since then, we’ve explored the role of gluten intolerance, vitamin D deficiency, supplemental iodine, blood sugar imbalances, adrenal stress and a leaky gut in perpetuating the autoimmune attack and disrupting thyroid function. We’ve discussed why dietary changes are always the first step in treating Hashimoto’s, and why replacement thyroid hormone is often necessary for a successful outcome.

What we haven’t discussed yet, however, are specific strategies for bringing the immune system back into balance. That will be the focus of this article.

Originally, I planned to go into considerable detail on the specific mechanisms of immune dysfunction that occur with Hashimoto’s, including a review of immunology, immune system classification (i.e. Th1 or “cell-mediated” immunity vs. Th2 or “humoral immunity”) and immune cell organization. It quickly became clear that such an approach would require an entire series of its own.

So, as fascinating as all of that stuff is, I decided to cut to the chase and focus on the practical, clinical applications. But there’s a caveat. Although I’ll be offering some general guidelines here for how to balance the immune system, if you have Hashimoto’s (or any other autoimmune condition) it’s in your best interest to find someone who understands immunology and is current with the latest nutritional and botanical protocols for treating autoimmune disease.

Why? Because autoimmune disease is not only extremely complex, but also highly individualized. Hashimoto’s in one person is not the same as Hashimoto’s in the next person. In one person, Hashimoto’s could present as a Th1-dominant condition. In another, it may present as Th2 dominant. In still another, both the Th1 and Th2 systems might be overactive, or underactive. And each of these cases requires a different approach. For example, botanicals like echinacea and astragalus stimulate the Th1 system. If someone with Th1 dominant Hashimoto’s takes these herbs, they’ll quite possibly get worse. On the other hand, antioxidants like green tea and Gotu Kola stimulate the Th2 system, and would be inappropriate for those with Th2 dominant Hashimoto’s. (For more information on the specifics of Hashimoto’s autoimmune physiology, see this article on Dr. Kharrazian’s blog and pick up a copy of his book.)

The good news, though, is that there are general approaches to balancing the immune system that are suitable for all types of Hashimoto’s regardless of the specific pattern of immune dysregulation. These approaches can be broken into three categories: removing autoimmune triggers, enhancing regulatory T cell function and reducing inflammation.

Removing Autoimmune Triggers

We’ve already discussed the role of gluten, iodine, stress and a leaky gut in triggering an autoimmune response. Other potential triggers include estrogens, infectious agents, and environmental toxins.

Estrogen fluctuations can trigger the gene expression of Hashimoto’s in the presence of inflammation and genetic susceptibility. In addition to turning on the genes associated with Hashimoto’s, estrogen surges have been shown to exacerbate the autoimmune attack on the thyroid. This may explain why the expression of Hashimoto’s is so common during pregnancy and perimenopause – both times when estrogen may be fluctuating wildly.

Environmental toxins are associated with autoimmune disease, and Hashimoto’s is no exception. Certain antigens like mercury that bypass our barrier system cause a potent immune response that can become chronic and overactive. If you suspect environmental toxicity may be contributing to your condition, it’s probably a good idea to get a test for chemical haptens and heavy metal antibodies.

Autoimmune thyroid disease has also been associated with a variety of infectious agents, including Rubella, Rubeolla, Epstein-Barr Virus, Retrovirus, Influenza B virus, Coxsakie virus and Yersinia. The mechanism in all cases is theorized to be cross-reaction between thyroid stimulating hormone (TSH) receptors and infectious agents. Once again, if you suspect an infectious agent is involved in your condition, a screening for these pathogens is a good idea.

Enhancing Regulatory T Cell Function

These strategies are all designed to enhance the function of regulatory T cells (also referred to as the Th3 system). Regulatory T cells are used to balance the activity between T-helper cells (Th1 & Th2) and T-suppressor cells (which “turn off” the immune attack).

Vitamin D has been shown to influence regulatory T cells, which in turn modulate T helper cell expression and balance the Th1 and Th2 response. For more on this see The Role of Vitamin D Deficiency in Thyroid Disorders.

The gut flora play a significant role in both cell-mediated (Th1) and humoral (Th2) immunity. Studies show that this protective role can be maintained and modulated by taking probiotics. Specific probiotic strains can influence the secretion of cytokines to help direct naïve helper T cells towards either a Th1 dominant, cell-mediated immune response or towards a Th2 dominant, humoral immune response.

Acupuncture has recently been shown to regulate the Th1 and Th2 immune response. In this study of patients with depression, both Prozac and acupuncture were shown to reduce inflammation. But only acupuncture restored the balance between the Th1 and Th2 systems. In another study, acupuncture reduced inflammation and lessened the symptoms of asthma by regulating the balance between Th1 and Th2 cytokines.

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Reducing Inflammation

Essential fatty acids (EFAs) play an important role in preventing and reducing inflammation. I’ve written an entire series of articles on this topic, which I’d recommend reading if you haven’t already.

The ideal ratio between omega-6 and omega-3 fatty acids is between 1:1 and 3:1. The average American ratio is closer to 25:1, and as high as 30:1, thanks to diets high in processed and refined foods. The result of this imbalance is – among other things – inflammation.

