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A Functional Medicine H-Pylori Protocol: Testing, Diagnoses, and Treatment

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A Functional Medicine H-Pylori Protocol: Testing, Diagnoses, and Treatment

Helicobacter pylori is a bacteria that resides in the digestive tracts of over two-thirds of the world's population. A higher prevalence of infection is noted in developing countries, people of low socioeconomic status, and the Hispanic and African American populations. This bacteria is often found in the stomach of infected individuals and can cause inflammation, ulceration, and increased risk of stomach cancer. Therefore, it is recommended to treat infection in symptomatic individuals when identified. This article will discuss H. pylori infection and functional medicine considerations for testing and treating infection. (1, 10)


What Is H. pylori?

Helicobacter pylori (H. pylori) is a spiral-shaped bacteria found in the gastrointestinal (GI) tract, commonly the stomach, of up to 75% of people globally. Most people don't know they have H. pylori because they never develop symptoms. However, in susceptible individuals, an infection can cause significant GI symptoms, peptic ulcer disease (PUD), gastritis, and stomach cancer. (1, 2)

H. pylori Symptoms

Although it's not fully understood why, up to 90% of people with H. pylori infection will never have any signs or symptoms. When symptoms do occur, they are typically related to gastritis (inflammation of the stomach lining) or a peptic ulcer (a sore within the lining of the stomach or small intestine) and may include (1):

  • Burning abdominal/stomach pain
  • Nausea and vomiting
  • Loss of appetite
  • Frequent burping
  • Heartburn, reflux, or GERD
  • Gas and bloating
  • Unintentional weight loss
  • Black or bloody stools caused by bleeding ulcers

What Causes H. pylori?

H. pylori infection occurs when the bacteria is spread from one person to another, typically during childhood, through direct contact with stool or saliva. Because of this, person-to-person transmission is common within families. H. pylori may also be spread through contaminated food or water. Once the H. pylori bacteria has gained access to the stomach, it uses its various virulence factors (cellular structures and molecules) to burrow into the stomach's lining and induce gastric inflammation. (1)

Hypochlorhydria, or low stomach acid, increases the risk of H. pylori infection because it creates a welcoming non-acidic environment in the stomach, allowing bacteria to adhere to the stomach wall more easily.

How Is H. pylori Diagnosed?

Per the American College of Gastroenterology (ACG) guidelines, screening for H. pylori infection should be performed in patients with an active or past history of PUD, gastric mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, and indigestion (5).

Endoscopic culture and biopsy of the stomach mucosa can be used to diagnose H. pylori infection. Given this procedure's cost and invasive nature, it is typically reserved when endoscopic imaging is indicated for other reasons.

The urea breath test is the most accurate non-invasive testing method for diagnosing H. pylori infection. The breath test involves the patient collecting a baseline breath sample, swallowing a urea-containing pill or liquid, and collecting a second breath sample 15 minutes later. The breath test measures and compares the carbon dioxide levels in each sample to determine the presence of infection. To prevent false negative results, patients should discontinue antibiotics and bismuth compounds for at least four weeks and proton pump inhibitors and sucralfate for at least two weeks before testing. (3)

A stool antigen test is another popular non-invasive testing method. It is cheaper than the urea breath test but slightly less accurate (3). This test measures immunogenic proteins (antigens) in the stool that are associated with H. pylori infection. Like the breath test, antimicrobials, proton pump inhibitors, and bismuth preparations can lead to a false-negative result; patients should discontinue these for at least two weeks before performing the test.

A serum IgG antibody test is the third non-invasive diagnostic test for H. pylori. This test cannot distinguish between an active and past infection and has the lowest accuracy rate. It may be recommended for patients with PUD or who cannot stop taking medications that affect the accuracy of breath and stool testing. (4, 5)

Functional Medicine Labs That Help Individualize Treatment for H. pylori Patients

Functional medicine labs help providers thoroughly assess GI health, rule out factors contributing to GI inflammation and symptoms, and customize H. pylori treatment for maximum efficacy.

Comprehensive Stool Test

A comprehensive stool test can holistically assess gastrointestinal health and function to adjunctively support gut healing and a balanced microbiome as needed and indicated by results.

