The Gut Infections That Can Cause Hashimoto’s

Is a gut infection harming your thyroid?

Is a gut infection harming your thyroid?

I might be biased, but I think the best practitioners are those who have been sick themselves…

They know what it’s like to be in the trenches – and how it feels to be well again.

Dr. Izabella Wentz is one of those practitioners – she was diagnosed with Hashimoto’s Thyroiditis, healed herself, and now helps others facing thyroid problems.

Today, she is sharing an article with us about one of the most overlooked causes of thyroid problems – underlying gut infections.

If you’re struggling with thyroid disease, please take this chance to learn from someone who has been where you are.

[Enter Izabella]

If you’ve been diagnosed with an autoimmune condition and told to consider your gut health, your first thought was probably, “What’s the gut got to do with it?”

That’s certainly the question I had when I was diagnosed with Hashimoto’s thyroiditis at age twenty-seven.

Sure, I could identify some of my symptoms as gut-derived—my irritable bowel syndrome had practically turned my bathroom at work into my second office. But how was this connected to the war being waged against the tiny, butterfly-shaped gland at the base of my neck?

What I soon found out was that the gut controls the immune system and most diseases of autoimmunity – like Hashimoto’s, MS, RA, and Graves’ – are linked to gut health in some way.

The “Big Bang” of Autoimmune Disease

People with Hashimoto’s thyroiditis and other autoimmune diseases often also have increased intestinal permeability, or leaky gut. A leaky gut will interrupt the immune system’s ability to regulate itself, and put the body into a perpetual attack mode.

For this reason, a critical part of my approach to healing myself from Hashimoto’s and now helping others do the same is repairing the gut.

To accomplish this, I use what I refer to as a “Gut Balancing Protocol.” The protocol includes removing reactive foods, supplementing with enzymes, balancing the gut flora with probiotics, and nourishing the gut with healing foods and nutrients like L-glutamine, zinc and fish oils.

Sticking to this plan (along with the implementation of strategies focused on the liver and the adrenal glands) can minimize and even eliminate symptoms related to Hashimoto’s.

But what about if you’ve already changed your diet and added in supplements – and you still have autoimmune symptoms?

You must dig deeper to discover what may be the underlying cause or trigger of the ongoing attack on your thyroid. If the trigger—which you might think of as the Big Bang of your condition—isn’t removed, remission will not be possible.

One of the most common “Big Bangs” for Hashimoto’s I see with my clients who don’t feel better after changing their diet is an underlying gut infection.

Up to 80 percent of my clients who don’t go into remission with dietary changes have tested for one or more infections using functional medicine testing.

Tackling Gut Infections and Leaky Gut: A Two-for-One Approach to Healing

Since gut infections can lead to intestinal permeability, removing the infection can be the missing link in gut repair. The key is to identify what type of infection is present, which can be tricky if you don’t know where to start. And this is where anecdotal evidence can help.

While many infections have been implicated in triggering Hashimoto’s, the most common ones I see in my clients include: Blastocystis hominis, H. pylori, SIBO, yeast overgrowth, and reactivated Epstein-Barr virus, so we’ll focus on those here.

Blastocystis hominis

In 2015, 35 percent of my clients tested positive for this protozoal parasite, making it the most common I’ve encountered in people with Hashimoto’s. I personally had a Blastocystis hominis infection that had to be resolved before I felt completely well.

While it’s common in conventional medicine for the Blastocystis hominis parasite to be regarded as a commensal organism (i.e., there’s no need to treat it), research has connected its presence to hives and IBS—two conditions often seen in Hashimoto’s, as well as intestinal permeability, a factor in autoimmune disease.

Symptoms include: bloating, diarrhea, nausea, flatulence, variable bowel habits, abdominal pain, hives, and fatigue. This pathogen may also cause multiple food sensitivities. While true food sensitivities, like in the case of Celiac disease, will typically result in a resolution of symptoms once food is removed, people infected with Blastocystis hominis will have the opposite: they develop multiple food sensitivities, and once they eliminate one food, they’ll develop another sensitivity.

