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The Thyroid Gut Connection: How to Nourish Your Microbiome for Better Thyroid Health?

Medically reviewed by 
The Thyroid Gut Connection: How to Nourish Your Microbiome for Better Thyroid Health?

A healthy gut and its bacterial inhabitants (the microbiota) are essential for digestive and immune function and influence almost all aspects of the body, including the thyroid. The thyroid and gut are intrinsically connected, and many intestinal diseases are linked to thyroid issues.


How Does Gut Health Influence Thyroid Function?

The interactions between the gut microbiota and thyroid function are so intricate it has been termed the gut-thyroid axis.

Our intestinal bacteria influence micronutrient absorption, produce specific vitamins (vitamin K, folic acid, and B vitamins), break down dietary fibers, regulate the immune response, and impact neurotransmitters and signaling to our brain. All of these aspects affect the thyroid. (4)

Iodine, selenium, zinc, and iron are all needed for proper thyroid health. These nutrients must be assimilated appropriately to be utilized effectively by the thyroid.

The microbiota fermentation of dietary fiber leads to short-chain fatty acids (SCFAs), which serve as an energy source for our enterocytes (intestinal cells). These SCFAs, especially butyrate, also have been found to impact immune regulation (including the number of T-regulatory cells) and have anti-inflammatory effects. This would aid in preventing autoimmune thyroid disorders and support healthy thyroid output. (4)

Other connections between the gut and the thyroid are related to thyroid hormone levels. Iodothyronine-deiodinases are enzymes that converts thyroxine (T4) to reverse T3 (rT3), its inactive form. The activity of these enzymes has been found in the intestinal wall.

A healthy liver is also vital for thyroid hormone levels. (22-23)

Finally, microbiota affects neurotransmitters, including dopamine. Dopamine has been found to inhibit thyroid stimulating hormone (TSH), which can lead to alterations in thyroid levels. (4)

GI Disorders Associated with Thyroid Dysfunction

Hashimoto's Thyroiditis (HT) and Graves Disease (GD) are the most common autoimmune thyroid diseases (AITD) and often co-occur with Celiac Disease (CD) and Non-celiac wheat sensitivity (NCWS). (1-10)

In a small study with children, those with HT had higher markers of intestinal permeability, "leaky gut." (11-12)

Another connection to the thyroid-gut axis is that intestinal pathogens have been found at higher rates in those with thyroid disorders. Helicobacter pylori infections have been linked to HT. This organism, Yersinia enterocolitica, and other bacterial organisms have been associated with GD. (13-15)

Small intestinal bacterial overgrowth (SIBO) has associated with hypothyroid patients due to lower thyroid function, which slows digestive transit. Levothyroxine therapy has also been shown to increase bacteria overgrowth.

Furthermore, bariatric surgery, which impacts the absorption of nutrients, has been related to changes in thyroid stimulating hormone (TSH) and T3 levels. (16-18)

What Nutrients Are Important For Thyroid Function?

Iodine, selenium, zinc, and iron are all essential for thyroid function, and the microbiota impacts the uptake of all these nutrients. Associations between thyroid dysfunction and altered levels of these minerals have been found. (4, 24)


Iodine is perhaps the most recognized and debated nutrient for the thyroid. Approximately 15-20 mg of iodine is found in the average adult, most of it in the thyroid gland. Iodine is essential for thyroid function, and too little may result in goiter, thyroid nodules, and even thyroid cancer. (4)

Excess levels have also posed issues. Excess iodine intake can cause a transient reduction of thyroid hormone synthesis. Too much iodine has been found to induce hypothyroidism in high-risk patients and those with diets high in goitrogens. It can also cause hyperthyroidism in susceptible patients. Furthermore, areas with a high intake of iodine have been correlated to increased rates of papillary thyroid cancer. (4, 25)


60% of those with hypothyroidism are also diagnosed with iron deficiency, likely related to malabsorption. Iron is needed for proper iodine utilization and thyroid hormone synthesis.4, 26

Interestingly, due to incomplete absorption, iron supplements can increase colonic iron. This can alter the microbiota causing adverse effects on the thyroid. (4, 26)


