Gut-Thyroid Connection: How Your Gut Bacteria Influence Thyroid Health

Do you feel tired all the time, like you have no energy? Do you struggle to warm up or find it hard to regulate your body temperature?  Does your metabolism seem stuck in the wrong gear?

If you answered yes to any of the above questions, I’m not surprised. 

Thyroid hormone and autoimmune thyroid diseases are one of the most prevalent medical conditions. 

So much so that thyroid disease in general is an epidemic

Because thyroid dysfunction does not discriminate – it’s not just a first world problem.

Developed countries are dealing with dysfunction conditions like Hashimoto’s thyroiditis (TH)—affecting 10-12% of the population worldwide.

While structural thyroid conditions like the disfiguring goiter are endemic to many third-world nations deficient in iodine. Goiter alone is thought to affect 200 million people globally!

Thyroid health is an enormous problem. 


Because your thyroid is responsible for many of your crucial metabolic and body functions – like immunity, metabolism, and energy levels.

But before we get too deep into the science, let’s have a better look at the little gland getting all this attention.

What is Your Thyroid?

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Just under your voice box sits your largest endocrine (or hormone) gland–the thyroid.

But it’s not at all big.

It’s shaped like a little bow tie or butterfly and weighs approximately 20g.

And it comprises many follicles—little spheres filled with thyroglobulin (TG) a protein bound to the thyroid hormones.

[We will talk more about our thyroid hormones shortly…]

Also tucked in behind each thyroid lobe (or butterfly wing) are even more thyroid glands—these are your parathyroid glands—there are 4 of them.

Parathyroid glands have cords rather than follicles. And they release parathyroid hormone (PTH) – important in regulating calcium.

Bone, kidneys and the intestine are PTH major targets.  Which raises an important point, not all tissues can detect all hormones. We will talk about this more later on.


But for now let’s investigate the thyroid hormones further.

Thyroid Hormones 101

Your thyroid secretes two major thyroid hormones, T3 and T4—which I’m sure you’ve heard of before.

In general, these increase your metabolic rate and are essential for normal growth. Most cells in the body respond to T3 and T4.


What’s the difference?

T4 is the inactive form and is then converted to T3 – for use in the body. 

This process creates a significant increase in free radicals – via oxidation reactions. We will look at minerals and supplements that fight these damaging free radicals a little later.  

Your doctor can request a simple blood test that measures your free T3 and T4 levels.

Next we have hormones that help create these thyroid hormones, let’s refer to them as thyroid helpers…

First, we will look at TSH.

TSH or thyroid-stimulating hormone does exactly what its name suggests—it promotes an increase in thyroid hormone synthesis.

And to work, TSH needs a series of biochemical steps to occur in the thyroid—the first (and most important) is the availability of iodine.


Another important thyroid helper is TBG.

TBG—thyroid-binding globulin, is bound to T3 and T4 when circulating in the blood.

The liver makes TBG, and it acts to increase the lifespan of our thyroid hormones by allowing the concentration of T3 and T4 to remain steady in our cells. 

And finally, we will mention TRH—thyroid-releasing hormone.

TRH comes from the hypothalamus (in your brain) and together with TSH function to increase T3 and T4 secretion.

As you can see, it’s not only the thyroid responsible for creating thyroid hormones – it’s a group effort.

And it becomes clear why thyroid problems are so prevalent…

… We need a complex balance for optimal function.

Why Thyroid Hormones Matter

Remember how we mentioned that not all tissues respond to all hormones? Well, thyroid hormones affect nearly every tissue in the body!

But not all tissues react the same way—some respond with metabolic consequences, others with growth. The following are some important metabolic functions of thyroid hormone:

  • Metabolism—increases rate of glucose, fat and protein uptake
  • Blood cholesterol level reduction
  • Body temperature increase—via increased sodium and potassium ion exchange
  • Mitochondria activity and numbers—affecting energy and heat production

Normal metabolism and body temperature need enough thyroid hormone to work properly.

Low levels have the opposite effects.

Now let’s look at the growth effects of thyroid hormone. The following body areas require adequate growth hormone to mature:

  • Bones
  • Hair
  • Teeth
  • Connective tissue—includes muscles
  • Nerves
  • Brain

There are a few important organs in there! Which emphasises why thyroid health is so important.

So what happens when thyroid health goes wrong?

Thyroid Related Disease Explored (with symptoms)

There are two general directions thyroid hormones can go awry.

Up and down.

We refer to these as hyper- and hypo-thyroidism.

Hyper meaning too much—and hypo is not enough.

You can read the general symptoms of both below.