Once I was successful in removing this parasite from my own gut, my thyroid antibodies dropped, I felt better, and I could once more tolerate grains and eggs—two types of food I couldn’t eat before. And my clients have reported similar transformations in tolerance.

Testing for Blastocystis hominis: Functional medicine stool tests that test for this include the BioHealth Lab 401/401H test, the GI-MAP test from Diagnostic Solutions Laboratory, the Doctor’s Data Comprehensive Stool Analysis, the GI Pathogen Plus Profile from DRG Laboratory, and the GI Effects Comprehensive Stool Profile (most of these tests can be ordered here). [1 – 9]

Helicobacter pylori

H. pylori is a spiral-shaped bacterium that burrows into the stomach lining and secretes urease, a neutralizer of stomach acid. The toxic by-product of urease and stomach acid, along with other chemicals produced by this bacterium, can damage the epithelial cells that form the lining of the intestines. When epithelial cells are damaged, inflammation occurs and the tight junctions of the intestinal wall are disrupted. And this is the story of how leaky gut begins.

H. pylori can trigger an immune response and has been implicated in numerous autoimmune conditions, including Hashimoto’s, thyroid nodules and Graves’ disease.

Symptoms include: Because H. pylori can contribute to low stomach acid, it can lead to poorly digested foods, which in turn can lead to the development of multiple food sensitivities. H. pylori has also been implicated in ulcers, although only about 5 to 10 percent of those infected with the bacterium will develop an ulcer. Others may have acid reflux, constipation, stomach aches – or they might not have any symptoms at all.

Testing for H. pylori: The presence of H. pylori can be revealed through a breath, blood, or stool test, or through the endoscopy procedure. I recommend the stool antigen test because it is a more sensitive test and will even reveal low grade infections that may be missed by the other tests. In 2015, 20 percent of my clients tested positive to H. pylori. Labs that utilize the stool antigen test include the BioHealth Lab 401/401H test, the GI-MAP test from Diagnostic Solutions Laboratory, the Doctor’s Data Comprehensive Stool Analysis, the GI Pathogen Plus Profile from DRG Laboratory, and the GI Effects Comprehensive Stool Profile. Order tests here. [10, 11]

Small Intestine Bacterial Overgrowth (SIBO)

As the name suggests, SIBO is an overgrowth of bacteria in the small intestine. Though technically, SIBO is not an infection, rather it is an overgrowth of commensal and even beneficial bacteria, though in the wrong place in the body. The healthy and well-functioning small intestine is supposed to contain very low levels of bacteria. This excess of bacteria can promote intestinal permeability as the body attempts to get rid of the bacteria. Bacterial overgrowth can be caused by antibiotic or acid-suppressing medication use, low stomach acid, slowed GI transit, and food poisoning.

According to a study published in 2007, SIBO can be present in up to 54 percent of people with hypothyroidism. [1]

Symptoms include: acid reflux, bloating, belching, and irritable bowel syndrome (diarrhea, constipation, or mixed type). SIBO may also cause a depletion of vitamin B12 and iron and of certain digestive enzymes, such as lactase (digests lactose in dairy) and amylase (digests starch). When these enzymes are depleted, you will have difficulty digesting a long list of foods.

Testing for SIBO: You will need to have a breath test done to determine the presence of gas-producing bacteria. It’s possible to find a gastroenterology center that has a breath-testing machine, but if that’s not an option, you can order a SIBO breath test kit that uses Lactulose to stimulate the bacteria to release their giveaway gases. These tests are available from Commonwealth Laboratories, BioHealth Laboratory, and Genova Diagnostics. You can order a breath test here. [12]

Yeast Overgrowth

Yeast is an opportunistic organism that is present in small amounts in certain parts of your body, including the intestinal tract. Yeast can be beneficial, helping with digestion and nutrient absorption, but too much of it is not a good thing. Yeast production can go into overdrive when your immune system is compromised or overall health weakened.

Most people with Hashimoto’s will have a high degree of yeast overgrowth, especially of the Candida genus. Treating this overgrowth can be very helpful in restoring health. In some cases, there may be an underlying cause of the yeast overgrowth, which must be addressed before the overgrowth can be completely remedied.