Two steps are required to bring this ratio back into balance. First, dramatically reducing consumption of omega-6 fats, and second, moderately increasing consumption of omega-3 fats. I explain how to do this in considerable detail in this article.

Another benefit of increasing intake of omega-3 fatty acids is that they have also been shown to help balance the Th1 and Th2 systems.

Aside from ensuring a proper balance of omega-3 and omega-6 fatty acids, following an anti-inflammatory diet/lifestyle and avoiding dietary triggers like gluten and iodine is essential.

Putting these general approaches to balancing the immune system into action should give you a good start towards getting the autoimmunity under control. But if you don’t see the results you’d like, I’d recommend working with someone who knows how to address your particular immune imbalance more specifically.

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Join the conversation

  1. Symptoms of Sjogren’s Syndrome can vary from one person to the next. Always consult with your doctor and dental specialist before rolling out improvements in your medicines. You may want to explore Sjogren’s Syndrome Natural Treatment alternatives.

  2. So, the article doesn’t really say what foods are high in omega 3, vs says what foods are high in omega 6.
    I have Hashimoto’s, and my specialist says I fluctuate between both Hyper and Hypo…plus, I am going through early menopause…GOOD TIMES!
    (It’s everything “they” said it would be…and more)
    But, I would like to know which one I should lean toward, just take a supplement for both, take it easy on those foods that are high in either.
    Also, I don’t understand the attached chart with the foods.
    I would just simply like to know what foods to avoid, eat more of and/or minimize.
    Thanks to anyone who can point me in the right direction.

  3. “To krill or not to krill, that is the question….” — Shrimpspear

    You and others (including Dr. K) recommend EPA/DHA in fish oil to combat inflammation & brain fog and also recommend against excessive iodine intake for those diagnosed with Hashimotos. I have both Hashimoto’s & chronic inflammation.

    Obviously I don’t take cod liver oil (anymore); too high in iodine.

    So, here is the rub: do I take fish oil for anti inflammatory and neuroprotective effect, or should I avoid it because of iodine content?

    I pray for an answer, Internet Oracle.

    • Hi MAS,

      Cod Liver Oil is NOT high in iodine. Fish Oil is high because they basically grind up everything inside the fish, but CLO is only the ground up fish liver, which has only trace iodine.

    • A year plus later…. The iodine issue you raised troubled me as well, so I did a lot of research, which resulted in the following. Iodine would be come an issue in the absence of Selenium, just like vitamin K2 can be come an issue in the absence of Vitamin D. So if you supplement with 200mcg of Selenium for one month (once a week after that), you can introduce iodine in the form of Potassium iodide, starting with ~50mcg and not over 225mcg – but don’t take my word for it and look it up….assuming you get to read this. From what I read (people in the know), balancing the two has a positive effect on TPO. I have Hashimoto and started slowly while monitoring my symptoms and looking at blood test. On the issue of cod liver oil, keep using it. I like to skip a day and use krill oil.

      I would like to hear from Chris, if there’s such a thing as omega 3 overdose. Based on chron-o-meter, my intake of code liver oil (one tsp ) and other nutrients, far exceed that of omega 6 (I’m mostly on high fat diet).

  4. Everyone recommends fatty acids but I have SIBO and because of that I am not able to absorb fat soluble vitamins well or not at all, but I am not sure. Most of my ailments are fatty acid deficient diseases and fat soluble vitamin deficiencies, such as dry eyes, sinus polyps, osteoporosis, etc. Because of my SIBO, will I be able to absorb a supplement, that is the question in my mind. Fixing the SIBO will fix me I think but no one knows how to do that yet and as time goes on, my allowed list of foods has shortened to meat and lettuce.

    • Cheryl,
      I have been managing my sibo several ways pretty effectively. When symptoms are bad I take a coarse of xifaxen and flagyl together . When they start to creep up I use 1000 mg of olive leaf, oregano oil capsules and deodorized garlic 2 x a day for a few weeks. I avoid gluten and Un fermented dairy . No corn syrup extra but I do ok with a lot of the stuff the specific carb diet says don’t eat I take a double dose of probiotics the kind with at least 8 types of bacteria

  5. I kinow the view by docs these days is that iodine and hashimoto’s don’t mix. Is that because Hashimoto’s is discovered to at times (in the Japanese for example, who eat lots of fish?) be an outcome of eating huge amounts of iodine-filled food? I wonder, because I did Swanson’s thriple iodine complex for eight months straight; my cholesterol dropped 35 points without any other explanation. My Hashimoto’s antibodies though remained at 500, To me, that is problematic. I assume these Hashi-toxins are bad for my body. Rights?

    • Swanson’s 12,500mcg is way too much; the recommendation is 225mcg from potassium iodide without any other additives. Kelp is easy to come by but isn’t recommended.

  6. Hi, my daughter was diagnosed with Hashimotos last May. Gone to functional medicine doctor. He says her goiter is due to bacteria in the mouth. We did test her and tests came back positive. I’ve been told that these tests not very accurate. Any advise? I’d like to help my daughter minimze the swelling in her neck, but due to Hashimotos , I’m concerned about stimulating her immune system.
    Thank you for your help