Is Your Thyroid Causing Your Digestive Problems? + 7 Ways to Heal Your Thyroid & Gut!

Do suffer from hypothyroidism or know someone who does? Chances are you know a little bit about the gastrointestinal (GI) symptoms that go along with it. I know. Fun, right? Thyroid digestive problems and intestinal issues, unfortunately, tend to go hand in hand. Here’s why that is and 7 ways to help heal.

Hypothyroidism, a condition in which there is too little thyroid hormone present in the body, can result in a number of GI symptoms, including the potential for overgrowth of bacteria, yeast or an imbalance in gut flora.

Small Intestinal Bacterial Overgrowth, or SIBO is a condition in which there is too many bacteria present in the small intestine. Studies have shown that SIBO may be present in more than half of patients with hypothyroidism!

SIBO generally presents as bloating, gas, diarrhea, constipation, and abdominal pain, although there are asymptomatic cases. The condition is a malabsorption syndrome as the bacteria cause damage to the small intestine and create an environment in which they (the bacteria) preferentially absorb your nutrients. That basically means your body isn’t receiving the full benefits from all of that delicious, nutritious food you’re eating. Read more about SIBO here.

There are three main mechanisms in place to protect your small intestine from becoming overrun with bacteria— stomach acid, intestinal motility (the spontaneous and independent movement of food/waste via the gastrointestinal tract), and the immune system. When any one of these mechanisms fail, you are at risk for SIBO.

4 Ways The Thyroid and Gut Connect

Stomach Acid

One of the main mechanisms inhibiting the overgrowth of bacteria in the upper intestine is stomach acid.

Elevated TSH (signifying hypothyroidism) and even subclinical hypothyroid cases have been associated with lowered stomach acid production, which can cause a host of symptoms, not least of which is the possible proliferation of bad bacteria in the gut.

H. pylori-induced gastritis, acid-blocking medications (over the counter or prescription), other autoimmune conditions, malnutrition, and aging all can cause failure of the gastric acid barrier.


Motility and transit time are compromised in patients with hypothyroidism, as well in other conditions that cause inflammation. This causes constipation, a common symptom among those with untreated hypothyroidism. And as we know, compromised motility may cause or exacerbate SIBO.


Hypothyroidism is also connected to the immune system, the third mechanism in place to protect from the overgrowth of bacteria.

Chances are, even those with subclinical hypothyroid may have immune system dysregulation and 90% of those presenting with hypothyroid are producing antibodies to thyroid tissue, a condition known as Hashimoto’s. So, you can see how a sluggish thyroid may trigger or exacerbate bacterial overgrowth!

SIBO Can Make Hypothyroidism Worse

We’ve established that patients with hypothyroidism may suffer from decreased stomach acid and impaired motility, which may result in the formation of SIBO over time. But can SIBO actually worsen hypothyroid?

We do know that an overgrowth of bacteria can interfere with levothyroxine absorption. This means that even those who are diagnosed with hypothyroid and taking a thyroid replacement hormone may not be receiving the intended dose of thyroid hormone.

SIBO, Leaky Gut and Autoimmunity

We also know that damage in the small intestine (this is where bacterial overgrowth wreaks the most havoc) is closely related to autoimmune diseases of all kinds. “Leaky gut” or intestinal permeability and SIBO are closely linked, and leaky gut is found in all cases of autoimmunity.

Damage in the small intestine can lead to immune activation, food particles in the bloodstream, and ultimately, a systemic problem that can result in autoimmunity or perpetuate the immune system’s attack on healthy tissues.

7 Ways To Heal Your Thyroid & Your Gut and Cure Digestion Problems & Intestinal Issues

Have Appropriate Lab Testing.

You can determine SIBO with a lactulose breath test. A stool culture, breath test for H. pylori or another testing may be indicated for your condition.

In addition, nutrient deficiencies, inflammation, and other blood markers. Specifically, in conjunction with your history to form a complete picture of your health.

