Is H. pylori driving your thyroid autoimmunity?

Helicobacter pylori (H. pylori) is the most common infection in the world and has been linked to autoimmune thyroid disease (AITD). Most people won’t have any symptoms, though some may experience significant upper GI bloating, pain, nausea, or burping.

Given its prevalence and connection to AITD, should testing for H. pylori be part of an initial workup for thyroid autoimmunity? It’s something I routinely discuss with my clients. Today’s blog is a resource for anyone who has tested positive, explaining why addressing this infection can be an important piece of your thyroid health puzzle.

H. pylori is a gram-negative bacterium that embeds into the stomach lining, causing inflammation and damage. It affects about 50% of the global population and has a remarkable ability to survive the stomach’s acidic environment.

The infection spreads through contact with infected bodily fluids, poor hand hygiene, and contaminated food or water.

Because of this, household members may also need testing to prevent reinfection, and sharing drinks, food, and utensils should be avoided.

Most people are asymptomatic, but around 30% may experience:

• Stomach pain or burning
• Upper GI bloating shortly after eating
• Gas and frequent burping
• Nausea
• Feeling full quickly, loss of appetite, or weight loss
• Development of new food sensitivities: H.pylori can reduce stomach acidity and impair digestion of proteins, which can make the gut more reactive

In a small number of cases, the infection can increase the risk of stomach cancer. It is classified as a Group 1 carcinogen by the International Agency for Research on Cancer.

H. pylori can also affect other systems beyond the stomach. Research links it to brain and nerve disorders (stroke, Alzheimer’s), skin conditions (rosacea, psoriasis), allergies (asthma, chronic hives), respiratory infections including COVID-19, blood issues like iron deficiency anemia, heart disease, certain types of glaucoma, and endocrine/metabolic conditions such as autoimmune thyroiditis and diabetes [Source].

In short, H. pylori doesn’t just stay in the stomach — it may influence multiple systems throughout the body.

How is it diagnosed?

The first-line test is usually a stool antigen test, ordered via a doctor or naturopath (I offer this service 😉). If results are negative but symptoms persist, a C-13 urea breath test is the next step.

This test measures carbon dioxide in the breath after taking C-13-labeled urea. H. pylori produces an enzyme called urease, which breaks down urea into ammonia and CO₂ — if detected in the breath, it confirms infection. Breath testing is considered the gold standard but requires referral to a gastroenterology clinic in New Zealand.

Conventional treatment

If positive, typical treatment is triple therapy: a proton pump inhibitor (acid blocker) plus two antibiotics (usually clarithromycin and amoxicillin or metronidazole) for 14 days, with 70–85% effectiveness [Source].

Quadruple therapy adds a fourth medication to the protocol: bismuth subsalicylate.

However, resistance to these antibiotic treatments is on the rise. In New Zealand, clarithromycin resistance has doubled since 1999 [Source]. This is partly due to the bacteria’s ability to form biofilms, which make it harder for antibiotics to penetrate, as well as genetic mutations that alter antibiotic targets.

Another consideration is that the therapy itself can be intense and may heavily disrupt the gut microbiome, leading to dysbiosis.

The H.pylori–autoimmune thyroid link

A 2024 study [Source] explored the connection between H. pylori infection and thyroid autoimmunity. Two hundred people took part — half with an active H. pylori infection and half healthy controls.

Each participant was tested for:

• Thyroid-stimulating hormone (TSH)
• Thyroid hormones (T4 and T3)
• Anti-thyroid peroxidase antibodies (TPO)
• Thyroglobulin antibodies (Tg)
• H. pylori-IgG (antibodies against H. pylori)
• cagA-IgG (antibodies against a more aggressive strain of the bacteria, linked to ulcers and stomach cancer)

The results: people with an H. pylori infection showed notable differences in their thyroid markers compared to those without infection.

• They had higher levels of TSH, suggesting the thyroid was under-active
• They had higher levels of thyroid antibodies (TPO and Tg), which are consistent with autoimmune thyroid conditions like Hashimoto’s
• They had lower levels of T4 and T3, indicating reduced thyroid hormone production

In short H. pylori infection was associated with signs of an under-active or inflamed thyroid.

Not only that, the higher the H. pylori antibody levels, the more disrupted the thyroid markers — suggesting the bacteria may play a role in driving thyroid autoimmunity.

🦠 This is just one study I’ve chosen to highlight; there are others, and H. pylori infection has also been linked to Graves’ disease.

How might this happen?

H. pylori damages the stomach lining and triggers inflammation, over-activating the immune system. Sometimes, antibodies targeting H. pylori mistakenly attack the thyroid due to structural similarity.

Other times, gut damage allows proteins from food to enter the bloodstream, confusing the immune system and prompting thyroid attack. Both mechanisms can contribute to autoimmune thyroid disease.

A natural approach to eradication

For those who test positive, there’s the conventional antibiotic pathway or complementary approaches. Some choose the natural route after failing conventional therapy, while others start with it for gentler gut support.

This approach often includes:

• Supporting the nervous system and stress management, since chronic stress reduces secretory IgA, a key immune defence in mucosal tissues
• An anti-inflammatory diet and removal of trigger foods (caffeine, alcohol, gluten, dairy, sugar, processed meats)
• Herbal antimicrobials: mastic gum, licorice root, black cumin (Nigella sativa), green tea (EGCG), broccoli sprouts, and pure cranberry juice (there are more!)
• Short-term use of N-acetyl cysteine (NAC) to thin the stomach mucus, allowing herbs to act directly on H. pylori
• Nutrients like vitamin C and zinc carnosine
• Specialty probiotics such as Lactobacillus reuteri DSM17648 (PyloGuard™), which helps detoxify H.pylori from the gut

After treatment, restoring beneficial microbes and healing the gut lining with nutrients like glutamine is important.

Final thoughts

A natural approach doesn’t mean using all interventions at once — it’s tailored to your individual needs. Clearing H. pylori is a crucial step toward addressing the complex puzzle of autoimmune thyroid disease, supporting your journey to better thyroid and gut health!

If you suspect this might be an issue for you, feel free to explore what working together could look like here.

Hugs,
Lauren