Gut repair in Hashimoto’s disease

As you already know from the post gut health and thyroid autoimmunity, low thyroid hormones make it difficult to heal the gut. At the same time, an inflamed intestine and leaky gut syndrome contribute to thyroid diseases such as hypothyroidism and Hashimoto’s thyroiditis.

In the process of restoring the integrity of the immune system, addressing the gut issues is often the first and most important step in taking control over an autoimmune disease such as Hashimoto’s.

Get tested

It is important to find out the causes of gut dysfunction and remove antigen that triggers over reaction of the immune system. Intestinal permeability test from Cyrex Labs is a new method of testing for leaky gut syndrome. This test is available through the True Health Labs and provides you with information what exactly is causing leaky gut so your practitioner knows what to specifically target for faster and more efficient gut repair.

Food allergies could also contribute to leaky gut syndrome. The food allergies test at True Health Labs  targets not only triggers of immediate (IgE) allergic reactions, but also of possible sources of delayed (IgG) reactions – the so-called “hidden allergies”. It helps to check for a possible allergic reaction to more than 90 different foods.

Comprehensive stool analysis at the True Health Labs evaluates digestion and absorption, bacterial balance and metabolism, yeast (candida) and immune status. For those with irritable bowel syndrome, indigestion, malabsorption, and other GI-related problems this test can pinpoint to the cause of the disease.

The repair phase involves the restoration of the damaged or destroyed intestine that could be done using the supplements and making dietary changes.


L-Glutamine is a semi-essential amino acid found mainly in the muscles. It comes in food such as beans, poultry, fish and dairy products and also can be manufactured by the body on its own.

There is an increased demand in glutamine when a person goes through metabolic stress situations like trauma, surgery or critical illness such as cancer, severe burns and autoimmune conditions.

L-Glutamine is an important metabolic fuel for the intestinal mucosal cells because it keeps villi and absorption surfaces of the intestines clean and helps to restore their functions.

Supplementing with L-Glutamine can decrease intestinal permeability, prevent undigested food particles from entering the bloodstream and reduce systemic inflammatory response.

According to Dr.D.Kharrazian, who is specialized in treatment for Hashimoto’s disease, taking micronized L-Glutamine 1500 mg three times a day on an empty stomach between meals could help in the repair of the intestine.


The integrity of the intestinal barrier can be restored with a special diet. The elimination of all foods that cause allergies and contain gluten allows the intestine to heal with time.

Excessive use of antibiotics in medicine and agriculture is one of the major causes of dysbiosis.  Chemical compounds found in foods interfere with thyroid function and increase digestive distress. Consumption of whole organic foods without hormones and environmental toxins contributes to quicker recovery.

Somebody who has Hashimoto’s disease and is just starting to address their gut issues may feel lost because of the numerous restrictions which are difficult to follow. A great thing is that you actually do not need to reinvent a completely new diet to improve your intestinal health.

There are currently 3 approaches to choose from that are most suitable for people with Hashimoto’s for the gut repair phase:

All these approaches can help to repair intestinal damage and overcome candida overgrowth.

However, many people with Hashimoto’s can improve by adopting less drastic dietary changes by going on the Paleo diet. Paleo diet has been found very effective in restoring digestive health, reducing inflammation and is an excellent choice as a life-long solution or as a maintenance after the repair of the gut is completed.

Paleo way of eating is based on foods we were genetically designed to eat such as lean meats, fish and other foods that made up the diet of our Paleolithic ancestors many years ago.

Paleo diet is especially beneficial for those with Hashimoto’s disease who show signs of multiple food allergies and need to eliminate all grains and dairy. This diet can successfully address these health issues and can be enough to slow down the progression of autoimmune conditions especially in those who are on the early stage of Hashimoto’s disease.

However, GAPS diet and Leaky Gut Cure program have better results in “healing and sealing” of the gut in advanced Hashimoto’s and those with digestive issues.