As you’d expect, hypo causes the opposite symptoms to hyperthyroidism. But both can ultimately cause the thyroid gland to enlarge.

So what causes these altered thyroid hormone states?

Let’s have a look at the various thyroid conditions in both an elevated or depressed state.

Hyperthyroidism is associated with these diseases:

  • Grave’s disease—characterised by goiter and protruding eyes with autoimmune links
  • Tumours—including pituitary (elevated TSH)
  • Viral thyroiditis
  • Thyroid storm—sudden thyroid hormone release (by surgery, stress, infection or from unknown causes)

And hypothyroidism is associated with the following conditions:

  • Iodine deficiency—causes inadequate thyroid hormone which increases TSH levels and results in goiter (thyroid hormone levels remain in low to normal range)
  • Goitrogenic substances—chemicals that inhibit thyroid hormone synthesis (some drugs, bio-mimicry chemicals like chlorine like to receptors)
  • Thyroid gland removal
  • Pituitary insufficiency—lack of TSH secretion
  • Hashimoto’s disease—autoimmune condition with depressed thyroid function

Besides all this, it is now also becoming clear that gut conditions are closely associated with thyroid conditions.

The Thyroid-Gut Connection

Did you know that the two most common autoimmune thyroid diseases (Hashimoto’s and Graves) often co-occur with Celiac disease and Non-Coeliac wheat sensitivity!

Let’s take a closer look at this connection.

Both these conditions show inflammation and a compromised gut lining.

A damaged (leaky) gut-lining can allow antigens and other reactive substances to pass through into the bloodstream, triggering immune reactions and sensitivities.

And on top of this, we know that thyroid hormones have a profound effect on the tight junctions in the gut. You can read more about tight junctions and the anatomy of the gut lining here.

We also know that TRH and TSH both influence the development of our GALT (gut-associated lymphoid tissue)—making up 70% of our immune system.


Additionally, microbiome (or gut) dysbiosis has been found in many thyroid diseases, including thyroid cancer. We will talk about specific gut bacteria later.

There are many gut-thyroid connections, and some raise the question of which came first… the disease or dysbiosis.

Because this imbalance further disrupts the availability of thyroid essential micronutrients—as gut bacteria influence their availability.

These micronutrients include:

  • Iodine, iron and copper—essential for thyroid synthesis
  • Selenium and zinc—both needed for T4 to T3 conversion
  • Vitamin D—regulates the immune response

Interestingly, these micronutrients are often deficient in people diagnosed with autoimmune thyroid diseases.

And if that weren’t enough, gut bacteria have even been shown to assist in the conversion of T4 to T3!

Gut Bacteria and Your Thyroid

Which brings us to the wonderful world of the human microbiome, the ecosystem in our gut.

If you didn’t know that your gut is teeming with trillions of bacteria (making approx. 2kg of your weight!) and you are interested in learning more, How to Improve Your Gut Health Naturally: The Ultimate Guide is a great place to start.

Let’s take a closer look at a few examples of how thyroid conditions connect with microbiome imbalance.

Hyperthyroid conditions have been linked with a significant decrease in levels of gut Bifidobacterium and Lactobacillus and an increase in Enterococcus levels.

Bifidobacterium and Lactobacillus play important roles in our microbiome, providing crucial metabolites like short-chain fatty acids (SCFAs) that reduce inflammation and help our gut lining cells thrive.

Fewer studies have been done on hypothyroid conditions however results so far are also pointing to gut imbalance.


The gut can reveal specific levels of bacteria, like Veillonella, that point to hypothyroidism.

SCFA production in hypothyroid guts is decreased, showing increased inflammation and interestingly increased blood levels of lipopolysaccharide levels (LPS).

LPS is a detrimental molecule to have floating around in your blood—it comes from gut bacteria. LPS is a normal structural component of some bacterial types cell walls.

When these bacteria are in abundance and the gut lining is ‘leaky’ these immune triggering troublemakers (LPS) can make their way into the bloodstream.

Also, LPS has been negatively linked with thyroid conditions in many ways:

  • Decreases thyroid hormone levels
  • Thyroid hormone receptors are reduced
  • Helps create autoimmune thyroiditis conditions (and goiter)
  • Reduces thyroid-stimulating hormone (TSH)
  • Increases inactive T3

As you can see, the gut and the thyroid are undeniably connected.

And there are many more than what we cover here… but to really get to the bottom of your gut issues whether thyroid related or otherwise a gut test definitely gives you a head start.

To learn more about your unique gut bacteria and your microbiome profile, our Gut Microbiome Testing offers a revolutionary approach to healing your gut. Many of my clients come to me with thyroid conditions. Click here to read some of my success stories.

