The Thyroid Gut Connection + 4 Steps to Heal Your Gut

Dr. Jolene BrightenPublished: Last Reviewed: Thyroid & Hormone Balance Leave a Comment

If you have thyroid symptoms, but your labs are normal, it may be that your gut function is impacting your thyroid health. Chances are if you've made a trip to your endocrinologist for your hypothyroidism you've heard that your condition is genetic, there's a prescription for it, and that's about all you can do. It's an autoimmune thyroid disease. Period. I'd even venture to guess that there was no mention of your gut health at all…let alone the thyroid gut connection. 

You may be wondering why would your endocrinologist talk to you about your gut? In the conventional medicine paradigm, the endocrinologist's job is to care for your hormones, while the gastroenterologist cares for your gut. But I'm here to tell you that they are connected and you must address both if you are to restore the function of your thyroid.

Leaky Gut and Hypothyroidism

Hashimoto's, or autoimmune thyroid, is the number one cause of hypothyroidism, underactive thyroid, in the United States. And while not all causes of hypothyroidism are well understood, we do know that if you have an autoimmune condition, then your immune system is not behaving as it should.

And where is the majority of your immune system located? Your gut!

Gut Immune Health and Hypothyroidism

Your gut has the important job of digesting and absorbing nutrients. But in addition to that, it is also tasked with regulating what passes through the lining of the intestine to enter your body and what must be kept out. 

It has been estimated that your gut houses anywhere from 70-80% of your immune system. This aspect of the immune system, known as the gut associated lymphoid tissue (GALT), contains B cells and T cells. The immune system can become triggered by infectious agents, food particles, and other proteins that make their way through the lining of the intestine and into the blood stream. When the intestinal lining substantially increases in permeability, in a condition known as “leaky gut” or in medical terms, intestinal hyperpermeability, this can cause the immune system to mount an attack against the foreign invaders. This is one mechanism that has been shown in the research to lead to autoimmune diseases like Hashimoto's thyroiditis, the number one cause of hypothyroidism.

Exposure to these “non-self” proteins or antigens stimulates the immune system to produce antibodies.The job of antibodies is to tag foreign proteins for destruction. However, in the case of molecular mimicry, the amino acid sequence of the non-self protein that has been tagged for destruction closely resembles an amino acid sequence of self proteins, aka your body tissues. When this happens, your immune system can mistake your tissues as foreign and begin to attack the target tissue, in addition to causing inflammation in the body.

The job of the gut mucosa or intestinal wall is to allow nutrients to pass through for absorption and utilization in the body. At the same time, the intestinal lining should keep harmful proteins from entering. But in cases of leaky gut, these proteins are able to cross this protective barrier and trigger an inflammatory response.

Over time, after repeat exposure, the body will respond by creating antibodies, which can set off a cascade of autoimmune destruction of the thyroid tissue — resulting in Hashimoto's and eventually autoimmune hypothyroidism. Hashimoto's is the most common autoimmune thyroid disorder in which the body creates thyroid antibodies, flagging the thyroid gland for attack by the immune system.

Interestingly, two brain hormones— thyrotropin releasing hormone (TRH) and thyroid stimulating hormone (TSH)—play a role in the development of GALT. And the thyroid hormone, T4, prevents inflammation in the gut. 

Download your FREE Hormone Starter Kit with Recipes to Heal Your Gut and learn more about how optimizing thyroid health 

thyroid support supplement

The Thyroid Gut Connection

The gut microbiome impacts thyroid hormone iodothyronine conversion and storage, intestinal absorption of key nutrients that affect thyroid function, and immune system regulation. 

It is possible to have intestinal infections, dysbiosis (an imbalance in gut flora), and other gut conditions – even Celiac disease – without any overt gut symptoms at all. In fact, estimates indicate that the majority of people newly diagnosed with Celiac disease do not present with gastrointestinal symptoms. In many adults, neurological symptoms are often the first sign of Celiac disease. 