Symptoms include: Numerous symptoms have been attributed to yeast overgrowth and they include gas, bloating, brain fog, sinus congestion, GI distress, itchy scalp, eczema, allergies, a white tongue, vaginal yeast infections, intestinal permeability and many more!

Testing for Yeast Overgrowth: Stool tests are best for detecting yeast overgrowth. Options for testing include BioHealth 401/401H test, the GI-MAP test from Diagnostic Solutions Laboratory, the Doctor’s Data Comprehensive Stool Analysis, the GI Pathogen Plus Profile from DRG Laboratory, and the GI Effects Comprehensive Stool Profile from Genova Diagnostics, as well as organic acids tests offered by various labs. Order these tests here.

Epstein-Barr Virus Reactivation

Most of us have had a prior infection of the Epstein-Barr virus (EBV), and many will recover without any lasting effects. In people with poor nutrition and vulnerabilities, however, the virus may deplete the body’s immune response and result in a low-grade latent infection. This lingering, unresolved infection can go on to contribute to multiple deficiencies and imbalances and leave the door open to the autoimmune process.

I suspect that many people with Hashimoto’s may have a hidden Epstein-Barr infection in the thyroid gland. Research out of Poland supports my informed hunch—a 2015 study done there found the virus in the thyroid cells of 80 percent of people with Hashimoto’s, while controls did not have the Epstein-Barr virus in their thyroid gland.

Symptoms include: Symptoms of an acute Epstein-Barr infection are easy to identify – the infection causes the debilitating condition known as Mononucleosis (“Mono”) or glandular fever. Symptoms include fatigue, swollen lymph glands and fever. Latent, chronic infections are more difficult to pinpoint and usually manifest as chronic fatigue and autoimmune disease, with occasional enlargement of lymph nodes. If you can identify that the last time you felt well was before you were struck with a viral infection, then likely EBV is a relevant trigger for you.

Testing for Epstein-Barr Virus Reactivation: Blood tests are the best way to determine if you have a reactivated infection. Test for all three, as only one may come out positive (you can order here).

  • EBV-VCA IgG/IgM by ELISA (Viral Capsid Antigen): IgG positive means you’ve had or have the infection; IgM positive means reactivated infection.
  • EBV-EBNA-1 IgG by ELISA (Nuclear Antigen): Positive test result usually associated with past infection.
  • EBV-EA-D IgG by ELISA (Early Antigen): Positive EA IgG may mean active infection or reactivated infection. [13, 14, 15]

What to Do About a Positive Test

So you have a gut infection, now what?

If you’ve reached a point where nothing you try seems to work, I would look for the silver lining in a positive test result—this means you finally have something to target with your efforts to recover your health.

No amount of food restriction will heal an infection, and no single increase in supplements or adjustment in thyroid medication will do it either. Most gut infections require targeted treatments, requiring various types of herbs, antibiotic, antifungal, antiviral or antiprotozoal agents to be eradicated.

As a student in pharmacy school, I learned that “every bug needs a different drug”—and this is certainly true when it comes to gut infections. In my book, Hashimoto’s Protocol, I share the most effective drugs, herbs and supportive therapies I’ve implemented with my Hashimoto’s clients.

As a trained pharmacist, I can recommend the most effective pharmacological treatments. But as someone who sought out natural medicine to help with my own recovery from Hashimoto’s, I’ve also immersed myself in the world of natural medicine and emerged with herbal and alternative treatments that can be equally effective in treating gut infections – and much more gentle.

In either case, supportive treatments should be considered, too. This can be dietary specifications that will support your recovery as your body works to remove the infection, along with strategic supplement use.

As you seek out to heal a gut infection, I recommend you keep an open and optimistic mind. I’ve coached and counseled over a thousand people with Hashimoto’s through the eradication of each of the gut infections discussed here and I can tell you that recovery is possible.

If you’re ready to take back your health, I encourage you to pick up a copy of my new book, Hashimoto’s Protocol: A 90-Day Plan for Reversing Thyroid Symptoms and Getting Your Life Back.

About the Author

Izabella Wentz, PharmD, FASCP is an internationally-acclaimed thyroid specialist and licensed pharmacist who has dedicated her career to addressing the root causes of autoimmune thyroid disease after being diagnosed with Hashimoto’s thyroiditis in 2009.

