Hashimoto’s Disease: The Link between Thyroid and Leaky Gut

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Hashimoto’s Disease: The Link between Thyroid and Leaky Gut

Hashimoto's Disease, Hashimoto's, Hashimoto, hashimotos, hashimoto's disease symptoms, autoimmune, thyroid, hypothyroidism, underactive thyroid, overactive thyroid, autoimmune diseases, autoimmune conditions, leaky gut, autoimmunity, immune system, auto-immune conditions, Graves' Disease, antibodies, stress, natural health
Dr. Doni explores the relationship between Hashimoto's Disease and Leaky Gut, and offers advice on addressing auto-immune hypothyroidism.

Part 10 of Dr. Doni’s Series on Leaky Gut

In this series, we are looking in detail at Leaky Gut, a condition that is very common, yet poorly understood. We have examined what it is, how to find out if you have it, and how to treat it—as well as how it relates to other common conditions such as IBS, depression, and heartburn.

This time, following on from last week’s article on how Leaky Gut causes autoimmunity, we will shine a light on how this autoimmune response can specifically attack the thyroid gland, causing it to either under- or over-perform and cause a whole raft of long-term health problems.

This is an extremely common problem, one that is becoming increasingly so, but is often not identified by standard medical exams and blood tests. So let’s try to understand the scale of the problem and what we can do about it.

Two Common Thyroid Conditions

One in twelve people in the U.S. will develop a thyroid condition during their lifetime. Women are more likely to have issues with their thyroid than men, but it occurs in both sexes and in children as well.

There are several possible causes of sub-optimal thyroid function, but the biggest cause is auto-immunity (when the immune system attacks the thyroid as if it shouldn’t be there). The two forms of auto-immunity to the thyroid gland are Graves’ disease and Hashimoto’s disease:

  • In Graves’ disease, the thyroid goes into overdrive and over-produces thyroid hormone. I’ll go into more detail about Graves’ next week.
  • With Hashimoto’s, on the other hand, the thyroid function decreases1 and this is what we’re going to focus on today.

Hashimoto’s is the most common cause of low thyroid function (hypothyroidism), affecting 90% of people with low thyroid function. Studies indicate that people with Hashimoto’s have auto-antibodies that attack their thyroid gland, destroying the gland itself and thus decreasing its production of thyroid hormone.

In many cases, the auto-antibodies are found in blood work before they have damaged the thyroid gland and before function has decreased. Once the body starts making auto-antibodies, it is more likely to make antibodies to multiple organs and cells causing other auto-immune conditions such as Celiac, Crohn’s, Type 1 Diabetes, and/or pernicious anemia. This is borne out by research that shows that many people with Hashimoto’s also test positive for other auto-immune conditions.2, 3

Most practitioners are not trained to address the underlying causes of Hashimoto’s. The standard medical approach is to simply fill in for your damaged thyroid gland with synthetic thyroid hormone, most often a prescription medication called Synthroid.

So when you visit your doctor’s office, they may not even test for, or mention, thyroid auto-antibodies because it doesn’t change their treatment.

Still, for millions of people, if the tests are never completed, or if their results are considered “within range,” they may never be diagnosed. Others may take a dose of Synthroid for decades without ever feeling better.

How to Know If Your Thyroid Is Under-Functioning

One of the key tests is for levels of Thyroid Stimulating Hormone (TSH) produced by the pituitary gland in the brain. This is the hormone that tells the thyroid gland to produce thyroid hormone.

If the brain perceives too little thyroid hormone, then the TSH level will increase in order to tell the thyroid to make more. T4 is the inactive thyroid hormone that is converted into the active thyroid hormone T3. 

That conversion occurs in cells throughout the body and is dependent on iron, selenium, zinc, and other nutrients. In the case of nutrient deficiencies, stress, elevated cortisol, or low mitochondrial function, the conversion to T3 is decreased, and an inactive form, called reverse T3 may be overproduced.

All of these thyroid hormones should be tested to better understand the state of your thyroid activity. Ask your doctor to check: TSH, free T3, free T4, and reverse T3.