The most common autoimmune thyroid diseases are Hashimoto's Thyroiditis and Graves Disease (overactive thyroid), which often accompany both Celiac Disease and non-celiac wheat sensitivity.

Other gut conditions can present with rashes, headaches, mood swings, fatigue, cough, sinus congestion, agitation and more.

As gut pathogens, diseases, and dysbiosis go undetected or ignored, sometimes for years or even decades, the intestines become damaged and the mucosal lining is not able to do its job. For some patients, the diagnosis of an autoimmune disease is the first sign that there's even something wrong with the gut.

This is why gut health is a primary area of focus in reversing autoimmune disease. But beyond autoimmunity, your gut also supports your thyroid health in other ways.

Your Gut and Thyroid Hormone Conversion

The majority of the hormones your thyroid gland produces is mostly T4, which is inactive. It requires other tissues, like your gut to convert it to its active hormone T3, which is responsible for your energy, metabolism, body temperature and much more.

About 20% of thyroid hormone conversion takes place in the gut and it is the job of your healthy gut flora to make sure you get the amount of T3 you need. The bacteria in your gut can affect thyroid hormone levels via an enzyme called intestinal sulfatase.

Within the digestive tract, T4 is converted into two forms of T3—T3 sulfate (T3S) and triidothyroacetic acid (T3AC). Bacterial sulfatase in the gastrointestinal tract is the enzyme that converts T3S and T3AC into the active T3 that the cells use.

The conversion of T3S and T3AC into active T3 requires an enzyme called intestinal sulfatase. The health and balance of intestinal bacteria and flora is important in maintaining optimal thyroid hormone levels.

In some studies, Lactobacillus species have been shown to be beneficial to both gut and thyroid health. This is one way in which a probiotic may be helpful for thyroid hormones.

If your gut is not functioning optimally you can experience common symptoms of hypothyroidism, even if you thyroid is healthy due to the gut thyroid connection. Poor gut health can be a reason for thyroid symptoms.

Hypothyroidism Iodine and Gut 

A popular treatment for hypothyroidism is iodine supplementation. However, I caution patients with hypothyroidism against iodine supplementation for a number of reasons. One of which being that iodine supplementation may be toxic to the intestinal bacteria responsible for thyroid hormone reservoirs and T3 activation. 

It is recommended to keep iodine supplementation to 100 mcg or less if not pregnant and 200 mcg or less during pregnancy.

Gut Inflammation Inhibits Active Thyroid Hormone

Your microbiome regulates inflammation by inhibiting pro-inflammatory cytokines, like IL-6, TNF-alpha, NFK-b, and promoted anti-inflammatory cytokines like IL-10. If you're not familiar with these terms, don't worry. All you need to know is that the more these things proliferate, unregulated in your system, the more inflammation in the body.

When inflammation goes up, the adrenal gland hormone cortisol follows and this down-regulates the conversion to T3. The result can be common thyroid symptoms such as low heart rate, cold intolerance, constipation or infrequent bowel movements, fatigue, anxiety, and joint pain. 

While addressing gut health, it may also be necessary to also utilize Adrenal Support in order to facilitate thyroid function. 

Constipation Reduces Thyroid Hormone

Constipation is one gut symptom that can create hormone imbalances that lead to increased levels of estrogen. As estrogen levels increase, so do proteins aimed at keeping the hormone bound—specifically sex hormone binding globulin (SHBG). The same mechanisms that lead to excess estrogen being bound can cause thyroid hormone to also become unavailable and bound to the protein thyroid binding globulin (TBG).

Low levels of circulating thyroid hormone can cause impaired gut motility and constipation, which can perpetuate the vicious cycle of hormone imbalance.

This is another example of how gut function is crucial to having adequate levels of thyroid hormone available.