10 Benefits of Paleo diet for Hashimoto’s patients

  • A Paleo diet is naturally casein and gluten free
  • Using good fats decreases omega-6 to omega-3 ratio and reduces inflammation
  • A Paleo diet is an anti-candida diet
  • A Paleo diet consists of whole foods that give maximum nutritional value. It is high in nutrients, vitamins and minerals which are necessary for optimal health and long term recovery
  • A Paleo diet does not normally contain foods that cause common food intolerance and allergies
  • With healing of the gut and the reducing of intestinal permeability you may improve your food intolerance
  • A Paleo diet improves blood pressure, stabilizes blood sugar, increases insulin sensitivity, lowers  total cholesterol, low-density lipoproteins (LDL) and triglycerides
  • A Paleo diet may help you to reduce body fat and lose weight
  • A Paleo diet has delicious recipes, is easy to follow and does not require calorie counting
  • A Paleo diet improves energy levels

How to replenish good bacteria?

Good intestinal bacteria prevents colonization of pathogens on the skin, the epithelium of eyes, nose, oral cavity, pharynx, urethra, penis and vagina. In addition to supportive thyroid and gastro-intestinal tract function, beneficial bacteria maintain a healthy immunity. Probiotics modulate both Th1 and Th2 immune responses in a positive way.

The practical and inexpensive way to prevent dysbiosis, restore intestinal flora and support immune system is to get more good intestinal bacteria  through a probiotic-rich diet.

The fermented dairy products, such as yogurt, buttermilk, kefir and others do not cause lactose intolerance or allergies as much as regular pasteurized milk does. Combining such products, especially kefir, with Paleo diet produces a synergetic effect in the healing of the gut, improvement of digestion and prevention of constipation.

Yogurt and kefir contain different bacterial cultures. Bacteria in yogurt keep the digestive system clean and provide food for the friendly bacteria that reside there. Kefir contains several major strains of beneficial bacteria which are not commonly found in yogurt such as:

  • Lactobacillus Caucasus
  • Leuconostoc
  • Acetobacter species
  • Streptococcus species

It also contains beneficial yeasts, which fight pathogenic ones and restores intestinal flora. Kefir provides the highest amounts of beneficial bacteria among the fermented dairy products. You could use kefir grains or a kefir starter kit with dry bacterial cultures to make kefir at home.

Good bacterial cultures are also available in probiotic supplements which could be an alternative approach for those who have dairy allergies and still cannot tolerate fermented dairy products.

About 65 to 80 billion of the beneficial bacteria are necessary to consume daily for optimal health and digestion with all food and supplements combined.

This equals approximately 150 to 200 ml of kefir per day or two capsule of Kendy Nutraceuticals Acti Flora Plus Prebiotic Probiotic taken on an empty stomach before meals. Acti Flora Plus comes in form of a pill and is a convenient and practical solution for those who have dairy allergies or are frequent travellers.

Article Gut health and thyroid autoimmunity


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

Restoring your digestive health by J. Rubin, J. Brasco, Twin Streams, 2003

Primal body, primal mind: Beyond the Paleo diet for total health and a longer life by a Certified Nutritional Therapist (CNT) and Board-certified in Holistic Nutrition Nora T. Gedgaudas, Healing Arts Press, 2011


Deep Nutrition: Why Your Genes Need Traditional Food by Dr. C. Shanahan, L. Shanahan, Big Box Books, 2008

The Paleo solution diet: The original human diet by R. Wolf, L.Cordain, Victory Belt Publishing, 2010

The Paleo diet for athletes: A nutritional formula for peak athletic performance by L. Cordain, J. Friel, Rodale Books, 2005


 The ultimate nutrient Glutamine by Judy Shabert, Avery; First Printing edition, 1994

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

Effect of glutamine on change in early postoperative intestinal permeability and its relation to systemic inflammatory response. World J Gastroenterol. 2004 Jul 1;10(13):1992-4

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