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Microbiome and chronic thyroid inflammation

What Do Bacteria in Our Gut Have to Do with Hashimoto's?

As shortly mentioned in our previous article on "Treatment-Resistant Abdominal Pain and SIBO," today we want to explain how SIBO (Small Intestinal Bacterial Overgrowth) and Leaky Gut (Syndrome of a Leaky Gut) are related to the autoimmune disease Hashimoto's thyroiditis (chronic thyroid inflammation).

Several studies have shown that SIBO can be an underlying cause for half of all people suffering from Hashimoto's and hypothyroidism.

First and foremost, it's important to understand that Hashimoto's is an autoimmune disease, which primarily means that it's not a problem of the thyroid itself but of the immune system.

Hashimoto's Thyroiditis: When the Immune System Attacks the Thyroid. (3)

Autoimmune diseases occur when the immune system turns against the body's own tissues and attacks them. In the case of Hashimoto's, the antibodies produced by the immune system attack the thyroid gland.

This results in inadequate hormone production, which slows down metabolic processes and leads to symptoms such as fatigue, constipation, hair loss, and what is often referred to as "brain fog."

Hair loss can also be a symptom of Hashimoto's. (4)

So, in a real sense, the thyroid is just an innocent "bystander" caught in the crosshairs of the immune system. The true "culprit" in this case is the immune system itself.

Why does the immune system attack the thyroid?

Dr. Alessio Fasano, a world-renowned gastroenterologist and researcher, has found that all autoimmune diseases share three common factors:

  1. Genetic susceptibility
  2. Antigen exposure (substances that antibodies bind to)
  3. Increased intestinal permeability

Increased intestinal permeability, also known as Leaky Gut, means that the tight junctions of the intestinal barrier become compromised. This allows bacteria, toxins, viruses, and food particles from the digestive tract to enter the bloodstream.

Leaky Gut occurs when the so-called tight junctions in the intestine break down (5).

Because these microbes and particles are not normally present in the bloodstream, the immune system identifies them as invaders, prompting it to go into attack mode.

This leads to a significant inflammatory response as the immune system essentially goes into “overkill” mode trying to neutralize these threats.

However, beware! Eventually, the immune system becomes overwhelmed. It "throws its hands up in the air" out of exhaustion, unable to handle the burden placed upon it, and starts attacking anything and everything.

This is how the thyroid becomes a target and triggers conditions like Hashimoto's.

So, what does SIBO have to do with all of this?

SIBO: Colon bacteria in the wrong place in the small intestine (6).

SIBO occurs when there is an increased number of "unexpected" (colon) bacteria in the small intestine or when the ecosystem goes through changes in the abundance of specific microbes.

By "unexpected" bacteria, we mean that the overgrowth is usually not due to bad bacteria but due to good bacteria that are in the wrong location.

When these otherwise “good” bacteria from the colon colonize the small intestine, where they don't belong, a range of symptoms and complications, including bloating, abdominal pain, nutrient deficiencies, and food sensitivities can be triggered.

But, even worse, this disruption of the ecosystem in the small intestine damages the intestinal lining, causing Leaky Gut and thus initiating a cycle of chronic inflammation. The immune system responds as mentioned before, and Hashimoto's begins to manifest.

Thyroid hormones play a significant role in many bodily processes (7).

Thyroid hormones play a crucial role in gut motility (movement of the gut) by regulating the enteric nervous system (our "gut brain") and the migrating motor complex (MMC; flows through the intestines between meals to move food further along the digestive tract).

In general, this means that thyroid hormones influence the speed at which food is digested and moves through the intestine.

However, when Hashimoto's is present, and thyroid hormone levels are low, this entire process slows down, leading to constipation as one of the typical symptoms of Hashimoto's (8).

Constipation is typical of Hashimoto's. (8)

Anything that gets stuck in the small intestine, as a result, becomes a feast for bacteria, exacerbating negative bacterial growth.

As with any complex, chronic condition, the key to relief lies in identifying and addressing the root causes that triggered the dysfunction.

Hashimoto is currently considered incurable, but improving clinical symptoms can lead to the discontinuation of chronic medications and an improvement in the quality of life.

For example, more and more research shows a connection between the consumption of gluten and the occurrence of Hashimoto's, not only in celiac patients but also in individuals with gluten sensitivity.

Your microbiome is happy about exercise and a healthy diet. (9)

Once again, it becomes evident how important it is to pay close attention to our microbiome and digestive system and to maintain a balance through a healthy diet and exercise!

Do you already know the state of the tiny inhabitants in your gut? No? Then test your gut microbiome now with myBioma and gain valuable insights and useful information to improve your gut health.


This article is intended for informational purposes only and is not to be construed as medical information or instructions for action. The recipes are for inspiration and are not intended as a therapeutic measure. If you have any health problems, we recommend that you contact a doctor or other expert immediately.


  • https://grassrootsfunctionalmedicine.com/blog/sibo-hashimotos/
  • Fasano, A. (2012). “Leaky gut and autoimmune diseases.” Clin Rev Allergy Immunol 42(1): 71-78.
  • https://www.netdoktor.at/krankheit/hashimoto-thyreoiditis-7954
  • https://i.onmeda.de/haarausfall_frau_buerste-635×355.jpg
  • https://www.glutenfreesociety.org/dr-fasano-on-leaky-gut-syndrome-and-gluten-sensitivity/
  • https://feelycenter.com/2019/05/05/sibo/
  • https://www.peak.ag/de/classic/peak-blog/schilddrusenhormon-das-stoffwechselhormon
  • https://www.onmeda.de/krankheiten/verstopfung.html
  • https://www.ausmed.com/cpd/articles/human-gut-microbiome-explained
Medical Doctor and Microbiome Expert
Ina is a medical doctor and is passionate about analysing the gut microbiome and its importance for health!