It is important to not that if you are perimenopausal or in menopause, estrogen hormone replacement therapy can also lead to lower levels of available thyroid hormone and a potential increased thyroid medication dose need. This may also be true for those who are taking oral contraceptive pills or hormonal birth control

Nutrient Deficiencies 

Several nutrients play a key role in healthy thyroid hormone levels. Iodine deficiency can impact thyroid hormone levels, but as discussed previously, it may have a negative impact on beneficial bacteria.

Copper and iron are both necessary for thyroid hormone production, but in some cases, low stomach acid that accompanies hypothryoidism may lead to deficiencies in both. Iron deficiency anemia can be found in those with low thyroid hormone. 

Zinc and selenium absorption can also be impacted by low thyroid hormone. But without these two micronutrients, the conversion from T4 to T3 can be impaired. 

Vitamin D is important in regulating immune response, including the function of immune cells. Low vitamin D has been shown to be a risk factor in the development of autoimmune thyroid disease. In some people with autoimmune thyroid disease, vitamin D supplementation may prove to be beneficial in helping resolve the autoimmune disorder.

All of these micronutrients are often deficient or low in patients with hypothyroidism and autoimmune thyroid disorders, which further contribute to poor thyroid function. Supplementing with these nutrients as part of a comprehensive thyroid supplement may be an important step in healing the thyroid. 

You'll find many of the key nutrients for thyroid health in my Thyroid Support formula

It is important to speak with your healthcare provider about potential nutrient deficiencies.

Thyroid-Gut Axis

In those with thyroid disorders, intestinal pathogens have been found to be present in higher rates than those without thyroid disease—underscoring the importance of the thyroid-gut axis in disease development. 

thyroid gut connection

Healing Your The Thyroid Gut Connection

You must heal your gut if you are going to improve thyroid health, balance hormones and reverse your autoimmune condition.

As a board certified naturopathic endocrinologist, I work with women in developing a treatment protocol that is specific to their individual needs. It is also important to begin with lab testing to create a more targeted treatment plan, which can also ensure healing is not delayed. I recommend working with a licensed health care provider who understands the importance of conventional and functional lab testing and can interpret them in conjunction with your symptoms.

In addition, it is important to have a licensed health care provider that has the ability to prescribe thyroid medications should you need them. Not all medical providers are permitted to prescribe medications and as such, they do not have the educational background to provide you the informed consent you need.

Here are some of the recommendations I make to my patients wanting to heal their gut and improve their thyroid health. Again, it's always best to do the work to understand what is at the root of your symptoms before you begin supplementing.

Four Phases to Gut Healing

1. Remove

All Potential Food Triggers.

Remove any possible food sensitivities for 3-6 weeks. One of the best ways to do this is with an elimination diet. This involves removing the top food allergens and other possible aggravators from your diet for 3-4 weeks. These are: Gluten, Dairy, Corn, Soy, Nuts, Beans/Legumes (including peanuts), and stimulants like chocolate, black tea, and coffee.

Don't hate me for saying coffee. I know no one likes to let that one go, but coffee may cross-react with gluten, irritating your intestines and well, you just don't know if it is making your symptoms worse until it has been removed.

You may or may not need to eliminate all of these. Most patients report feeling improvements in symptoms with a gluten free diet.

Unnecessary Medications.

Remove NSAIDs, proton pump inhibitors (PPIs), unnecessary antibiotics, and birth control. These medications can disrupt the gut thyroid connection on multiple levels. Talk with your doctor before discontinuing meds.

Life Stressors.

Like we mentioned above, chronic stress can actually change the makeup of your microbiome. It also disrupts the HPA-axis (hypothalamic-pituitary-adrenal), which affects pretty much all the hormones in your body.

Bacteria, Yeast, Parasites.

Ask your doctor to test for and treat any potential bacterial or yeast overgrowth and to assess for any parasites or pathogens. Again, some of these critters can live on happily undetected. If you're having any chronic gut or thyroid issues, best to test.