Endocrinology journals indicate that TSH levels in blood work should optimally be between 0.5 and 2.5 (when taking thyroid hormone, it should be between 0.5 and 1.5), and a higher number indicates lower thyroid function.4

Keep in mind however, that TSH is produced by the brain in response to how much thyroid hormone is available in the pituitary gland and is not considered to be the be-all and end-all when it comes to determining thyroid function or thyroid hormone activity because it does not necessarily reflect thyroid function in other areas of the body.

It is important to also consider symptoms and body temperature (part of the role of your thyroid is to regulate your body temperature), as well as free T4, free T3, and reverse T3 when determining whether you may have lower thyroid function.

The auto-antibodies that can be tested in the blood are thyroglobulin antibody (ATA or TGAb), thyroid peroxidase antibody (TPO), and thyroid stimulating antibody (TSI). TPO and TSI can trigger Graves’ disease, while ATA and TPO cause Hashimoto’s disease.

Testing for these auto-antibodies will help you to know whether autoimmunity is an underlying cause so that you can address it. The best way to address it is to understand what causes it, so let’s discuss that more first.

Why is Hashimoto’s Becoming More Common?

Two reasons: Stress and Leaky Gut.

As humans, we live in a constant state of risk for Leaky Gut. Our lives are filled with stresses, day in and day out. We are exposed to toxins in our homes, during our commute, when traveling, and in our office environments.

Medications are commonly prescribed to address infections, belly-aches, headaches, joint pain, tooth repair, and even for screening exams that damage our intestinal lining and make it harder for our bodies to keep up.

Then, on top of all that, we are bombarded with processed and fast foods that are too often gluten-based—and not just any gluten, but super-concentrated gluten that is chewier and tastier than it used to be and far worse for our digestive systems.

As we saw in my article on acid reflux, all these things—stress, toxins, gluten, and medications (especially antibiotics and NSAIDS)—can cause Leaky Gut. And Leaky Gut is associated with autoimmunity (as we discussed in the prior article).5

We know that genetics play a role in Hashimoto’s, and certainly by having a family history of Hashimoto’s, you are more likely to have it yourself. However, it is stress that turns on genetic mutations and stress itself—whether emotional stress (like a death, divorce, or trauma) or physical stress (like injury, lack of sleep, or any other condition that triggers a stress response in your body)—also causes autoimmunity.

When we look beyond thyroid function and combine it with adrenal distress (where cortisol levels soar or plummet, negatively affecting thyroid hormone production) and psycho/emotional and physical stresses (which are known to both lower thyroid function and increase the likelihood of auto-immunity), it is easy to see why hypothyroidism and Hashimoto’s are becoming so common.

And just in case you need more convincing, here are some other reasons why Hashimoto’s is increasing:

  • Anxiety makes it more likely that you’ll also have Hashimoto’s.6
  • Cigarette smoking is a known toxin and a stress on the body. It is also known to increase the likelihood of both Graves’ and Hashimoto’s.
  • Gluten sensitivity (which affects 1 in 4 people) and Celiac disease (which affects 1 in 111) involve the production of antibodies to gliadin (the protein in gluten) which looks similar to the thyroid gland, and this leads the immune system to attack the thyroid.7

And it doesn’t stop there. Even if you don’t smoke, and even if you eat gluten-free, you are still at risk of developing Hashimoto’s unless you fully engage in a lifestyle that involves getting plenty of sleep, stress recovery, organic produce, and high-quality nutrients.

How Does Low Thyroid Function Feel In Your Body?

This is an important question because these are symptoms that develop slowly over time and, taken separately, are not that serious.

These symptoms are easy to take for granted or not even notice. Taken them all together however, we start to see a pattern that could lead us to a diagnosis of hypothyroidism and treatment that will make you feel better.

There is a further complication in that not everyone experiences the same symptoms and many of the symptoms associated with an underactive thyroid could also be caused by other conditions.

