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Hashimoto’s Disease

Hashimoto, thyroiditis, autoimmune disease, thyroxin, hypothyroidism, gut bacteria, infection
Hashimoto’s Disease

What is Hashimoto’s Disease?

Hashimoto’s, Hashimoto’s Disease or Hashimoto Thyroiditis (HT) is medically defined as an autoimmune disease, where the body turns on itself and slowly destroys the thyroid. When the immune system does this, the thyroid makes less and less thyroxin, a hormone which controls metabolism in the body.  This is called hypothyroidism. The medical solution is to reach for the Levothyroxine, a synthetic thyroid hormone.

Causes of Hashimoto’s Disease?

Hashimoto’s is seven times more likely in women than in men, suggesting it may be related to a human ‘estrogen’ issue. Certainly some experts believe that Hashimoto’s is linked to estrogen dominance – either too much estradiol,  and/or not enough balancing progesterone. It has long been known that there is a link between estrogen and thyroid function (6).

However, HT is also increasing in prevalence in our modern world and a finger has been pointed at xenoestrogens, or chemical estrogens, as found in herbicides, pesticides and in home products, and toiletry and personal care products. 

Radiation may also be a factor since it is known to affect the thyroid. Equally, low or high iodine levels have been quoted as causes, depending on the source.

However, being an ‘autoimmune disease’, research is now increasingly pointing the finger at a damaged gut microbiome, including infection, as a major cause (1). There seems to be a reciprocal relationship between thyroid autoimmunity and gut microbiota. The whole biochemistry and homeostasis of the thyroid seems dependent upon the health of the body’s microbiome.

Symptoms of Hashimoto’s Disease?

  • Fatigue
  • Joint and muscle aches
  • Weight gain
  • Hair loss
  • Depression  
  • Slowed heart rate, or irregular heart beat
  • Constipation
  • Feeling of cold all the time
  • Paleness or puffiness
  • Inability to get pregnant

Hashimoto’s and the microbiome?

As early as 2012  growing evidence (2) suggested a bacterial (and even a viral) involvement in Hashimoto’s. 

Hashimoto’s thyroiditis has now become the most common autoimmune disease in the world and is strongly linked to intestinal permeability, according to a 2021 research study from Brazil (3).  The researchers analyzed stool samples from 40 HT patients and 53 controls, and compared these to dietary records. The group with HT, consumed significantly less fruits, vegetables, and soluble fibre foods, but more foods that encouraged bacterial growth known to be linked to inflammation. Our sister site The Rainbow Diet, has research on exactly what foods increase bacteria that make anti-inflammatory compounds, and what foods make inflammatory compounds. We have linked the article below.

Other findings were that there was a significant increase in Bacteroides and a decrease in lactic acid producing Bifidobacterium in stool samples of patients with HT. Interestingly, members of the Lactobacillus family were higher in patients without thyroid hormone replacement, but depressed in those who use oral levothyroxine. This might link to the finding that Levothyroxine can increase the risk of breast cancer (4) – we know breasts with cancer have very low levels of Lactobacillus.

Other more general studies have firmly established that the mix of bacteria – both commensal and pathogens – in the microbiome is linked to inflammation and an immune response. Attack by the immune cells can cause ‘similar tissues’ or tissues which also have the infection inside, to also be attacked. Thus it is possible that simply an imbalance in the microbiome may link to Hashimoto’s and Thyroid problems.

The Small Intestine and Hashimoto’s

An interesting factor in Hashimoto’s seems to be SIBO, or small intestinal bacterial overgrowth. This is not technically an infection, more a case of bacteria being in the wrong place at the wrong time. After processing your food in the stomach, it passes to the small intestine from where your nourishment is absorbed. However, yeasts and bacteria can find their way into the small intestine and get in the way of this absorption. They gorge of the nutrients and can set up conditions similar yo those of IBS – including gas production, wind, diarrhoea, leaky gut, acid reflux and more. SIBO can also deplete iron and B-12 levels. A lot of experts fail to fully understand, but you can deal with SIBO. 

At the moment SIBO is known to be linked to Hashimoto’s but it is not known whether it is a cause or a consequence. One would feel it has to be the former. SIBO can be caused by antibiotic use and especially by Proton Pump Inhibitors like Omeprazole. It is also linked to poor ‘peristalsis’ (the electrical impulse that runs through the GI tract to keep food moving).

