SIBO vs. SIFO: Know the Difference, Heal Your Gut

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: SIBO vs. SIFO: Know the Difference, Heal Your Gut

• Podcast Review: Secrets to Sleeping Well and Aging Slowly with Dr. Lisa Merritt

• Ask Dr. Eric: Can healing the gut help to heal thyroid eye disease?

SIBO vs. SIFO: Know the Difference, Heal Your Gut

Under normal circumstances, the upper small intestine contains relatively few bacteria compared to other parts of the gastrointestinal tract. Small intestinal bacterial overgrowth (SIBO) occurs not just due to an increase in bacterial quantity, but also a shift in the type of organisms present.

For example, in a healthy small intestine, most bacteria are gram-positive. In SIBO, however, there is often a shift toward gram-negative organisms such as E. coli and Klebsiella pneumoniae, although certain gram-positive organisms like Enterococcus can also become overrepresented.¹

SIBO is a type of gut dysbiosis and is frequently associated with irritable bowel syndrome (IBS), particularly the diarrhea-predominant type (IBS-D).² While not all IBS cases involve SIBO, a significant number do.

The Link Between SIBO and Food Poisoning

Through my SIBO certification training with Dr. Allison Siebecker in 2017, I learned that food poisoning is the most common cause of IBS-D. This often results in damage to the gut’s migrating motor complex via an autoimmune response, impairing gut motility and setting the stage for bacterial overgrowth. Although this damage is currently irreversible, SIBO caused by food poisoning is still treatable—though it may require long-term prokinetic support to prevent recurrence.

How to Know If You Have SIBO

While symptoms can be informative, testing is the best way to confirm SIBO. Common symptoms include:

✅ Bloating or abdominal discomfort (especially after eating high-FODMAP foods)

✅ Gas, belching, or abdominal pain

✅ Diarrhea and/or constipation

✅ Unexplained weight changes

✅ Skin issues like eczema or rashes

The gold standard for diagnosing SIBO is a breath test, which measures levels of hydrogen and methane gases after ingestion of a sugar substrate (usually lactulose or glucose). Elevated levels of these gases suggest excessive bacterial fermentation in the small intestine.

Three Treatment Options for SIBO

Prescription Antibiotics. Rifaximin (Xifaxan) is commonly prescribed and is unique among antibiotics in that it typically does not disrupt beneficial gut flora. It may even increase beneficial strains like Bifidobacterium and Faecalibacterium prausnitzii.³ However, not all patients respond to rifaximin, and it’s generally not my first-line approach.

Herbal Antimicrobials. Natural options such as berberine, oregano oil, neem, and allicin can be effective. Allicin (from garlic) is often tolerated even by those with SIBO, though individual sensitivity varies. A clinical trial showed that herbal antimicrobials are as effective as rifaximin in treating SIBO.⁴

Elemental Diet. This therapeutic diet is designed to “starve” bacteria while providing easily absorbable nutrients. It typically includes amino acids, fats, simple carbohydrates (i.e. glucose), vitamins, and minerals. Though highly effective, it can be difficult to follow. The standard duration is 2–3 weeks, followed by retesting.

SIFO: Small Intestinal Fungal Overgrowth

SIFO is characterized by excessive fungal growth in the small intestine and is often overlooked. Symptoms mirror those of SIBO and include:

✅ Gas, bloating, belching

✅ Indigestion, nausea, diarrhea

✅ Fatigue, brain fog, joint pain, and skin issues

Unlike SIBO, SIFO can’t be diagnosed via breath testing. The gold standard is an aspirate and culture from the small intestine, which is not widely available. If someone has SIBO-like symptoms but tests negative, or fails to respond to typical SIBO treatments, SIFO should be considered.