Zinc is a cofactor of thyroid hormone production and for the enzyme 1,5′-deiodinase, which converts T4 to T3 and reduces metabolic rate. It also assists with oxidative stress as part of the superoxide dismutase enzyme and for hormone binding transcription factor, which is important for gene expression. (4)


Selenium helps regulate the immune system and is involved in several thyroid functions. It is part of various enzymes that protect the thyroid gland from free radicals and has been linked to microbiota balance. Some studies suggest it may lower levels of antithyroid antibodies, improve thyroid function and structure, and relieve clinical symptoms. (4, 27)

Vitamin D

Vitamin D has been stated to influence the thyroid through its immunomodulatory effects. Human studies often find a correlation between hypothyroid patients and thyroid hormones (TSH and T3) and lower levels of vitamin D. (4)

Overall nutrient status and microbiome support also may benefit the thyroid. Hashimoto's Thyroiditis (HT) and Grave's Disease (GD) patients commonly have altered microbiota, including Lactobacillaceae and Bifodacterium spp. Interestingly, it has been found that these bacteria also influence iron, selenium, and zinc levels. (4, 28)

How the Thyroid Influences the Digestive System

Thyroid hormone interacts with the gastrointestinal tract in several ways. For example, thyroid hormones indirectly impact digestive motility through catecholamines on the muscle cell receptors. Reduced motility has been found in hypothyroidism, and increased motility in hyperthyroidism. This can cause diarrhea and malabsorption in hyperthyroidism and constipation in hypothyroidism. (29-31)

Hypothyroid patients may also experience delayed gastric emptying due to autoimmunity or changes in the gastric mucosa. This can result in trouble swallowing (dysphagia) or heartburn. Impaired esophageal motility can also occur with both hyper- and hypothyroidism. (30, 31)

Thyroid disorders have been associated with autoimmune gastritis and esophageal compression. (30, 31)

Too much TSH decreases bile acids (BA) synthesis in the liver. Bile acids are needed to regulate lipids, glucose, and metabolism. (32)

The Thyroid/Gut Autoimmunity Connection

Autoimmune Thyroid Disease (AITD) is believed to be the result of the interaction of genetic predisposition, immune impairment, and environmental factors (i.e., micronutrients, gut microbiota). The gut microbiota regulates the immune system, modulates both the innate and the adaptive immune system, and impacts the development of gut-associated lymphatic tissue (GALT), where more than 70% of the entire immune system is situated. (4, 33-34)

An imbalance of commensal and pathogenic bacteria in the gut can lead to a loss of immune tolerance. It has been found that butyrate, through T-regulatory cells, may enhance immune balance and positively influence symptoms of AITD. (4, 34)

Celiac Disease is an autoimmune intestinal disease where the protein in gluten, gliadin, triggers an immune reaction that leads to severe inflammation of the intestine, atrophy in the absorptive surface of the small intestine, and increased intestinal permeability. Non-Celiac gluten sensitivity has similar symptoms and gut manifestations but likely activates the innate immune system. (4)

The resulting dysbiosis, bacterial overgrowth increasing intestinal permeability, and a shift to proinflammatory cells all impact nutrient absorption and immune regulation of the thyroid and result in AITD.(4,33-34)

How to Test for Thyroid Health

A comprehensive thyroid panel that includes TSH, T3, T4, FT3, FT4, reverse T3, and appropriate antibody testing (Anti-TPO, Anti-Tg) will provide objective measurements of how the thyroid functions. Functional reference ranges can be found here.

Hashimoto's Thyroiditis often has elevated thyroid-stimulating hormone (TSH), low levels of free thyroxine (fT4), and increased antithyroid peroxidase (TPO) antibodies. Early on in the disease, the patient may display signs of hyperthyroidism. This is why clinical symptomology and assessing labs are essential for proper treatment. (35)

It is also important to note that antibodies can fluctuate throughout the course of the disease. Thyroid treatment solely to treat antibodies is controversial regarding exact ranges and influence on symptoms, hypothyroidism manifestations, and mortality rates.(35-36)

The Top Comprehensive Thyroid Panels Ordered by Rupa Health Practitioners

How to Test for Gut Health

A comprehensive stool test that assesses digestive function, intestinal inflammation, the intestinal microbiome, and intestinal permeability will help to determine if these key components that impact the thyroid-gut axis need to be addressed.