So what can we do to support our thyroid health?

Food & Lifestyle Changes for Thyroid Health

There are many things you can do every day that will naturally help balance your microbiome, heal your gut and support your thyroid function.

Please note these are general recommendations and not tailored to your unique microbiome profile. For those looking for a personalised plan and individual guidance—my Gut Microbiome Programs are found here.

Here are a few practical food and lifestyle thyroid health tips to consider:

  • Iodine—iodine is essential to make thyroid hormone, getting enough iodine in your diet is crucial for thyroid health.

    Rich food sources: Fish and seafood, seaweed (kelp, nori, kombu, wakame), eggs
  • Iron & Selenium—iron is needed for iodine absorption and thyroid hormone synthesis, iron deficiency is also common in hypothyroidism. Selenium is a potent antioxidant critical in removing free radicals generated during thyroid hormone synthesis.

    Rich food sources: Cashews, almonds, pumpkin seeds, Brazil nuts (selenium too), leafy greens, organ meats
  • Zinc – you need zinc to convert T4 to T3—zinc deficiency is a common presentation with thyroid conditions. Zinc is mainly absorbed in the gut, so gut health here is critical.

    Rich food sources: Oysters (highest), red meat, poultry, beans, nuts
  • Vitamin D – the form vitamin D2 is found in food  and the form of vitamin D made by sunlight in the skin is D3. As we know vitamin D is crucial for calcium balance (bone health) but it also regulates the immune system and protects against autoimmunity. Low levels are seen in hypothyroidism.

    Rich food sources: oily fish, red meat, liver, egg yolks
    Lifestyle tip: top up your recommended daily vitamin D intake with a healthy dose of sunshine.
  • Glutathione –  glutathione is known as a master antioxidant and plays an important role in T4 to T3 conversion. It helps keep the free radicals at bay and assists in maintaining thyroid tissue health.

    Rich food sources: sulfur foods (garlic, onion, fish, cruciferous veg), vitamin C foods, avocados, spinach, tomatoes, carrots
    Lifestyle tip: reduce or eliminate NSAIDs (like paracetamol) that deplete the livers stores of glutathione
  • Probiotics & Fermented Foods – help to balance the microbiome by providing beneficial Lactobacillus and Bifidobacteria (and many more) packaged up with the very food they thrive on. In particular, Lactobacillus reuteri has been connected with better thyroid health.

    Rich food sources: kimchi, sauerkraut, fermented vegetables

    Lifestyle tip: if you are not making your own ferments (it’s really easy!) – read the label to ensure your purchase is not pasteurised (heat treatment destroys the good bacteria)
  • Fermentable Fibre – any fibre or resistant starch that is fermented by bacteria in your colon is called fermentable fibre. The by-product of this fermentation are the powerful protective short-chain fatty acids – in particular butyrate works to provide gut cell energy and many other benefits.

    Rich food sources: read 27 High Fibre Low Carb Foods

    Lifestyle tip: it’s easy to include more fibre in your diet – start a salad habit and sprinkle with the fibre-full toppings – like chia, flax and pumpkin seeds
  • Reduce Inflammation Triggers – removing common inflammation triggers is an important practice in gut healing. Gluten, dairy, processed foods and grains can be triggers for those with overactive immune systems and thyroid issues.

    Lifestyle tip: try eliminating inflammatory food groups yourself or work with a qualified health practitioner to guide you on your healing journey
  • Balance Your Gut – one of the most powerful actions you can take for thyroid health is to balance your microbiome. Eliminating the trouble makers that feed inflammation and nurturing those that support you is crucial for thyroid wellbeing.

    Lifestyle tip: Gut testing allows you to see where you need balance and exactly what is going on in your gut.

Putting It All Together

There really are so many things you can do to assist and support your thyroid.

We have covered a lot of thyroid science here and hopefully you now understand how your gut is connected to your thyroid health.

And also understand the various thyroid conditions a little deeper. 

We all need to be mindful to support our gut health – it really is the root cause of most health concerns.

If you’re interested in finally getting to the bottom of your personal concerns once and for all, I highly recommend our Gut Microbiome Testing Program

I help so many clients get absolutely amazing results. 

We work together with their gut profile and with their unique symptoms to craft a truly tailored and unique 3-month program. Fully supported with 8 weeks of meal plans and delicious recipes, a handful of specific supplements and much more.

If you want to get back to feeling your best and have exhausted all other options, I’d love for you to be my next success story.

Here’s that link again, you can read more about the programs here.


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