I felt a great disturbance in the microbiome…

Relationship between disturbance of microbiome and Hashimoto’s thyroiditis
What is Hashimoto’s Thyroiditis?

Hashimoto’s thyroiditis is an autoimmune disorder in which the immune system of the body attacks the thyroid gland, a gland which is located beneath the Adam’s apple in your neck. This gland forms a part of the endocrine system of the body which secretes various hormones to coordinate multiple functions of the human body.
Inflammation due to Hashimoto’s thyroiditis, which is also referred to as chronic lymphocytic thyroiditis, results in hypothyroidism. Hashimoto’s thyroiditis is the most common cause of hypothyroidism or underactive thyroid in the USA. It usually affects females in the middle age-group but it may occur in males and females of any age group and also in children.

What are the causes of Hashimoto’s thyroiditis?

Hashimoto’s thyroiditis is an autoimmune disease in which the immune system produces antibodies, which damage the thyroid gland. It is not clear what causes the immune system of the body to attack the thyroid gland. According to the belief of some scientists a bacterium or virus may trigger this response while according to others it may occur due to a genetic mutation. Ultimately like most autoimmune conditions it appears a triad of genetics, environment and triggers create a perfect storm with resulting tissue damage and symptoms (even if TSH is balanced within the normal range).

How is the thyroid affected by the microbiome?

There has been growing evidence that imbalances or dysbiosis of intestinal microbiome and over abundance of unfriendly bacteria in the gut can negatively affect functioning of thyroid gland and may even trigger autoimmune diseases including Hashimoto’s thyroiditis.

The thyroid majorly produces the hormone T4 which is the inactive form and it requires to be converted to the active form T3 before it can be used by the body cells. 20% of T4 hormone is activated or converted to T3 in the intestines by the friendly bacteria present there. Imbalance in gut microbiome will affect the active hormone available for use by the cells, resulting in a state of low thyroid or hypothyroidism.

One of the main roles of friendly bacteria present in the gut is of strengthening the walls of the intestines, protecting it against pathogenic organisms and preventing the occurrence of leaky gut. When that barrier is not present large food particles and foreign matter pass out of intestines into your body starting a response by the cells of the immune system. Presence of prolonged immune response in the body can trigger production of antibodies against healthy cells and tissues resulting in autoimmune disorders such as Hashimoto’s thyroiditis.

When the intestinal microbiome is imbalanced, long-term damage and inflammation may occur in the body, which may result in production of cortisol (the stress hormone) by the adrenal glands. Over time, excessive cortisol may suppress the function of thyroid gland, reduce the quantity of hormones secreted by the thyroid and also inhibit the conversion of inactive T4 to its active form T3.

A study published in the journal Biomedicine and pharmacotherapy demonstrated that patients with Hashimoto’s thyroiditis have intestinal microbial dysbiosis and they showed an increased growth of the harmful bacteria E. coli. Another study published in discovery medicine concludes that dysbiosis in the gut may result in autoimmunity that may lead to Hashimoto’s thyroiditis.

How can we determine there is a problem with the microbiome?

Stool testing (I prefer a 3 day collection from Drs Data) can pick up on both functional and pathologic changes. It can tell us about inflammation, absorption and whether there is a healthy microbial balance. Pre and post stool testing is one of the most important tests in functional medicine because we have as much as 70% of our immune system in the gut! Treatment can be customized with the information found in this lab and it many times can pinpoint the trigger creating the autoimmune storm.

How to restore your intestinal and microbial health?

Prebiotics are the foods on which your gut bacteria thrive. Prebiotics such as bananas, garlic and onions contain dietary fiber and nutrients to feed intestinal bacteria and release by products of metabolism such as short chain fatty acids which help in maintaining health and preventing disease. Some of the prebiotic foods are:

  • Garlic
  • Onion
  • Jicama
  • Asparagus
  • Artichokes (Jerusalem)
  • Bananas
  • Pulses (beans, lentils, chickpeas etc.)
  • Fermented dairy & Ghee (butyric acid)

Probiotics are a kind of good bacteria, which on administration will keep your intestine healthy. They may be present in certain fermented foods that contain active live bacterial cultures such as yogurt.

Eating a diet rich in prebiotics and probiotics with live cultures plays a vital role in maintaining the balance of your gut flora. You can also eat fermented foods like kimchee, kefir, sauerkraut and kombucha as they contain live microbes and help in improving the health of the intestinal microbiome. Ensure that you get fermented foods with live cultures and not foods that are pasteurized.

