Hippocrates said that all disease begins in the gut, and my experience has shown that this is largely the case. Yet gastrointestinal (GI) dysfunctions are the most overlooked, and exceedingly common disorders today, affecting many Australians, accounting for millions of dollars in annual sales of over the counter digestive aids. While these medications can offer immediate relief, the underlying cause of the dysfunction, whether it is acid reflux, or constipation, go ignored. And people end up with far worse problems down the road. Since most of the immune system is situated in the digestive tract, a problematic gut leads to a problematic immune system. Because the lining of the digestive tract is an important immune barrier, poor gut health is a significant factor in triggering autoimmune diseases such as Hashimoto’s, as well as functional hypothyroidism.


One of the first things to go in a poor digestive environment is the balance of a healthy gut flora in the intestines, and 20% of healthy thyroid activity depends on healthy gut bacteria. Poor digestive function depletes the body of nutrients that support thyroid health, particularly zinc, tyrosine, selenium and vitamin A and D. Also, faulty digestion is believed to be a leading cause of autoimmune disorders, including Hashimoto’s, since at least 60% of the immune system is located in the digestive tract. An inflamed GI tract and parasitic infections exhaust the adrenal glands, which in turn drags down thyroid function. Constipation from poor GI health makes it difficult for the body to eliminate unneeded hormones, so estrogen accumulates which slows down thyroid function. These are just a few reasons why supporting gut health is paramount to successfully managing an autoimmune thyroid condition, and supporting functional hypothyroidism


Hypothyroidism can lead to hypochlorhydria, a condition in which the stomach produces too little stomach acid, or hydrochloric acid (HCl). For someone with acid reflux this may sound like a good thing, but in fact hypochlorhydria often causes that problem. When food is not digested thoroughly by sufficient stomach acid it putrefies, ferments, and becomes rancid in the stomach. The small intestine naturally tries to refuse entry to this rotting food, so it backs up in the oesophagus, irritating the delicate tissue and causing heartburn. Also because the food is not sufficiently acidic, although it’s certainly acidic enough to burn the oesophagus, it does not stimulate the gallbladder to secrete bile to emulsify fat, nor does it signal the pancreas to secrete digestive enzymes for further digestion. The poorly digested rotting food moves through the intestines, eventually causing inflammation, infection and intestinal permeability. Whenever a pattern of hypochlorhydria is observed, thyroid disorders should be ruled out, and anytime thyroid malfunction is observed hypochlorhydria must be considered. In either case supplemental hydrochloric acid should be used until the pattern resolves.


Many don’t realise it, but the gallbladder is an important digestive organ, because it secretes bile to emulsify fats so that the body can easily assimilate them. When the fats are sufficiently emulsified by bile they transport minerals, and they don’t go rancid in the GI tract, which would cause inflammation and infection. Hypothyroidism has been shown to impair gallbladder function, causing the organ to become distended and contract sluggishly, thus not releasing enough bile. A sluggish gallbladder also causes the liver’s detoxification pathways to become sluggish and backed up, so that the organ cannot effectively detoxify hormones, toxins and other metabolites. It is important to support hypothyroidism and cleanse the liver and gallbladder to restore gallbladder function.


Ideally, food takes 19 to 24 hours to move through a healthy digestive tract. Hypothyroidism has been shown to slow this transit time, as well as impair intestinal absorption rates. This frequently results in constipation, bowel inflammation, malabsorption, and the growth of too much harmful gut bacteria.


As mentioned earlier, 20% of thyroid function depends on a healthy balance of gut flora. We carry approximately 2kg of healthy bacteria in our colons. These bacteria serve many functions, one of which is to facilitate the conversion of T4 to active T3 hormone. When diets are poor and digestion falters, dysbiosis (an overabundance of bad bacteria) occurs crowding out the beneficial bacteria and hampering thyroid function. Interestingly some studies have found connections between the senior Yersinia enterocolitica and Hashimoto’s. Researchers have found that antibodies to these bacteria, which indicate exposure to it, was 14 times higher in people with Hashimoto’s than in those without the disease. Testing for and removing this particular bacterium can be another effective tool in managing Hashimoto’s disease.


Many people have an overabundance of harmful bacteria in their guts. Studies have shown that the bacteria cell walls, called lipid polysaccharides (LPS) impact thyroid metabolism in numerous ways; they reduce thyroid hormone levels, dull thyroid hormone receptor sites, increase the amount of inactive T3, decrease TSH and promote autoimmune thyroid disorders. The strain of LPS on the immune system can also promote an abnormal relationship between the thyroid and pituitary glands. When I have a patient complaining of digestive disorders, chronic pain and inflammation and excessive immune activity (multiple food intolerances or an autoimmune disease, for instance) I know that bacterial infections in the gut are likely wreaking havoc on thyroid function.


Another way poor digestive function contributes to hypothyroidism is by contributing to the excess oestrogen accumulation. Dysbiosis and poor digestion prevents the body from successfully eliminating unnecessary oestrogen, and toxic levels of this powerful hormone builds in the body. This increases the risk of a number of undesirable outcomes, including hypothyroidism, that won’t show up on a blood test and an increase in breast and uterine cancer risks. Excess oestrogen binds the thyroid transport protein so that the thyroid hormones cannot get into the cells to do their job, causing hypothyroidism symptoms.


A healthy GI tract is a tightly woven mesh of tissue that does not allow the absorption of bacteria, harmful foods, or undigested food particles into the bloodstream. However, chronic inflammation brought on by poor diet, poor blood sugar control and chronic stress loosens these junctions so that harmful substances and undigested food leak into the bloodstream. This is called intestinal permeability. But it’s more commonly known as leaky gut. Once in the bloodstream these particles are recognised as foreign invaders or antigens, which the immune system attacks. Unfortunately for many people, especially those with insulin resistance who are most prone to having leaky gut, this response happens almost every time they eat, resulting in chronic inflammation, and an immune system that never gets a break. This sets the stage for the development of an autoimmune disease such as Hashimoto’s, when the overwhelmed immune system confuses the thyroid gland with gluten, which was allowed in through the leaky gut. The first step to repairing the GI tract is to remove the foods that are creating chronic immune responses, with an elimination and rechallenge diet. This diet helps to single out which foods are stoking your immune system so that you know what to avoid until your gut integrity is restored. Unfortunately these foods are typically people’s favourites such as ice cream, pasta, cheese and bread. Also because of the resemblance of the gluten molecules to thyroid tissue, I always have my patients with Hashimoto’s immediately remove gluten from their diets.


To get started on the path toward restoring your gut health and managing your autoimmune or functional thyroid condition, seeing a holistic health practitioner is vital to getting you symptom free and feeling great again.

While the gut is not the only body system to affect the thyroid, healing the gut is one of the core solutions for preventing and healing from Hashimoto’s, and preventing hypothyroidism from developing into Hashimoto’s.

Complete gut healing can take time but doesn’t have to be complicated. Results often start to happen quickly, so you can feel improvements in your digestion, energy, mental clarity, and many other areas, in as short as 2 to 4 weeks if you’re on the right track.

In good health