Potential Causes of Leaky Gut:

Between the cells of the intestinal lining is what is called the tight junctions. The tight junctions exist where the membranes of the cells come together to create a impermeable barrier in the intestinal lining. When these junctions are compromised, potential pathogenic bacteria and organisms, along with otherwise benign undigested food particles are allowed to pass through making their way into the blood stream. This is what is referred to as leaky gut and can be triggered by a myriad of factors.

Low Thyroid Hormone

Your gut depends on your thyroid hormones for it's health. It is essential in the function of the gallbladder, stomach acid production, and the integrity of the gut lining. Poor gallbladder function can inhibit liver detoxification and influence hormone imbalances. Low T3 and low T4, which occur in hypothyroidism, have been associated with the formation of gastric ulcers, along with abnormal reverse T3 levels. 


Long-term, regular use of NSAIDs (non-steroidal anti-inflammatory drugs) like ibuprofen can cause damage to the intestinal lining.

Birth Control Pill.

Birth Control Pills are one of the most common medications women take that can contribute to leaky gut. The pill induces inflammation and leaky gut within the intestines and can increase the risk of certain autoimmune diseases.

Read more about in this article: Is Birth Control Bad for Your Gut?

Antibiotic Use.

Antibiotics disrupt the normal healthy bacteria in your gut and leave it susceptible to harmful organism overgrowth.

Mom's exposure to antibiotic due to C-section or Group B Strep will cause disruption of both mom and baby's gut. Antibiotic use in general can disrupt intestinal flora and gut lining for 6-12 months.

However, keep in mind that antibiotic use can be necessary and lifesaving. Remember to discuss any medication changes or use with your healthcare provider.

Chronic Stress.

Stressors from work, life, and even exercise or strict dieting can alter your microbiome and lead to leaky gut.

High Sugar Diets.

Diets high in processed grains and sugars can lead to damaging hormonal swings, not to mention feed yeast, bad bacteria, and pathogens in the gut. There are so many reasons to cut down on the sugar.

Low Fiber Diets.

Diets rich in fiber, both soluble and insoluble, have been shown to reduce the risk of developing many gut pathologies, including leaky gut.

2. Replace

Digestive Enzymes.

Important digestive enzymes can become depleted with age or underuse. Taking targeted digestive enzymes for a period of time can be helpful when we're healing.

Betaine HCl.

If you have hypochlorhydria (low stomach acid) or become very full with meals, you may need the help of some Betaine HCl. Ask your doctor about adding this to your regimen.

Consider a Combination Digestive Aid.

I typically recommend digestive enzymes, HCL, and ox bile for the most comprehensive support.

Digest is comprised of a blend of digestive enzymes along with betaine HCL to support optimal digestion of proteins, fats, and carbohydrates. If you've ever been “glutened” and suffered the effects, know this product contains the special protease DPP IV that breaks down gluten and lactase to digest dairy. The use of Digest before meals may be helpful when patients experience gas and bloating after eating, constipation, or a feeling of fullness after eating only a small quantity of food.

Download your FREE Hormone Starter Kit with Recipes to Heal Your Gut and learn more about how optimizing thyroid health and learn more about how optimizing thyroid health

autoimmune thyroid disease bacterial overgrowth

3. Re-inoculate

Fermented Vegetables.

This is a great way to begin getting some beneficial bacteria going in your gut! Cultured, organic vegetables like pickles, sauerkraut, and other fermented vegetables like beets and carrots can promote the growth of good bacteria in the gut.


The effects of probiotics on gut health and immune system function can be incredibly beneficial in healing.

I recommend women with a thyroid condition consider oral spore based probiotics, lactobacillus and bifido species, along with a other beneficial organisms. I typically start my patients with Women's Probiotic as I've seen this provide great results.

Saccromyces boulardi is one strain that has been shown to protect against pathogens, increase beneficial immune response, protect gastrointestinal barrier function, and promote enzymatic activity so you can better absorb nutrients from your food!