Some of the most commonly reported issues I hear from my patients who have low thyroid function are:

  • Fatigue—feeling tired all the time
  • Weight gain and difficulty losing weight
  • Constipation
  • Coarse hair and/or hair loss
  • Dry skin
  • Feeling cold often, such as cold hands and feet
  • Frequent colds and other infections
  • Frequent headaches
  • Joint pain
  • Menstrual irregularities (missing periods or severe cramps)
  • Difficulty conceiving a pregnancy
  • Mental fog
  • Depression or low mood

Some people, but not all, have thyroid nodules. Others may have an enlarged thyroid, called a goiter. But many people may not have any reason to think their thyroid is struggling unless they are to be tested for thyroid auto-antibodies: anti-thyroglobulin and thyroid peroxidase antibody.

Once you know whether your immune system is making these antibodies, whether you are taking thyroid replacement medications or not, you can start taking steps to decrease the production of these antibodies that are attacking your thyroid and shift the immune response back to what it should be doing – protecting you from bacteria and infection.

4 Steps to Address Hashimoto’s Disease

Here are four steps you can take to begin this shift:

  • Step 1: Avoid gluten and dairy products. Both gluten and lactose (the sugar in dairy products) have been associated with the development of thyroid antibodies.7,8,9 If you’d like help doing this, consider using the guided elimination diet that I have developed, which I call the Stress Remedy Program (7-day or 21-day version).
  • Step 2. Identify Leaky Gut and start addressing it. Leaky Gut is known to make auto-immunity more likely in general, and furthermore, inflammation from Leaky Gut as well as the imbalanced digestive flora that often occurs with Leaky Gut are both associated with Hashimoto’s.10,11 For information on how to address Leaky Gut, go back to the 2nd article in this series (here) where I talk about how to test for Leaky Gut and then the 3rd article (here) about how to treat it.
  • Step 3. Take Selenium.* 200 to 400 mcg is the dose that has been shown to effectively reduce thyroid antibodies.12 Be sure to choose a high-quality selenium-methionine such as this product that you can find in my online store.
  • Step 4. Optimize adrenal health. As we’ve discussed, when cortisol levels are higher than they should be due to exposure to stress, this will disrupt your immune system, digestion, as well as your thyroid function. Based on my approach described in my book The Stress Remedy, you can bring your cortisol levels back to optimal which is essential for bringing Hashimotos to a halt.

There are more treatment options available, and they may be necessary for your case, but in my practice I’ve seen thousands of cases of Hashimoto’s completely resolve with just these 4 steps.

To achieve these same results, be sure to choose a practitioner with extensive training and experience with autoimmunity, Leaky Gut, adrenal stress patterns, and thyroid conditions.

Getting Help with Hashimoto’s Treatment and Ongoing Care

For a comprehensive overview, The Living with Hashimoto’s Summit is a good place to start. Even if you can’t attend live, you’ll get access to the recordings if you register here.

This Summit as an online event where those living with Hashimoto’s or those who have thyroid conditions, can gain tools, insights, and perspectives from top experts to live with fewer or even no symptoms at all.

leaky gut, digestion, healing

As I always emphasize, everyone is unique and may need more specific treatment. For individual help, please consider setting up a comprehensive breakthrough session with me. During this session, I will review your case and we can decide on the best approach for you, whether that’s my specially developed Leaky Gut Package, or my Signature Wellness program. Either way, I encourage you to start taking your health into your own hands and making choices that will benefit your future.

It is possible to feel better. And it is possible to calm an autoimmune response to the thyroid.

Please subscribe to my newsletter to be sure you don’t miss future articles, and with it I’ll send you a free ebook – A Guide To Adrenal Recovery.

Next week, I’ll go deeper into Graves’ Disease and hyperthyroidism — what happens when your thyroid is over-producing.

–Dr Doni
24th September 2015

*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.