Tests for candida antibodies or organic acids (e.g., elevated arabinose) can suggest fungal overgrowth but cannot pinpoint its location. Still, if symptoms suggest fungal overgrowth and lab markers support it, a low-sugar diet combined with antifungal support (herbal or pharmaceutical) may be warranted. Nystatin is a common antifungal medication, but many practitioners (myself included) often start with natural antifungals first.

Conclusion

SIBO and SIFO are underrecognized yet common causes of chronic digestive and systemic symptoms. Breath testing remains the go-to method for diagnosing SIBO, while SIFO often requires a more nuanced clinical approach. Whether bacterial or fungal in nature, identifying the underlying cause of gut overgrowth can be transformative for patients with IBS, thyroid autoimmunity, skin conditions, and more.

While treatment options vary, a personalized strategy that may include herbal antimicrobials, dietary therapy, or even prescription medications can make a significant difference in outcomes—especially when combined with long-term gut support and lifestyle strategies.

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 podcast episode I had a conversation with my friend and chiropractor, Dr. Lisa Merritt, a functional medicine expert and holistic health educator, shares how seemingly harmless habits can disrupt sleep and accelerate aging. We talk about strategies for calming a racing mind, improving vagal nerve tone, and setting up an environment that supports deep, restorative rest. You’ll also hear how to spot anti-aging fads that waste time and money, and the simple shifts that create lasting benefits for your body and mind.

Listen now to discover how to reclaim your nights and protect your health for years to come.

Ask Dr. Eric

During every issue I'll answer a question or two 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: CAN HEALING THE GUT HELP HEAL THYROID EYE DISEASE?

Dr. Eric, how important is healing the gut when someone is dealing with thyroid eye disease?

Thanks for your question! Thyroid Eye Disease (TED), also referred to as Graves’ orbitopathy or ophthalmopathy, is a chronic inflammatory condition affecting the eye tissues—most notably the muscles and connective tissues behind the eyes. It is commonly associated with Graves’ disease.

In TED, the same thyroid-stimulating immunoglobulins (TSI) that target the thyroid gland in Graves’ disease also bind to receptors in the eye tissues. This triggers inflammation, swelling, and a cascade of immune activity that can result in symptoms such as:

• Eye bulging (exophthalmos)

• Eye pain or pressure

• Redness and swelling

• Double vision

• Dry or gritty eyes

TED is more than just a cosmetic concern—it can have significant impacts on vision, comfort, and quality of life. While conventional treatments often focus on managing the symptoms (e.g., corticosteroids, Tepezza), some people seek a root-cause approach to address the underlying immune dysfunction.

The Gut-Immune Connection: Why It Matters in TED

Many who have been reading this newsletter for awhile already know that approximately 70% of the body’s immune system resides in the gut. This means that your gut microbiome plays a pivotal role in regulating immune balance.

In autoimmune conditions like Graves’ disease and TED, this immune regulation is compromised. Intestinal permeability (a.k.a. "leaky gut"), dysbiosis (imbalance of gut flora), and chronic inflammation can all contribute to immune system dysfunction and heightened autoimmunity.

Therefore, optimizing gut health isn’t just beneficial—it’s essential in reversing TED.

The Goal: Remove Triggers and Restore Gut Integrity

Just as with Graves’ disease, the primary goal when addressing TED from a functional medicine perspective is to identify and remove the triggers that are driving the autoimmune response. These may include:

✔️ Chronic infections (H. pylori, Epstein-Barr virus, gut parasites)

✔️ Food sensitivities (gluten, dairy, corn, soy)

✔️ Environmental toxins (mold, heavy metals, chemical exposure)

✔️ Stress and trauma

Addressing these root causes while supporting gut repair through diet, targeted supplements, and lifestyle changes can lead to meaningful improvements in both thyroid and eye health.

Additional Thyroid-Related Resources

Click Here for Secrets to Sleeping Well and Aging Slowly (episode 212)

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/22262197/ 

(2) https://pubmed.ncbi.nlm.nih.gov/32754068/

(3) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504364/ 

(4) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030608/

That’s a wrap