Hashimoto’s Root Cause: How Leaky Gut, Anti-Gliadin Antibodies, and H. pylori Trigger Autoimmunity

Hashimoto’s thyroiditis is one of the most common autoimmune conditions in the United States. It is often treated as a thyroid-only disorder. Medication may stabilize hormone levels, but many patients continue to struggle with fatigue, brain fog, weight changes, hair thinning, infertility, and inflammation.

As a functional medicine practitioner, I approach Hashimoto’s differently.

Instead of asking only how to replace thyroid hormone, we ask:

Why is the immune system attacking the thyroid in the first place?

More often than not, the answer leads back to the gut.

What Is Hashimoto’s Thyroiditis?

Hashimoto’s is an autoimmune thyroid condition where the body produces antibodies commonly TPO and thyroglobulin antibodies that attack thyroid tissue. Over time, this can lead to hypothyroidism.

However, the thyroid is often the target, not the root cause.

Hashimoto’s is fundamentally an immune dysregulation condition and the immune system is deeply connected to the gut.

The Gut-Thyroid-Immune Axis

Approximately 70–80% of the immune system resides in the gut-associated lymphoid tissue. The intestinal lining acts as both a digestive surface and an immune barrier.

When gut integrity is compromised (often referred to as increased intestinal permeability), immune activation increases. Undigested food particles, microbial fragments, and toxins can enter circulation, triggering systemic immune responses in genetically susceptible individuals.

In clinical practice, when we test patients with Hashimoto’s, we frequently uncover gut-driven immune triggers.

One of the most valuable tools for evaluating this is the GI-MAP, a comprehensive stool analysis that assesses:

• Microbiome balance

• Pathogens and opportunistic bacteria

• Immune markers

• Secretory IgA

• Anti-gliadin antibodies

• H. pylori

• Inflammatory markers

Common GI-MAP Findings in Hashimoto’s Patients

Elevated Anti-Gliadin Antibodies

One of the most common findings we see clinically in Hashimoto’s patients is elevated anti-gliadin antibodies on GI-MAP testing.

Gliadin is a component of gluten. Even in patients who do not have celiac disease, immune reactivity to gliadin is common in autoimmune thyroid cases.

Why this matters:

• Gluten exposure can increase zonulin, which affects intestinal permeability.

• Increased permeability allows immune exposure to gliadin fragments.

• Molecular mimicry may occur where immune cells mistake thyroid tissue for gliadin.

• This perpetuates autoimmune activation.

When anti-gliadin antibodies are elevated, we often implement a structured gluten elimination protocol alongside gut repair — not arbitrarily, but based on objective immune data.

Elevated Secretory IgA (sIgA)

Secretory IgA is the primary antibody of the mucosal immune system.

On GI-MAP testing, elevated sIgA often indicates:

• Ongoing immune activation in the gut

• Chronic antigen exposure

• Food sensitivities

• Microbial imbalance

Autoimmune conditions like Hashimoto’s are rooted in immune dysregulation. If the gut immune system is constantly stimulated, systemic immune imbalance often follows.

H. pylori and Autoimmune Thyroid Disease

Another pattern we frequently identify is overgrowth of Helicobacter pylori.

H. pylori can:

• Disrupt stomach acid production

• Impair nutrient absorption (iron, B12)

• Promote systemic inflammation

• Stimulate immune activation

Chronic infections are well-known immune triggers. When present, they must be addressed strategically and in phases to avoid further immune stress.

Epstein-Barr Virus (EBV) as an Immune Trigger

We also commonly see correlations between Hashimoto’s and prior infection or reactivation of Epstein-Barr virus.

EBV has been associated with several autoimmune conditions. While not always the root cause, viral stress can act as a catalyst in immune-driven disorders.

Why Thyroid Medication Alone Is Often Not Enough

Thyroid replacement therapy can be life-changing and necessary. However, it does not:

• Repair intestinal permeability

• Reduce food-based immune triggers

• Address microbial imbalance

• Remove chronic pathogens

• Regulate mucosal immune activation

Without addressing upstream drivers, antibodies may remain elevated and symptoms may persist.

Our Integrative Functional Gut Health Package

At Integrative Wellness Center of Jacksonville, we developed our Integrative Functional Gut Health Package specifically for patients who need a structured, root-cause approach including those with Hashimoto’s and other autoimmune conditions.

This package is designed to move beyond symptom suppression and identify the drivers of immune activation.

Rather than guessing or applying generic protocols, we use testing to create a strategic plan.

For many Hashimoto’s patients, this means:

• Identifying gluten reactivity that standard labs missed

• Reducing immune overactivation

• Restoring microbial balance

• Supporting gut barrier repair

• Improving nutrient absorption

• Calming antibody activity

When the gut environment improves, we often see improvements in energy, mental clarity, digestive function, inflammation levels, and overall thyroid stability.

Why Testing Is the First Step

Functional medicine is data-driven. The first step in working with Hashimoto’s from a root-cause perspective is comprehensive testing.

The GI-MAP provides insights that standard blood work simply cannot.

If you are struggling with:

• Persistent thyroid antibodies

• Fatigue despite medication

• Digestive symptoms

• Food sensitivities

• Brain fog

• Autoimmune flares

A comprehensive gut evaluation may be the missing piece.

Hashimoto’s does not begin in the thyroid it begins in the immune system.

And in many cases, the immune system is reacting to something happening in the gut.

Through comprehensive testing, strategic gut repair, and immune regulation, it is possible to address upstream triggers rather than simply managing downstream symptoms.

If you are ready to take a root-cause approach to Hashimoto’s and understand what your immune system is responding to, our Integrative Functional Gut Health Package is designed to provide clarity, precision, and a structured path forward.