H. Pylori Is Not Always The Villain

When H. pylori shows up on a stool test, panic is common. But not everyone with H. pylori has a problem and not every problem needs the same 'Kill Bill' solution. Think of H. pylori like a roommate: sometimes quiet, sometimes messy, occasionally destructive.

Helicobacter pylori is a spiral-shaped bacterium that can live in the stomach lining. It survives by releasing urease, an enzyme that neutralises stomach acid so it can 'hang out' in what should be an acid bath. This trick helps the bug, and lowers your acid too, which can ripple into:

• Poor protein breakdown

• Iron & B12 malabsorption that can look like anaemia, fatigue, hair shedding

• Impaired enzyme/bile signalling which can result in bloating, reflux, 'brick belly'

• Gastritis (inflamed stomach lining) or ulcers (sores)

H. pylori can also adhere to tissue (gastric mucosa, even vascular endothelium), produce exotoxins and cause local and systemic inflammation.

Many people carry H. pylori with no symptoms. Only approximately 15% develop ulcers, 1–3% progress to gastric cancer. Some researchers even frame it as potentially commensal (part of the microbial community) in low levels. So a positive test does not mean automatic treatment. The real question is: Is it causing trouble in you right now?

Symptoms and red flags

Common symptoms (may overlap with reflux/gastritis):

• Reflux/heartburn, frequent belching, bitter/sour taste

• Burning or gnawing upper-abdominal pain

• Nausea or early fullness (food 'just sits there')

• Bloating after meals

• Low iron or B12, anaemia, fatigue

• Ulcer-type pain: after meals (gastric) or 2–4 hours later/at night (duodenal)

Red flags – see a doctor promptly:

• Unintentional weight loss

• Black/tarry stools, vomiting blood

• Severe anaemia, persistent/worsening pain

• Ongoing vomiting, difficulty swallowing

Testing

Frontline (active infection):

• Urea breath test: you drink labelled urea, the H. pylori urease makes labelled CO₂ , which is measured in the breath. This is a non-invasive test, which is good for diagnosis and eradication checks.

• Stool antigen test: detects current infection.

When there are red flags/complications:

• Endoscopy and biopsy: get a direct view of the tissue, and also take a culture if needed. It is invasive but definitive.

Exposure only (not activity):

• Blood antibodies (IgG): this shows if you’ve ever had it but can’t tell if it’s active.

Functional big-picture:

• GI-MAP (PCR): very sensitive; detects DNA and the virulence factors (genes that can make strains more aggressive), plus overall microbiome and downstream clues (such as low elastase suggesting poor pancreatic output, dysbiosis, and overgrowths).

  However, this PCR test can pick up tiny, clinically irrelevant traces. So interpretation of the test must be done in context. At the New School, we don't treat the test, we 'treat' the individual.

Preparation is key: Proton Pump Inhibitors (PPIs), bismuth and antibiotics can skew breath/stool antigen results. Usually stopping these for approximately 4 weeks is advised by your clinicians before testing or re-testing.

Summary of the tests

Test	What It Shows	Pros	Cons
Urea breath test	Active infection (bug metabolising urea)	Non-invasive, accurate, widely used	Must stop PPIs/antibiotics first
Stool antigen test	Active infection	Affordable, simple, non-invasive	Less accurate if on acid blockers
Endoscopy and biopsy	Direct look + tissue sample	Gold standard, detailed	Invasive, expensive
Blood antibodies (IgG)	Past or present exposure	Cheap, simple	Can’t tell if the infection is active
GI-MAP (PCR Stool)	DNA + virulence factors + gut ecosystem	Comprehensive functional tool	Can over-detect tiny irrelevant traces

Best bets for active infection: Breath or stool antigen.

Most comprehensive picture: GI-MAP (if interpreted carefully).

Gold standard (but invasive): Endoscopy with biopsy.

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The Terrain: Some reasons as to why H. pylori thrives

1) Stress and the HPA axis

A hyper-vigilant HPA axis keeps you in 'predator mode', even if the 'predator' is a toxic job, deadlines, or life load. The body diverts from rest-and-digest to fight-or-flight, which suppresses stomach acid (HCl). Low HCl means easier entry/expansion for H. pylori.

2) Medications

• PPIs (Proton Pump Inhibitors) & H2 (histamine) blockers: suppress acid, thereby 'weakening' a primary defence

• Antibiotics: reduce protective competitors, allowing the H.Pylori the opportunity to 'take advantage'

• NSAIDs (ibuprofen, aspirin, steroids): injure the mucosa, setting up gastritis/ulcers

3) Nutrient deficiencies which lead to HCl acid deficiency

• Zinc is required to produce HCl

• Sodium (chloride) provides the chloride in hydrochloric acid

• Protein intake signals acid release

• Ultra-processed diets reduce nutrients that aid digestion

4) How we eat

• Chew thoroughly, digestion starts in the mouth, it 'tells' the stomach to prepare the acid and enzymes

• Sit and slow down to eat (parasympathetic mode is the digestion mode)

• Avoid eating on the run, hunched posture, or grazing mindlessly, as these can result in weak digestive signalling.

Functional Gut Test by Genova

When to treat H. pylori

The decision isn’t a 'positive test equates 'kill it'. It is about context.

Treatment usually makes sense if:

• You have ulcers or gastritis

• There’s iron/B12 deficiency or anaemia

• Symptoms are strong and persistent

• Virulence factors are present on PCR stool tests

• You have high risk of gastric cancer

Treatment options:

• Conventional: triple antibiotic therapy (often effective, but intense)

• Nutritional/Herbal: oregano, berberine, mastic gum, Oregon grape, Chinese goldthread, DGL (deglycyrrhizinated licorice), plus soothing herbs like aloe, marshmallow, slippery elm to protect the stomach first.

Timing is crucial: if the stomach lining is inflamed, a qualified practitioner will heal and soothe gut lining first, then 'treat'.

Re-test to ensure it has been eradicated.

To health!

From the team at the New School Of Nutritional Medicine

Learn about the Founder & Principal of the New School of Nutritional Medicine, Dr Khush Mark PhD, HERE.