Maldigestion measurements can help one assess if additional digestive support interventions, such as enzymes and bile salts, are needed to optimize the absorption and assimilation of vital nutrients that support thyroid functioning.  

AITD is correlated to both celiac disease and non-celiac gluten sensitivity, which both are caused by deregulations in immune function and intestinal permeability markers.

A SIBO test, H.pylori, and additional pathogens (infectious markers) can also be considered due to their connections to thyroid disorders and absorption markers, especially HT.

Top Comprehensive Gut Health Test Ordered by Rupa Health Practitioners

Micronutrient Testing

Over time, micronutrient-related malnutrition can lead to disorders like thyroid dysfunction but also are linked to anxiety, irregular heartbeats, neurological disorders, and low immune function. Many symptoms of chronic disease are further worsened by nutrient depletion.

The Cellular Micronutrient Assay by Cell Science Systems includes measurements for all the nutrients that support thyroid health covered in this article, Vitamin D, iron, iodine, zinc, and selenium.

The Top Rupa Micronutrient Panels Ordered by Rupa Health Practitioners

Root Cause Treatment for Thyroid Gut Connection

After a full health history and comprehensive labs, one can then embark on root cause treatment to address the underlying issues leading to thyroid and gut dysfunction.

The results of the GI Map or comprehensive stool panel can help one verify specific supplementation to address any digestive imbalance and microbial imbalance:

  • Digestive enzymes, bitters, bile salts, and intestinal integrity support (glutamine) can be used as necessary to support nutrient balance and improve gut health. (37)
  • Prebiotics and probiotics can help to assist with microbial diversity and balance the immune response.(4)
  • Saccharomyces boulardii helps to support intestinal permeability, SIgA (a marker of intestinal health and immunity), microbial balance, and has evidence for treating diarrhea. The latter can be important for hyperthyroid patients. (38)
  • Grapefruit seed extract has antibacterial and antifungal properties, which can support digestive health and may help with particular pathogen invasions. (39)
  • Ginger can be used to soothe the digestive tract and digestive distress. Scientific evidence supports that ginger can increase gastrointestinal motility, which is compromised in thyroid disorders. (40-41)
  • Omega-3 fatty acids with resolvins may assist with soothing inflammation and help with digestive issues. They have also been found to support vessel integrity which can be compromised by long-term, systemic inflammation. (42)
  • Essential oils such as peppermint and ginger, which have antimicrobial and gastrointestinal-supportive properties, can be implemented. They also have been shown to relax the mind-body and decrease stress, impacting gastrointestinal and thyroid function. (43)

A whole food, organic diet that incorporates a wide range of antioxidants from colorful fruits and vegetables is vital to replete thyroid nutrients. Plant polyphenols can also support gut health, intestinal barrier function, immune response, and microbiota balance.(44)

Supplementation with specific nutrients should be based on clinical symptoms and the result of micronutrient testing with particular attention to thyroid nutrients. (4)

If one is supplementing with vitamin D, it is important also to give its available cofactors, such as magnesium and vitamin K. This supports its bioavailability and activation and is essential for proper utilization and function of calcium. (45-46)

Decreasing stress and lifestyle factors such as sleep and supporting relationships should not be overlooked in their role in balancing thyroid and gut health. (47)

Finally, chemicals and environmental exposures are also something that may impact thyroid health and should be evaluated.


Simply treating thyroid hormonal levels with medication without assessing underlying root causes will not lead to the resolution of symptoms or heal the thyroid.

Serum thyroid hormones can help determine if there is dysfunction in thyroid hormone production, transport, receptor sensitivity, or thyroid utilization and removal.

Addressing gut health, determining optimal nutrient status, and optimizing nutrition and lifestyle factors from a personalized, functional medicine approach can help one regulate and regain balance of the thyroid-gut axis and is likely the missing link for many to regain better thyroid regulation.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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