Let Your Gut Soar,
Ian Hollaman, DC, MSc, IFMCP


  1. Ishaq HM, Mohammad IS, Guo H, Shahzad M, Hou, YJ, Ma C, Naseem Z, Wu X, Shi P, Xu J. Molecular estimation of alteration in intestinal microbial composition in Hashimoto’s thyroiditis patients. Biomedicine & pharmacotherapy. November 2017; 95:865-874.
  2. Hashimoto’s Disease. 2018. Available at: https://www.mayoclinic.org/diseases-conditions/hashimotos-disease/symptoms-causes/syc-20351855. Accessed June 29, 2108.
  3. What your gut bacteria need to thrive with Hashimoto’s. 2018. Functionalhealthnews. Available at: http://functionalhealthnews.com/2017/08/what-your-gut-bacteria-need-to-thrive-with-hashimotos/. Accessed June 29, 2018.
  4. The role of fermented foods & probiotics in gut health. Ignitenutritionca. Available at: https://ignitenutrition.ca/blog/fermented-foods-probiotics-help-gut-health/. Accessed June 29, 2018.
  5. Does the gut microbiota trigger Hashimoto’s thyroiditis? Discoverymedicine. Available at: http://www.discoverymedicine.com/Kouki-Mori/2012/11/27/does-the-gut-microbiota-trigger-hashimotos-thyroiditis/. Accessed June 29, 2018.
  6. Dysbiosis and thyroid dysfunction. All roads lead to the microbiome. Hypothyroidmom. Available at: https://hypothyroidmom.com/dysbiosis-and-thyroid-dysfunction-all-roads-lead-to-the-microbiome/. Accessed June 29, 2018.

The Thyroid Gut Connection


The Thyroid Gut Connection

So you were diagnosed with a thyroid condition or you suspect you have thyroid disease because you have constipation, cold feet or hands, hair and skin problems, terrible fatigue, weight gain and brain fog? Well, join the 40 million other Americans who suffer from Hypothyroidism. But is it really just a simple thyroid problem?  Do you suspect there is something more going on below the surface that has the thyroid entangled?

If you were diagnosed with hypothyroidism via an elevated Thyroid Stimulating Hormone, TSH, or you have some of the above symptoms, you most likely have an immune disorder called “thyroiditis” or “Hashimoto’s Hypothyroidism”. The American Endocrine society says that 90% of people who get diagnosed with hypothyroidism suffer from autoimmune thyroid. But what causes it?

The GutLike many problems in health, we need to “look to the gut” to understand why our immune system is so flared up and starting to attack our own tissue.
While researchers were studying Celiac disease, an autoimmune condition that attacks the gut, they uncovered the “holy trinity” of autoimmune conditions. That is, that anyone with autoimmunity must have three things: 1) genetic predisposition, 2) an environment in the gut ripe for problems and 3) had a triggering event that turned on their genes to start making antibodies against their own tissue.

It goes something like this:

Mary Lou was born via C-section or did not breast feed very well. Or, maybe Mary Lou took a lot of antibiotics because of strep infections or had many yeast infections as a kid and also took a lot of antibiotics. Unfortunately for Mary Lou, she wiped out 80% of her immune system, which is really the healthy bacteria in the gut. Then she grew up, had kids, went through a highly emotional or stressful situation and she began to notice symptoms. Weight gain, gut problems, fatigue, feeling out of sorts and wanting to just lay in bed and let the world wash over her. On top of that Mary Lou’s hair was thinning, she was constipated and life felt like an endless fog that she was trying to part. Sound familiar? Mary Lou had just developed Leaky Gut and was suffering miserably. On top of that her doctor either told her “Here, take this thyroid hormone the rest of your life” or “Your tests only show minor elevations in TSH, there is nothing I can do for you but my friend the psychologist can give you his drugs if you would like”.
So what is going on? Well, like I mentioned, the gut is the root of the problem.  Many people have gut changing events like antibiotics, poor breast-feeding or elevated stress that suppresses our immune system. Then, pour on life with the high sugar, high fat standard American diet (SAD), not enough fiber and the constant deadline driven society and your gut barrier begins to break down.

