Gut Infections, H. Pylori Testing

Welcome to Healthy Gut Healthy Thyroid!

This is your weekly roundup of the BEST actionable steps for those people with thyroid and autoimmune thyroid conditions who want to restore their health…by healing their gut. Whether you have hyperthyroidism or Hashimoto’s you will benefit from the content in this newsletter.

In today's issue:

• Main Topic: Why Gut Infections Are Commonly Overlooked

• Podcast Review: Is it Possible to Heal Your Thyroid in 3 Months or Less?

• Understand Your Tests: Testing for H. Pylori

• Ask Dr. Eric: Is H. Pylori my trigger?

Why Gut Infections are Commonly Overlooked

Most functional medicine practitioners begin their protocols with foundational diet and lifestyle changes—and rightly so. This is why I identified inflammatory foods as “Roadblock #1” in Newsletter #11, where I discussed the top 5 gut healing roadblocks. I later expanded on that in Newsletter #12, diving deeper into the role of food in gut and thyroid health.

In Newsletter #13, I also explained how environmental toxins can damage the gut and thyroid, and how addressing these toxicants is essential to the healing process. Then, in Newsletter #14, I discussed the importance of stomach acid, and how low levels of gastric acid can be a hidden contributor to gut infections and microbial overgrowths.

But here’s the problem: gut infections are often missed, even in the natural health world. While dietary changes and detox strategies are common starting points, infections and microbial imbalances can persist beneath the surface—often without obvious digestive symptoms.

The Different Microorganisms That Can Disrupt the Gut

Let’s break down the primary categories of microorganisms that can affect gut health:

Viruses: Often cause acute digestive symptoms such as diarrhea and abdominal pain. These are typically short-lived.

Bacteria: Pathogens like Salmonella and E. coli are usually symptomatic, but others—like H. pylori—can be silent for years.

Parasites: Organisms like Giardia and Cryptosporidium may cause obvious symptoms or remain unnoticed, depending on the host’s immune response.

Fungi: Candida albicans is the most well-known yeast. While it’s a normal inhabitant of the gut, overgrowth can lead to systemic issues.

Infection vs. Overgrowth: What’s the Difference?

Some microorganisms are considered opportunistic, meaning they live in the gut normally, but can overgrow and cause problems when conditions allow—such as after antibiotic use, during chronic stress, or in the presence of low stomach acid.

For example:

SIBO (Small Intestinal Bacterial Overgrowth) involves excessive bacteria in the small intestine.

SIFO (Small Intestinal Fungal Overgrowth) refers to excessive yeast or fungal growth in the same area.

In contrast, a true infection involves pathogenic organisms (like Giardia or Salmonella) that are not meant to reside in the gut and can actively damage the gut lining or disrupt immune function.

Should You Test for Gut Infections or Overgrowths?

While not every patient needs immediate gut testing, it’s a critical step for many—especially those with persistent symptoms or autoimmune thyroid conditions like Hashimoto’s or Graves’ disease. Here are the most common tests I recommend:

Comprehensive Stool Panel: Assesses H. pylori, parasites, pathogenic and opportunistic bacteria, fungal markers, and inflammatory and digestive health markers.

SIBO Breath Test: Useful for those with gas and bloating, especially after eating high-FODMAP foods.

Organic Acids Test: Not gut-specific, but excellent for detecting yeast overgrowth and Clostridia species by evaluating metabolic byproducts.

Addressing Infections and Overgrowths

There’s no one-size-fits-all solution. While I often recommend herbal antimicrobials, the specific approach depends on the microorganism involved. For instance:

✔️H. pylori requires a different protocol than SIBO.

✔️Parasite protocols may include antiparasitic herbs not used for fungal overgrowths.

✔️Yeast overgrowths often respond well to targeted antifungals and dietary changes.

Conclusion

Although diet, stress management, and detoxification are essential for gut healing, they may not be enough if a hidden infection or microbial imbalance is present. This is why gut infections and overgrowths deserve more attention—especially in those with thyroid conditions. Proper testing, individualized protocols, and ongoing support can make the difference between temporary relief and lasting healing.

 Find Your Hashimoto’s Triggers

If you have Hashimoto’s thyroiditis, visiting an endocrinologist is likely to result in a prescription for thyroid hormone replacement. And while there is a time and place for thyroid hormone, the problem is that it doesn’t do anything for the autoimmune component of Hashimoto’s.

And so what happens is that many people will take thyroid hormone without doing anything to improve the health of their immune system, which means that over time further damage to their thyroid gland will take place.

The good news is that you can do things to reverse the autoimmune component of Hashimoto’s. And the best way to accomplish this is by finding and removing your triggers.

My book “Hashimoto’s Triggers” will show you how to do this. By reading this book you will discover the following:

• More than one dozen triggers of Hashimoto’s thyroiditis

• The different diet options, and how to detect your specific food triggers

• Everything you need to know to heal your gut

• How to reduce fatigue, brain fog, hair loss, lose weight, and address other common symptoms

• Strategies to lower thyroid antibodies when nothing else has worked

• Nutritional supplements and herbs for Hashimoto’s

• A comprehensive list of the blood tests you should get, along with other specific tests that can help detect your triggers

• What you need to do to achieve optimal adrenal health

• Natural treatment options for viruses, pathogenic bacteria, parasites, Candida, and SIBO

Click Here to order the book “Hashimoto’s Triggers”

Save My Thyroid Podcast Review

I have a podcast called "Save My Thyroid", where I discuss how people with hyperthyroidism and Hashimoto's can save their thyroid and regain their health. And during each edition of this newsletter I'll briefly discuss a recent podcast episode.

