Gut health and thyroid autoimmunity

Good bacteria perform a range of essential and health critical functions that support thyroid, digestive and immune systems. The intestinal lining is an important immune barrier that is responsible for more than 60% of the immune defence. Imbalances in digestion and intestinal flora causes the immune system to malfunction and can trigger autoimmune diseases including Hashimoto’s thyroiditis.

What dietary factors cause immune system imbalance?

The part of the immune system situated in the intestine is called gut-associated lymphoid tissue. It consists of several types of lymphoid tissues that store T- and B-cells.  These cells carry out attacks and produce antibodies against antigens to defend against potential threats.

Leaky gut syndrome, damage to the intestine, celiac disease or activity of bad bacteria causes an increase in permeability of the intestinal barrier and therefore compromises the natural defence mechanism of the immune system. The undigested particles of food, bacteria, parasites, molds and environmental toxins go undefeated through the barriers and trigger the autoimmune disease.

The following dietary factors could initiate an autoimmune response:

  • Overuse of medical drugs (antibiotics, NSAIDs, antacids). Treatment of re-occurring infections such as ear and nose infections often require antibiotics that lead to imbalance of the gut flora. Besides eradicating bad bacteria, antibiotics kill off the good bacteria as well as causing dysbiosis, overgrowth of bad bacteria (candida, helicobacter or parasites) and damage to the intestinal lining.
  • Poor digestive health, inflamed digestive tract and parasitic infections result in multiple illnesses such as indigestion, leaky gut, nutritional deficiencies, autoimmune diseases including Hashimoto’s, diabetes, lupus, multiple food intolerances and allergies that may first appear in adulthood. For example, H. pylory is a gut bacteria that can trigger overreaction of the immune system and lead to Hashimoto’s disease.
  • Food allergies contribute to the increase of intestinal permeability. The most common foods that cause allergies are dairy, eggs, gluten, soy, corn and food additives. Recent studies show that people with Hashimoto’s tend to have gluten intolerance or full-blown celiac disease that can trigger thyroid autoimmunity, malbsorption of many nutrients and nutritional deficiencies of selenium, magnesium, complex B vitamins, iron, vitamin D and many others.
  • Crossreactivity to foods other than gluten can cause irritation and damage to intestinal walls. Gluten has been shown to have a crossreactivity with 24 other common foods such as dairy, amaranth, yeast, chocolate, potatoes, sesame seeds and coffee. It means that those with gluten sensitivity can also react to these foods as they react to gluten and increase overreaction of thyroid autoimmunity.
  • Gluten-like proteins in other grains can also cause allergic reaction in sensitive individuals. According to research studies and Dr. Peter Osborne, corn gluten can cause damage to intestine in people with celiac disease and gluten intolerance. He noticed that about a half of his patients who followed gluten-free diet did not improved until they excluded ALL grains from their diets.
  • Another study that was published in the Journal of the American Dietetic Association found out that many packaged gluten-free grains and grain product are cross contaminated with gluten and are actually not gluten-free. If you have gluten intolerance or celiac disease you can show allergic reaction and cause intestinal damage by consuming those “gluten-free” foods.
  • Excessive iodine in the diet can cause goiter and trigger autoimmune thyroiditis in genetically susceptible individuals and can worsen an existing condition. It is advisable to make a reliable iodine test because iodine deficiency can also trigger Hashimoto’s.
  • Eating excessive amounts of sugars, flour and a diet high in refined and processed foods causes blood sugar swings which stimulate bacterial overgrowth and suppress immune function.  
  • Bad fats. Consumption of products high in trans-fats (margarine), omega 6 fatty acids (canola oil) and polyunsaturated and hydrogenated fats found in most processed foods promote chronic inflammation and autoimmune over reaction.
  • Environmental toxins in foods and water can interfere with thyroid function, contribute to digestive problems and penetrate the intestinal barriers causing the autoimmune response.

The dietary factors listed above contribute to adrenal exhaustion causing further complications in treatment of hypothyroidism and autoimmune thyroiditis. High cortisol levels suppress the immune function and promote conversion of active T3 thyroid hormone in its inactive form reverse T3.

Imbalances of the intestinal flora

Normal intestinal flora is comprised of hundreds of varieties of bacteria, which are specific to the human body. Besides leaky gut there are other intestinal imbalances contributing to low thyroid function and autoimmunity:

  • Dysbiosis

The deficiency or absence of good bacteria in the intestinal flora called dysbiosis or disbacteriosis. Up to 20% of thyroid hormone conversions from T4 to T3 take place in the intestines but only in the presence of the good bacteria. Having not enough benefical bacteria makes less active T3 hormone available.

  • Bacteria overgrowth

An abnormally high level of invaders such as candida, heliobacter pylori and parasites in the small intestine is called bacterial overgrowth. Bad bacteria can suppress the good bacteria, diminish thyroid function and interfere with absorption of thyroid medication and nutrients.

In the following video Dr. Bryan Walsh the author of educational program Fat is Not Your Fault designed specially for patients who have weight issues, explains how by producing toxins called lipopolysaccharides bad bacteria wreak havoc on multiple aspects of our physiology. He introduces 18 ways how gut dysbiosis ruins your health and negatively impacts thyroid function.

How thyroid function affects gut health?

The production of hydrochloric acid decreases with hypothyroidism causing hypochlorhydria. Food, especially containing protein does not digest properly increasing intestinal permeability, inflammation and susceptibility to infections.

Low thyroid hormones affect the function of the gall bladder and detoxification processes as well as impairing the conversion of T4 to T3 thyroid hormone in the liver. In addition, hypothyroidism slows transit time of the digested food leading to constipation, which in turn increases inflammation, infections and malabsorption.

Article Gut repair in Hashimoto’s disease

P.S. There is a lot more to discover about Hashimoto’s thyroiditis, so sign up for Outsmart Disease blog updates and get FREE e-mail course Nutritional guide for Hashimoto’s disease to learn more.


Why do I still have thyroid symptoms? When my Lab tests are normal: A revolutionary breakthrough in understanding Hashimoto’s disease and hypothyroidism. D. Kharrazian, Morgan James Publishing, 2009

Fiber menace: the truth about fiber’s role in diet failure, constipation, hemorrhoids, irritable bowel syndrome, ulcerative colitis, crohn’s disease, and colon cancer. K. Monastyrsky, Ageless Press, 2005

Good gut bugs: How the healing powers of probiotics can transform your health by K. Marsden, Little, Brown Book Group, 2010

Bacteria for breakfast: Probiotics for good health by Dr. Kelly Dowhower Karpa, Trafford Publishing, 2006

Association between hypothyroidism and small intestinal bacterial overgrowth. J Clin Endocrinol Metab. 2007 Nov;92(11):4180-4.

About Marina Gutner, PhD

Marina Gutner, PhD, researcher, medical writer, thyroid blogger, founder and Admin of Outsmart Disease who writes about life-changing treatments for hypothyroidism, Hashimoto's thyroiditis and autoimmune disease and how to balance hormones in women