If your digestive symptoms get worse or you experience extreme gas or bloating when eating probiotic foods or you suspect it's the effects of probiotics, spore based probiotics may be more tolerable. That's because in some cases of hypothyroidism, small intestinal bacterial overgrowth or SIBO, can also be present. In those cases, lactobacillus may make gut symptoms worse. This is when I will opt for a purely spore based probiotic instead of one that contains lactobacilli. 

4. Repair

Curcumin Extract.

While eating and drinking turmeric is beneficial to your overall health, I recommend supplementation with the active constituent, curcumin, while healing the gut.


Glutamine feeds the cells of your intestine, helping create a healthy intestinal lining.

Ginger Root.

Ginger root contains a number of constituents that help to reduce irritation and inflammation.

Zinc Carnosine.

A combination of the mineral zinc and the amino acid carnosine, this supplement increases healing time and boosts immune function.

Marshmallow Root.

Marshmallow root soothes and healing the intestinal lining and is good for the acute treatment of both constipation and diarrhea.

Aloe Vera.

Aloeis a potent anti-inflammatory that has been used with success in patients with Irritable Bowel Disease.

Getting to the root of your gut issues is an important step to healing your thyroid and your health. In my practice, I understand the importance of conventional and functional lab testing and can interpret them in conjunction with your story. I can help guide you on your next steps and help you understand your thyroid a whole lot better in my Thyroid Master Class.

Gut Healing Recipes

If you're looking for recipes to support thyroid and gut health, please download a free copy of my popular hormone balancing recipe guide

Turmeric-Ginger Glazed Salmon

The recipe combines the rich flavors of turmeric, ginger, and glazed salmon to create a delicious and nutritious dish that provides glutamine, zinc, curcumin, and ginger to support your gut health. It's easy to prepare and perfect for a satisfying and wholesome meal.


For the Turmeric-Ginger Glaze:

  • 1/4 cup extra-virgin olive oil
  • 1 tablespoon grated fresh ginger
  • 2 cloves garlic, minced
  • 1 teaspoon ground turmeric (contains curcumin)
  • 1 tablespoon honey (optional)
  • Salt and pepper to taste

For the Glazed Salmon:

  • 2 wild-caught salmon fillets (6-8 ounces each)
  • Salt and pepper to taste
  • 1 tablespoon coconut oil or ghee for searing

For the Zinc-Rich Side:

  • 2 cups baby spinach
  • 1/4 cup pumpkin seeds (pepitas)
  • 1/4 cup sliced almonds
  • Lemon wedges for garnish


  1. Prepare the Turmeric-Ginger Glaze:
    • In a small saucepan, heat the olive oil over medium heat.
    • Add the grated ginger and minced garlic and sauté for 1-2 minutes until fragrant.
    • Stir in the ground turmeric and honey (if using).
    • Season the mixture with salt and pepper to taste.
    • Remove the glaze from heat and set it aside to cool.
  2. Glaze the Salmon:
    • Season the salmon fillets with salt and pepper on both sides.
    • Heat the coconut oil or ghee in a skillet over medium-high heat.
    • Place the salmon fillets in the skillet, skin-side down, and sear for about 3-4 minutes until the skin is crispy.
    • Flip the salmon fillets and brush the turmeric-ginger glaze generously over the top.
    • Continue cooking for an additional 3-4 minutes or until the salmon is cooked to your preferred level of doneness and the glaze caramelizes.
  3. Prepare the Zinc-Rich Side:
    • While the salmon is cooking, place the baby spinach in a serving bowl.
    • In a dry skillet, lightly toast the pumpkin seeds and sliced almonds over medium heat for 2-3 minutes or until they become fragrant.
    • Sprinkle the toasted seeds and almonds over the spinach.
  4. Serve:
    • Place the glazed salmon fillets on a bed of the zinc-rich spinach and nut mixture.
    • Garnish with lemon wedges for a fresh burst of flavor.
  5. Enjoy:
    • Serve your Paleo Turmeric-Ginger Glazed Salmon immediately, and savor the combination of flavors and nutrients that support your health while adhering to a Paleo diet.