In a recent Q & A podcast episode I answered the question “Is it Possible to Heal Your Thyroid in Three Months or Less?” Through my personal and clinical experience, I break down why most thyroid conditions take many months to truly stabilize. You'll learn the difference between having ‘normal labs’ and real healing, why looking beyond TSH matters, and how hidden imbalances in the gut, adrenals, or immune system can slow down your progress. This talk isn’t for discouragement—it’s about knowing the general experience so you know what’s possible for your own journey.

If you're tired of chasing fast results and ready to understand what true healing looks like, this episode is a must-listen, so tune in now!

Understand Your Tests

Testing for Helicobacter Pylori

Because H. pylori can serve as a potential trigger for both Graves' disease and Hashimoto's, I recommend testing for this bacterium in most of my autoimmune thyroid patients—even in the absence of overt digestive symptoms. There are several diagnostic methods available, each with its own advantages and limitations:

Blood Antibody Test. This test measures antibodies to H. pylori in the bloodstream. However, a significant limitation is that H. pylori antibodies can remain elevated long after the infection has been eradicated. As a result, it is not reliable for determining an active infection, and for this reason, I rarely recommend blood testing for H. pylori.

Urea Breath Test (Patient Test #1). This test leverages H. pylori’s unique ability to convert urea into carbon dioxide, which can then be detected in a breath sample. The urea breath test is considered highly accurate and is frequently used in conventional medical settings to diagnose active H. pylori infections.

Stool Antigen Test (Patient Test #2). This test detects H. pylori antigens in a stool sample. It is also regarded as a highly sensitive and specific method for identifying active infection. That said, false negatives can occur, particularly if the patient has recently taken antibiotics, proton pump inhibitors (PPIs), or certain herbal antimicrobials.

PCR Stool Test (Patient Test #3). Polymerase chain reaction (PCR) testing detects H. pylori DNA in the stool. One of the more widely used PCR-based tests is the GI-MAP by Diagnostic Solutions. In my clinical experience, this test sometimes detects H. pylori when both the urea breath test and stool antigen test yield negative results.

However, the presence of H. pylori on a PCR test does not automatically warrant treatment. I typically only recommend treatment when H. pylori is both detectable and elevated, as not all colonization is clinically significant.

Ask Dr. Eric

During every issue I'll answer one or two questions that I think can benefit most people with a thyroid or autoimmune thyroid condition. If you'd like for me to consider your question for a future edition of this newsletter email your question to [email protected].

QUESTION: HOW DO I KNOW IF H. PYLORI IS MY TRIGGER?

Dr. Eric, I recently tested positive for H. pylori on a GI-MAP, but since I'm not experiencing any digestive symptoms I'm wondering how can I tell if this is my trigger?

The scientific literature shows a potential relationship between Helicobacter pylori (H. pylori) infection and autoimmune thyroid conditions, including Graves’ disease and Hashimoto’s thyroiditis.^1,2 While correlation does not necessarily imply causation, in my clinical experience—and that of many other functional medicine practitioners—H. pylori can be a significant trigger in the development or exacerbation of thyroid autoimmunity.

Even in non-autoimmune hypothyroidism, H. pylori may present a problem. It can interfere with the absorption of thyroid hormone replacement therapy by suppressing stomach acid production.³ This means that someone taking levothyroxine or other thyroid hormones might have reduced efficacy if they are unknowingly harboring an H. pylori infection.

Could H. Pylori Be Your Main Trigger?

For patients with autoimmune thyroid conditions who test positive for H. pylori, it’s not always clear whether the infection is the primary trigger. Autoimmune conditions are typically multifactorial, and it's common for individuals to have multiple triggers contributing to immune dysregulation.

That said, if H. pylori is positive—whether through a comprehensive stool test or a urea breath test—I generally recommend addressing it, even in the absence of classic gastrointestinal symptoms like heartburn, reflux, or bloating.

Antibiotics vs. Natural Approaches for H. Pylori

I just want to briefly mention the different treatment options:

Conventional Therapy: Typically involves triple therapy—two antibiotics plus a proton pump inhibitor (PPI). While often effective, this can significantly disrupt the gut microbiome and may contribute to longer-term imbalances in digestive health.

Natural Antimicrobials: These include mastic gum, black cumin, DGL licorice, and oregano oil, and they tend to be gentler on the microbiome but require more time and consistency. Most natural approaches take at least two months, and in some cases three or four months for full eradication. Occasionally, a follow-up test may still show H. pylori, requiring extended treatment or a change in strategy.

In my practice, I usually recommend starting with a natural protocol, especially for those with preexisting gut issues or microbiome imbalances. If the infection persists after two to three months, then the patient can decide whether to continue the natural approach or transition to conventional therapy.

Additional Thyroid-Related Resources

Click Here for “Is it Possible to Heal Your Thyroid In 3 Months or Less?” (podcast)

Click Here for 5 Gut Healing Roadblocks to Overcome (newsletter #11)

Click Here to access hundreds of thyroid-related articles and blog posts

Click Here to join the Graves’ disease and Hashimoto’s community

Click Here to purchase one of Dr. Eric’s thyroid-related books

Click Here to work with Dr. Eric and his team

References:

(1) https://pubmed.ncbi.nlm.nih.gov/31906000/

(2) https://pubmed.ncbi.nlm.nih.gov/37568552/

(3) https://pubmed.ncbi.nlm.nih.gov/21435090/

That’s a wrap