Dr. Wentz is the author of the New York Times best-selling patient guide Hashimoto’s Thyroiditis: Lifestyle Interventions for Finding and Treating the Root Cause and the forthcoming protocol-based book Hashimoto’s Protocol: A 90-Day Plan for Reversing Thyroid Symptoms and Getting Your Life Back.

As a patient advocate, researcher, clinician and educator, Dr. Wentz is committed to raising awareness on how to overcome autoimmune thyroid disease through The Thyroid Secret Documentary Series, the Hashimoto’s Institute Practitioner Training, and her international consulting and speaking services offered to both patients and healthcare professionals.


  1. Sugiyama A, et. al. Hashimoto’s disease is a frequent comorbidity and an exacerbating factor of chronic spontaneous urticaria. Allergol Immunopathol (Madr). 2014 Jul 31.
  2. Fakkar NM et al. Study of Blastocystis hominis isolates in urticaria: a case-control study. Clinical and Experimental Dermatology, 36, 908–910.
  3. Blastocystis Research Foundation.
  4. Nagel R, Bielefeldt-Ohmann H, Traub R. Clinical pilot study: efficacy of triple antibiotic therapy in Blastocystis positive irritable bowel syndrome patients. Gut Pathogens. 2014;6:34. doi:10.1186/s13099-014-0034-0.
  5. Poirier P, et. al. New Insights into Blastocystis spp.: A Potential Link with Irritable Bowel Syndrome. PLoS Pathogens. March 2012.
  6. Biedermann T, et al. Hypersensitivity to nonsteroidal anti-inflammatory drugs and chronic urticaria cured by treatment of Blastocystis hominis infection. British Journal of Dermatology, 146, 1102–1117
  7. Dinleyici, E.C., et al., Clinical efficacy of Saccharomyces boulardii or metronidazole in symptomatic children with Blastocystis hominis infection. Parasitology Research, 2011. 108(3): p. 541-5.
  8. Levy, Y (06/2003). “Chronic urticaria: association with thyroid autoimmunity.” Archives of disease in childhood (0003-9888), 88 (6), 517.
  9. RAJI?, B., ARAPOVI?, J., RAGUž, K., BOšKOVI?, M., BABI?, S., MASLA?, S. Eradication of Blastocystis hominis prevents the development of symptomatic Hashimoto’s thyroiditis: a case report. The Journal of Infection in Developing Countries, North America, 9, Jul. 2015. Available at: <>. Date accessed: 03 Oct. 2015.
  10. Aghili R, Jafarzadeh F, Bhorbani R, Khamseh ME, Salami MA, Malek M. The association of Helicobacter pylori infection with Hashimoto’s thyroiditis. Acta Med Iran. 2013;51(5):293-296.
  11. Franceschi F, Satta MA Mentella MC. Helicobacter pylori infection in patients with Hashimoto’s thyroiditis. Helicobacter. 2004;9(4):369.
  12. Lauritano EC, Bilotta AL, Gabrielli M, Scarpellini E, Lupascu A, Laginestra A, et al. Association between hypothyroidism and small intestinal bacterial overgrowth. J Clin Endocrinol Metab. 2007;92:4180–4.
  13. Janegova A, Janega P, Rychly B, Kuracinova K, Babal P. The role of Epstein-Barr virus infection in the development of autoimmune thyroid diseases. Endokrynol Pol. 2015;66(2):132-136.
  14. Draborg AH, Duus K, Houen G. Epstein-Barr virus in systemic autoimmune diseases. Clin Dev Immun. 2013;2013:535738. doi: 10.1155/2013/535738. Epub 2013 Aug 24.
  15. Nagata, K, Nakayama Y, Higaki K, et al. Reactivation of persistent Epstein-Barr virus (EBV) causes secretion of thyrotropin receptor antibodies (TRAbs) in EBV-infected B lymphocytes with TRAbs on their surface. Autoimmunity. 2015;48(5):328-335.

Did You Like this Article?

Subscribe to our newsletter to receive email notifications, some ways to find relief, and next steps.