This dish not only tastes fantastic but also provides essential nutrients like glutamine, zinc, curcumin, and ginger in a Paleo-friendly way. It's a perfect choice for a nutritious and satisfying meal that fits within the Paleo dietary guidelines.

If you want to dig deeper to explore your root cause and find out more about how to heal your thyroid, please consider attending my Thyroid Master Class.

Dr. Brighten Essentials

Get Your FREE Hormone Starter Kit with

7 Day Meal Plan & Recipe Guide

This starter pack is exactly what every woman needs to bring her hormones back into balance!

Hormone Starter



  1. Arafah BM. Increased need for thyroxine in women with hypothyroidism during estrogen therapy. N Engl J Med. 2001. 344(23). 1743-9.
  2. Marqusee E, Braverman LE, Lawrence JE, Carroll JS, Seely EW. The effect of droloxifene and estrogen on thyroid function in postmenopausal women. J Clin Endocrinol Metab. 2000. 85(11). 4407-10.
  3. Tarique Hussain, Ghulam Murtaza, Dildar H. Kalhoro, Muhammad S. Kalhoro, Elsayed Metwally, Muhammad I. Chughtai, Muhammad U. Mazhar, Shahzad A. Khan. Relationship between gut microbiota and host-metabolism: Emphasis on hormones related to reproductive function. Animal Nutrition. 2021. Volume 7, Issue 1. 1-10.
  4. Al Bander Z, Nitert MD, Mousa A, Naderpoor N. The Gut Microbiota and Inflammation: An Overview. Int J Environ Res Public Health. 2020. 17(20). 7618.
  5. Fröhlich E, Wahl R. Microbiota and Thyroid Interaction in Health and Disease. Trends in Endocrinology & Metabolism. 2019. Vol. 30, No. 8.
  6. Knezevic J, Starchl C, Tmava Berisha A, Amrein K. Thyroid-Gut-Axis: How Does the Microbiota Influence Thyroid Function. Nutrients. 2020. 12(6). 1769.
  7. Freeman HJ. Neurological disorders in adult celiac disease. Can J Gastroenterol. 2008. 22(11). 909-11.
  8. Arrieta MC, Bistritz L, Meddings JB. Alterations in intestinal permeability. Gut. 2006. 55(10). 1512-20.
  9. Czarnywojtek A, Florek E, Pietrończyk K, Sawicka-Gutaj N, Ruchała M, Ronen O, Nixon IJ, Shaha AR, Rodrigo JP, Tufano RP, et al. The Role of Vitamin D in Autoimmune Thyroid Diseases: A Narrative Review. Journal of Clinical Medicine. 2023. 12(4). 1452.
About The Author

Dr. Jolene Brighten

Facebook Twitter

Dr. Jolene Brighten, NMD, is a women’s hormone expert and prominent leader in women’s medicine. As a licensed naturopathic physician who is board certified in naturopathic endocrinology, she takes an integrative approach in her clinical practice. A fierce patient advocate and completely dedicated to uncovering the root cause of hormonal imbalances, Dr. Brighten empowers women worldwide to take control of their health and their hormones. She is the best selling author of Beyond the Pill and Healing Your Body Naturally After Childbirth. Dr. Brighten is an international speaker, clinical educator, medical advisor within the tech community, and considered a leading authority on women’s health. She is a member of the MindBodyGreen Collective and a faculty member for the American Academy of Anti Aging Medicine. Her work has been featured in the New York Post, Forbes, Cosmopolitan, Huffington Post, Bustle, The Guardian, Sports Illustrated, Elle, and ABC News. Read more about me here.