Our small intestine consists of 25 feet of tubing that has a shag carpet lining called the “microvilli”. This is where we absorb our food and where the outside world interacts with the inside world. This barrier has the surface area equivalent to a doubles tennis court! It is covered by an immune system barrier called secretory IgA. This helps to grab onto bacteria and food and slows down items as they try to pass through our barrier. Like I said previously, stress begins to wear this immune system down and we have large food molecules trying to get into our body coupled with bad bacteria and yeast. What prevents a flood of material into the gut are proteins called “tight junctions”. These guys are the glue between our enterocytes, the single cell layer that separates the outside world from within.  What keeps these guys tight? Vitamin D! Vitamin D, which is also called “the sunshine hormone”, keeps these tight junctions working normally. With low levels of Vtamin D, coupled by inflammation in the gut, we start to widen the space between intestinal cells. Then, materials start to pour through, more inflammation results and we call in the immune system to defend ourselves! Guess what? Leaky gut just started!

So now our immune system recruits “antibodies” which are really lock-and-key proteins that fit around invaders, foods or bacteria and help to flag and destroy threats to our immune system. Unfortunately this process is supposed to be short term, but with a leaky gut, the immune system continues producing antigens. Our immune system gets tired as it constantly deals with a barrage of foods and bacteria coming through the small intestine cells. When we get fed up with this process we start to turn our attack against the gatekeepers, those tight junctions, which help regulate the flow of traffic. Our immune system is pretty smart overall but because it is getting so overwhelmed with this leaky gut it starts to attack the very structures that are regulating traffic, the tight junctions. This is actually the first autoimmune event. Then over time as the process continues these newly formed “self antibodies” flow through the rest of your bodies’ circulatory system and find their way into and around thyroid tissue. It just so happens that the tissue in your gut, look very similar to that thyroid tissue and BANG! Now you are creating antibodies against the gut tissue AND your thyroid. In research it’s called “molecular mimicry” but in real life its called Hashimoto’s hypothyroidism because now your immune system is attacking your own tissue and with nothing to stop the process you begin to suffer from thyroid symptoms: brain fog, depression, fatigue, hair loss, constipation and weight gain. Sound familiar?

The bad news is this can move on and target other tissue like joints, nerves, skin and even the brain. The good news is Functional Medicine can create a targeted approach to address the underlying cause and get you feeling optimal again!  But, this process is not for everyone. It takes work, diet changes and supplementation that help heal not only the gut, but also the inflamed immune system. You can try to just heal the gut but unfortunately you are still left with an angry red headed step-child (thyroid) and an immune system that is in disarray! So this is why Dr. Autoimmune developed a specific program to heal the gut and immune system for optimal results.

Here is what our program consists of:

  1. Contact our office to see if you qualify for care, set an appointment and submit paperwork 48 hours in advance of your appointment so Dr. Ian can thoroughly review your case
  2. At your New Patient Exam and Consultation we conduct a comprehensive neurologic and metabolic examination with a full health history and case review – the Functional Medicine process
  3. Any necessary labs are obtained to confirm our suspicions
  4. Your results from the Initial Exam are explained to you at the Report of Findings (the second visit), which you attend with your spouse/partner/parent/child/dear friend so you don’t have to play “telephone” to them and they can get their questions answered
  5. If we accept you for care and you are ready to tackle your health challenges, we begin a program that may consist of any or all of the following:
  • A 5R Elimination Provocation Diet customized to your needs
  • Additional lab work to uncover more triggers and mediators
  • Custom, pharmaceutical grade supplementation to speed healing
  • Therapies such as PeMF or Cold Laser to encourage tissue healing
  • Brain therapies like Neurofeedback or Functional Neurology
  • Environmental assessments and recommendations for remediation
  • Lifestyle recommendations to promote self-regulation
  • Exercise prescriptions to promote anti-inflammation
  • Nutritional Coaching to create lasting changes
  • Applied Kinesiology examination and treatments
  • Exit strategies so that you maintain your newfound health

Everyone is evaluated uniquely and his or her program reflects what is absolutely critical to solve the autoimmune process, not just bandage it. Our goal is to repeat labs at 8 weeks and definitively show regression and eventual remission. Isn’t that what we all want? See symptoms resolve but also know deep down we healed at the cellular level so we can thrive, not just survive!

What’s next?

If this peaks your interest please call 303-882-8447 for your free 15-minute consultation with Dr. Ian. Join us and let your health soar!

Ian Hollaman, DC, MSc, IFMCPSupporting complex, chronic thyroid and autoimmune diseases in the Denver-Boulder area