Both the gut lining and the gut microbiome play a role in the health of your thyroid and its hormones. The thyroid gland, shaped like a butterfly and based in the front of the neck, is critical to your energy production, and regulation of lipid absorption, and metabolism.

The gut lining and thyroid function

Anything that damages the gut lining, be it infection or irritation from foods, drugs, or toxins, may disrupt the integrity of the mucous membrane, aka intestinal permeability or “leaky gut”. Even emotional stress can affect the balance of the microbiome, which can trigger that initial irritation, inflammation and infection, looping back to physical stress. This creates a nasty cycle.

Intestinal permeability leads to consequences that activate the body-wide immune system which, in turn, has the potential to cross-react and damage tissues anywhere in the body, including the thyroid.  Evidently, thyroid diseases often co-occur with Celiac Disease (CD) and Non-celiac wheat sensitivity (NCWS).

The intestinal wall, when healthy, contributes to the conversion of the inactive T4 to active T3 thyroid hormone. This deiodinase activity contributes to total T3 availability.

Gut microbiome and thyroid function

Gut microbiota have an influence on the availability of essential micronutrients for the thyroid gland, ones often found deficient in cases of autoimmune thyroid disease. Here’s five reasons why micronutrients and a healthy microbiome matter to your thyroid function:

  1. Thyroid hormone synthesis requires: iodine, iron, and copper
  2. Converting inactive T4 to active T3 thyroid hormone selenium and zinc are needed
  3. Vitamin D assists in regulating the immune response.
  4. Supplementation of probiotics beneficially effects thyroid hormones and thyroid function
  5. Based on animal studies, supplementation of Lactobacillus and Bifidobacteria increase levothyroxine availability and stabilize thyroid function.

What are symptoms of low thyroid function?

  • slow speech
  • hoarse voice
  • puffy face
  • swollen thyroid gland
  • heavy menstrual periods
  • irregular menstrual periods
  • muscle and joint pain
  • difficulty thinking and processing
  • feeling depressed
  • forgetful
  • poor energy
  • muscle weakness
  • constipation
  • brittle fingernails
  • swelling in the lower legs, ankles, feet

Are there natural thyroid medications?

There is synthetic thyroid T4 replacements called levothyroxine or synthroid and T3 replacement called liothyronine. However, natural desiccated thyroid (NDT) may also be something to consider if diet and lifestyle changes don’t break through the fog. NDT provides both T4 and T3, which is good if there is an issue with conversion.

How can a naturopathic doctor help?

Naturopathic doctors ( ND’s) are medical trained and naturally focused. They treat the root cause. If there is an imbalance in the gut microbiome, or a leaky gut, the root cause of that, be it food sensitivity, infection, stress, or other irritation, will be addressed. ND’s run labs for microbiome analyasis, gut lining integrity, nutrient levels, thyroid stimulating hormone (TSH), T4, T3, and any antibodies to help rule out autoimmune thyroid disease. This helps determine what nutrients might be missing and what foods or nutraceutical dose to suggest and for how long. Naturopathic doctors with education in pharmaceuticals are able to prescribe natural desiccated thyroid. They are also very good at stress management and adrenal (HPA-axis) support with both nutrition, lifestyle and stress management programs. 


Knezevic, J., Starchl, C., Tmava Berisha, A., & Amrein, K. (2020). Thyroid-Gut-Axis: How Does the Microbiota Influence Thyroid Function?. Nutrients, 12(6), 1769.