What we do know is that roughly half of people with low thyroid function have SIBO and there’s even some evidence that levothyroxine can make matters worse!

Infection and Hashimoto’s

When you develop an infection, your immune system targets those specific microbes. However, in some cases, the immune system accidentally targets certain cells in your body that happen to look like the original microbe. Think of it as mistaken identity.

There seem to be at least 6 ‘infections’ that have been associated with Hashimoto’s.

  1. Yeasts – yeasts build up in the gut if you damage your commensal (good) bacteria. They are the cause of leaky gut, and can get into the blood stream and then pass round the body  colonising areas of the body, causing lowered oxygen. Yeast infections can happen in several ways, for example, after you have taken drugs (PPIs, antibiotics, chemotherapy, steroids and others), have food poisoning, if you eat badly, binge drink, smoke or are stressed. In some cases increased levels of yeasts can occur because of a parasitic infection.  Yeasts are known to be involved in SIBO. A simple fix can be found in the ‘Heal your Gut’ article; yeasts can be killed by taking oregano, caprylic acid, pau d’arco and/or artemisinin, for example.
  2. Helicobacter pylori – a bacterium that infests the stomach rather than the colon. This parasite is associated with stomach ulcers, stomach cancer and acid reflux. It can be killed off naturally by taking bismuth (in, for example, the antacid brand gastro-bismol) along with the herb goldenseal, or the blend Para-Free Plus. Oregano, fish oil, berberine and NAC are also helpful.
  3. Borrelia bergdorferi – is more usually associated with Lyme Disease, but has even been found in some brain tumours and seems linked to Hashimoto’s in some way. Artemisinin, or sweet wormwood, has an action against Borrelia.
  4. Yersinia enterocolitica – a bacterium found in contaminated seafood (mussels and oysters especially) and meats like pork, chicken and contaminated water and dairy products.  It occurs worldwide but is fairly uncommon. Antibodies to the bacterium have been found in 75% of patients with Hashimoto’s (5), as opposed to less that 8% of the general population. The surface proteins of Yersinia look exactly like those of the thyroid. The immune system of the body doesn’t distinguish between the two and attacks both.
  5. Epstein-Barr Virus (EBV) – is a Herpes virus that is common in 80% of us. It is held in control by the immune system.  The virus can re-activate inside the thyroid in people with a genetic issue. Helpful natural treatments include olive leaf extract, pau d’arco, and medicinal mushrooms especially cordycepin from cordyceps mushrooms.
  6. Hepatitis C – there is a higher risk of Hashimoto’s if you have HepC, possibly because the virus can also be present inside the thyroid, not just the liver.  There is little evidence for natural remedies for Hepatitis C.

Hashimoto’s – it starts in the gut

It is highly likely that, like all autoimmune diseases, the origins of Hashimoto’s thyroiditis emanate from a poor microbiome. And it may be that SIBO is involved in this and poor peristalsis is a factor. This Dysbiosis undoubtedly lies in yeast, bacterial and viral infections, complicated by an imbalance of oestrogen and progesterone.

Go to: Heal your Gut – Heal your Body

Go to: Progesterone – the natural protector



  1. Gut microbiota and Hashimoto’s thyroiditis – Camilla Virili et al; Endocr Metab Disord. 2018 Dec;19(4):293-300.
  2. Does the gut microbiota trigger Hashimoto’s thyroiditis? – https://www.ncbi.nlm.nih.gov/pubmed/23200063
  3. Detection of Alterations in the Gut Microbiota and Intestinal Permeability in Patients With Hashimoto Thyroiditis – Leonardo César de Freitas Cayres et al; Front Immunol. 2021 Mar 5;12:579140. 
  4. Is Levothyroxine and/or your thyroid driving your breast cancerhttps://www.canceractive.com/article/is-the-synthetic-thyroid-hormone-thyroxine-behind-your-cancer
  5. Antibodies to Yersinia enterocolitica in thyroid disease – https://www.ncbi.nlm.nih.gov/pubmed/1036668
  6. Interaction of estrogen therapy and thyroid hormone replacement in postmenopausal women – Norman A Mazer; hyroid. 2004;14 Suppl 1:S27-34.