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I felt a great disturbance in the microbiome…

gut problems
July 2, 2018

Relationship between disturbance of microbiome and Hashimoto’s thyroiditis
What is Hashimoto’s Thyroiditis?

Hashimoto’s thyroiditis is an autoimmune disorder in which the immune system of the body attacks the thyroid gland, a gland which is located beneath the Adam’s apple in your neck. This gland forms a part of the endocrine system of the body which secretes various hormones to coordinate multiple functions of the human body.
Inflammation due to Hashimoto’s thyroiditis, which is also referred to as chronic lymphocytic thyroiditis, results in hypothyroidism. Hashimoto’s thyroiditis is the most common cause of hypothyroidism or underactive thyroid in the USA. It usually affects females in the middle age-group but it may occur in males and females of any age group and also in children.

What are the causes of Hashimoto’s thyroiditis?

Hashimoto’s thyroiditis is an autoimmune disease in which the immune system produces antibodies, which damage the thyroid gland. It is not clear what causes the immune system of the body to attack the thyroid gland. According to the belief of some scientists a bacterium or virus may trigger this response while according to others it may occur due to a genetic mutation. Ultimately like most autoimmune conditions it appears a triad of genetics, environment and triggers create a perfect storm with resulting tissue damage and symptoms (even if TSH is balanced within the normal range).

How is the thyroid affected by the microbiome?

There has been growing evidence that imbalances or dysbiosis of intestinal microbiome and over abundance of unfriendly bacteria in the gut can negatively affect functioning of thyroid gland and may even trigger autoimmune diseases including Hashimoto’s thyroiditis.

The thyroid majorly produces the hormone T4 which is the inactive form and it requires to be converted to the active form T3 before it can be used by the body cells. 20% of T4 hormone is activated or converted to T3 in the intestines by the friendly bacteria present there. Imbalance in gut microbiome will affect the active hormone available for use by the cells, resulting in a state of low thyroid or hypothyroidism.

One of the main roles of friendly bacteria present in the gut is of strengthening the walls of the intestines, protecting it against pathogenic organisms and preventing the occurrence of leaky gut. When that barrier is not present large food particles and foreign matter pass out of intestines into your body starting a response by the cells of the immune system. Presence of prolonged immune response in the body can trigger production of antibodies against healthy cells and tissues resulting in autoimmune disorders such as Hashimoto’s thyroiditis.

When the intestinal microbiome is imbalanced, long-term damage and inflammation may occur in the body, which may result in production of cortisol (the stress hormone) by the adrenal glands. Over time, excessive cortisol may suppress the function of thyroid gland, reduce the quantity of hormones secreted by the thyroid and also inhibit the conversion of inactive T4 to its active form T3.

A study published in the journal Biomedicine and pharmacotherapy demonstrated that patients with Hashimoto’s thyroiditis have intestinal microbial dysbiosis and they showed an increased growth of the harmful bacteria E. coli. Another study published in discovery medicine concludes that dysbiosis in the gut may result in autoimmunity that may lead to Hashimoto’s thyroiditis.

How can we determine there is a problem with the microbiome?

Stool testing (I prefer a 3 day collection from Drs Data) can pick up on both functional and pathologic changes. It can tell us about inflammation, absorption and whether there is a healthy microbial balance. Pre and post stool testing is one of the most important tests in functional medicine because we have as much as 70% of our immune system in the gut! Treatment can be customized with the information found in this lab and it many times can pinpoint the trigger creating the autoimmune storm.

How to restore your intestinal and microbial health?

Prebiotics are the foods on which your gut bacteria thrive. Prebiotics such as bananas, garlic and onions contain dietary fiber and nutrients to feed intestinal bacteria and release by products of metabolism such as short chain fatty acids which help in maintaining health and preventing disease. Some of the prebiotic foods are:

  • Garlic
  • Onion
  • Jicama
  • Asparagus
  • Artichokes (Jerusalem)
  • Bananas
  • Pulses (beans, lentils, chickpeas etc.)
  • Fermented dairy & Ghee (butyric acid)

Probiotics are a kind of good bacteria, which on administration will keep your intestine healthy. They may be present in certain fermented foods that contain active live bacterial cultures such as yogurt.

Eating a diet rich in prebiotics and probiotics with live cultures plays a vital role in maintaining the balance of your gut flora. You can also eat fermented foods like kimchee, kefir, sauerkraut and kombucha as they contain live microbes and help in improving the health of the intestinal microbiome. Ensure that you get fermented foods with live cultures and not foods that are pasteurized.

Let Your Gut Soar,
Ian Hollaman, DC, MSc, IFMCP


  1. Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou, YJ, Ma C, Naseem Z, Wu X, Shi P, Xu J. Molecular estimation of alteration in intestinal microbial composition in Hashimoto’s thyroiditis patients. Biomedicine & pharmacotherapy. November 2017; 95:865-874.
  2. Hashimoto’s Disease. 2018. Available at: https://www.mayoclinic.org/diseases-conditions/hashimotos-disease/symptoms-causes/syc-20351855. Accessed June 29, 2108.
  3. What your gut bacteria need to thrive with Hashimoto’s. 2018. Functionalhealthnews. Available at: http://functionalhealthnews.com/2017/08/what-your-gut-bacteria-need-to-thrive-with-hashimotos/. Accessed June 29, 2018.
  4. The role of fermented foods & probiotics in gut health. Ignitenutritionca. Available at: https://ignitenutrition.ca/blog/fermented-foods-probiotics-help-gut-health/. Accessed June 29, 2018.
  5. Does the gut microbiota trigger Hashimoto’s thyroiditis? Discoverymedicine. Available at: http://www.discoverymedicine.com/Kouki-Mori/2012/11/27/does-the-gut-microbiota-trigger-hashimotos-thyroiditis/. Accessed June 29, 2018.
  6. Dysbiosis and thyroid dysfunction. All roads lead to the microbiome. Hypothyroidmom. Available at: https://hypothyroidmom.com/dysbiosis-and-thyroid-dysfunction-all-roads-lead-to-the-microbiome/. Accessed June 29, 2018.

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