If you need help getting lab testing or would like to chat about what labs may be indicated for you, contact my clinic here for a complimentary 10 minute consult.

Treat the Underlying Cause.

If you have dysbiosis, a state of flora imbalance, SIBO, yeast, parasite or any other non-commensal critter growing in your gut it is vital that you treat them. Work with an experienced practitioner to re-establish healthy gut flora and restore your gut’s terrain to prevent future infections.

There are many natural therapies, including herbs, to use to bring your gut back to health. I caution you from beginning herbal antimicrobial therapy without medical supervision from a licensed health practitioner. Although they are natural, they can do quite a bit of damage when dosed incorrectly or for too long.

You can download my free guide to thyroid labs here.

Avoid Gluten.

There are strong ties between gluten and gluten-containing grains and SIBO, gut dysbiosis, and leaky gut.

There is also a strong link between autoimmune thyroid conditions and celiac disease. If you’ve been diagnosed or suspect you are hypothyroid, I suggest first testing for celiac disease and then eliminating gluten from your diet.

Read more about the effects of gluten on the thyroid here.

You can download your guide to going gluten free here.

Overhaul Your Diet.

Diet is a huge component of gut and thyroid health. Once you’ve determined if you have SIBO, yeast overgrowth, and/or other gut infections/pathogens, work with a qualified practitioner. Together you can formulate a therapeutic diet that’s aligned with your specific goals.

Download your free guide to carbohydrates in SIBO treatment.

Increase Anti-inflammatory Herbs.

Herbs like ginger and turmeric can be consumed daily as tinctures, teas, capsules, or in drinks, soups, and stews. These potent anti-inflammatories have been proven in several studies to tamper inflammation and help heal the gut.

Research has also shown that ginger (a potent antimicrobial) possesses inhibitory action against pathogenic bacteria like Staphylococcus aureus, E.coli, and Salmonella, while stimulating the growth of friendly bacteria like Lactobacilli.

Both turmeric and ginger are also high in antioxidants to combat the oxidative stress of conditions like SIBO.

Consider Probiotics.

Lactobacillus, Enterococcus, and Bifidobacteria have the ability to reduce IBS symptoms. They are also involved in important immune system signaling that reduce inflammation and can help tame autoimmunity.

In some cases of SIBO, probiotics may make symptoms worse, especially if they contain prebiotics. If this is the case for you, you may need to reduce the bacteria in the small intestine and restore gut motility before using probiotics regularly.

Decrease Stress.

Stress has been shown to alter gut bacteria, favoring aerobic bacteria, while also decreasing beneficial bacteria such as lactobacilli.

Deep breathing, light exercise, and meditation/mindfulness are good places to start. Read more about stress reduction here. 

Talk to Your Doctor

If you are hypothyroid, have Hashimoto’s, or suspect you may have a thyroid or hormone imbalance, ask your doctor for a complete thyroid workup.

You can download my free guide to thyroid labs here.

You can also ask your doctor about the possibility of SIBO, intestinal permeability, or any possible pathogen or infection. All of which need to be healed whether you’re presenting with symptoms or not.

Chronic gastrointestinal issues in those with clinical or subclinical hypothyroid should not be ignored. By treating the gut and thyroid together, we can restore energy, improve digestive health, reverse autoimmune disease and create lasting health. 

This is what we do for patients in my clinic and we’d love to share more about how we can help you too. Schedule a free 10-minute consult and let’s have a chat about your health priorities.


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About The Author

Dr. Jolene Brighten

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Dr. Jolene Brighten is a licensed Functional Medicine Naturopathic Doctor, best selling author, speaker, and mother. Dr. Brighten specializes in women’s health, from fertility to postpartum care, adrenal and thyroid support, autoimmune conditions, and digestive disorders. In her patient centered practice, Dr. Brighten thrives on navigating the space between conventional and alternative medicine, all while working with patients to help them achieve optimum balance, health, and happiness.