  1. American Thyroid Association.
  2. Dong YH, Fu DG. Autoimmune thyroid disease: mechanism, genetics and current knowledge. Eur Rev Med Pharmacol Sci. 2014;18(23):3611-8.
  3. Pyzik A, Grywalska E, Matyjaszek-Matuszek B, Roliński J. Immune disorders in Hashimoto’s thyroiditis: what do we know so far? J Immunol Res. 2015;2015:979167.
  4. Wartofsky L & Dickey RA. The evidence for a narrower thyrotropin reference range is compelling. Journal of Clinical Endocrinology and Metabolism 2005 90 5483–5488.
  5. Fasano A. Leaky gut and autoimmune disease. Clin Rev Allergy Immunol. 2012;42(1):71-78.
  6. Carta MG, Loviselli A, Hardoy MC, Massa S, Cadeddu M, Sardu C, Carpiniello B, Dell’Osso L, Mariotti S. The link between thyroid autoimmunity (antithyroid peroxidase autoantibodies) with anxiety and mood disorders in the community: a field of interest for public health in the future. BMC Psychiatry. 2004 Aug 18;4:25.
  7. 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
  8. Jiskra J1, Límanová Z, Vanícková Z, Kocna P. IgA and IgG antigliadin, IgA anti-tissue transglutaminase and antiendomysial antibodies in patients with autoimmune thyroid diseases and their relationship to thyroidal replacement therapy. Physiol Res. 2003;52(1):79-88.
  9. Asik M, Gunes F, Binnetoglu E, Eroglu M, Bozkurt N, Sen H, Akbal E, Bakar C, Beyazit Y, Ukinc K. Decrease in TSH levels after lactoserestriction in Hashimoto’s thyroiditis patients with lactose  Endocrine. 2014 Jun;46(2):279-84.
  10. Mori K1, Nakagawa Y, Ozaki H. Does the gut microbiota trigger Hashimoto’s thyroiditis? Discov Med. 2012 Nov;14(78):321-6.
  11. Kyriacou A, McLaughlin J, Syed AA. Thyroid disorders and gastrointestinal and liver dysfunction: A state of the art review. Eur J Intern Med. 2015 Aug 7. pii: S0953-6205(15)00243-5.
  12. Gärtner R, Gasnier BC, Dietrich JW, Krebs B, Angstwurm MW. Selenium supplementation in patients with autoimmune thyroiditis decreases thyroid peroxidase antibodies concentrations. J Clin Endocrinol Metab. 2002 Apr;87(4):1687-91.
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  1. Dr. Doni has done such miracles with my Hashimoto’s, and leaky gut, and other autoimmune issues and my adrenals. She is absolutely amazing. If you are having problems, contact her!

  2. Thanks so much for this! I’ve been looking into thyroid disorders, and while I eliminated Graves’ disease, I didn’t know much about Hashimoto’s disease. I match most of the symptoms and will start taking Selenium right away, see if it helps. One last question–what kinds of tests would a doctor need to do to establish Hashimoto’s disease?
    Thanks a million for the straightforward information.

    • Hashimoto’s is established when the blood test for thyroid antibodies comes back positive or elevated. The most common two antibodies tested are anti-thyroglobulin and thyroid peroxidase antibody. I’m glad the info was helpful and I look forward to hearing what you notice with taking selenium.

  3. Due to at least 8 doctors ( including naturopath) I think I have been on about 9 months of elimination diets… none of which have helped my unexplained weight gain and inability to lose. I’ve had treatment protocols for leaky gut, blastocystis hominids, thyroid etc. but none of them have made the slightest difference and I’m guessing therefore didn’t ” heal” those problems. Needless to say eliminating soy, gluten, dairy, soy etc. hasn’t been the answer. From reading your blog that looks like what you would prescribe if I came to see you. I’m looking for a practitioner to help me but I already know that that type of elimination diet hasn,t worked for me at all… then what???

  4. drdoni
    Would you know if there is any research material available that indicates even after complete removal of thryoid that Hasimoto’s Disease is still active in the body? I’ve been trying to locate medical/scientific evidence to this.fact and Leaky Gut sounds a very logical solution.

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