The GI-MAP by Diagnostic Solutions is a popular stool testing option among functional medicine providers specifically for diagnosing and treating H. pylori. This panel includes DNA detection and quantification of H. pylori microbes, virulence factors, and antibiotic-resistant genes. The presence or absence of virulence factors and antibiotic resistance can change treatment option decisions to assist in the timely and successful eradication of infection.

Blood Tests for Hypochlorhydria

If hypochlorhydria is suspected or determined as a cause of H. pylori infection, ordering a panel that includes a CBC, CMP, iron panel, thyroid panel, vitamin B12, intrinsic factor, and anti-parietal cell antibodies can screen for causes and consequences of low stomach acid.

Food Sensitivity Testing

Food sensitivities contribute to gastrointestinal inflammation, exacerbating abdominal pain and other symptoms of H. pylori-induced gastritis and PUD. Antibody testing identifies foods to which an individual is sensitive so that they can temporarily remove them from the diet to palliate symptoms and facilitate the gut-healing process.

SIBO Breath Testing

Proton pump inhibitor (PPI) therapy is a mainstay treatment for H. pylori eradication, gastritis, GERD, and PUD. PPI use and hypochlorhydria are risk factors for small intestinal bacterial overgrowth (SIBO), contributing to low-grade GI and systemic inflammation and upper GI symptoms. SIBO can be diagnosed with an at-home breath test.

Conventional Treatment for H. pylori

Treatment should be initiated for all patients who test positive for active H. pylori infection. Standard conventional first-line antibiotic protocols for treating H. pylori include (5):

  • Clarithromycin triple therapy: PPI, clarithromycin, and amoxicillin or metronidazole for 14 days
  • Bismuth quadruple therapy: PPI, bismuth, tetracycline, and metronidazole or tinidazole for 10-14 days
  • Concomitant therapy: PPI, clarithromycin, amoxicillin, and metronidazole or tinidazole for 10-14 days

Functional Medicine Treatment Protocol for H. pylori

Nonprescription therapy usually has fewer side effects than antibiotics, is less likely to cause treatment resistance, and is effective when combining multiple natural agents. A dietary and natural supplement protocol for H. pylori eradication is described below.

Therapeutic Diet and Nutrition Considerations for H. pylori

No universally suggested diet is known to expedite the eradication of H. pylori. While preliminary research suggests a low-nickel diet may increase eradication rates in patients receiving antibiotic therapy, additional research is required to confirm this result. Otherwise, a well-balanced, whole-food diet is recommended to prevent nutritional deficiencies that may occur secondary to H. pylori infection and hypochlorhydria, including vitamins B12, C, E, and iron. (1)

Patients with identified or suspected gastritis or PUD could benefit from a 6-8 week elimination of food sensitivities and allergies to remove triggers exacerbating intestinal inflammation. During an elimination-rechallenge diet, food triggers should be removed for an allotted time and then individually reintroduced into the diet over a three-day challenge. The patient should be instructed to eat an average-sized serving of food in its purest form three times on the first day of the food challenge and then re-eliminate it for two days. During these two days, the patient will observe for any symptoms indicating an adverse reaction to the food. If no symptoms occur, the patient can reincorporate the food into the diet.

Foods rich in fiber, antioxidants, and flavonoids (e.g., whole fruits and vegetables) exert protective effects on the mucosal lining of the GI tract, reducing rates of peptic ulcers and expediting the gut-healing process. (8, 9)

Supplements Protocol for H. pylori

The sample protocol below explains botanical and nutritional supplements frequently recommended for the natural treatment of H. pylori infection.


Orthomolecular's Pyloricil formula combines four natural ingredients known to eradicate H. pylori and heal the stomach lining.

Mastic gum, obtained from the stem and leaves of the mastic tree (Pistacia lentiscus), has been used historically to support stomach health. Laboratory and clinical studies have supported and confirmed its bactericidal actions against H. pylori infection.

Bismuth is a naturally occurring mineral commonly utilized in conventional and functional medicine treatment protocols because it exerts direct bactericidal effects on H. pylori and helps heal ulcers. H. pylori resistance against bismuth has not been reported.

When complexed with carnosine, zinc's healing properties are enhanced. Zinc carnosine has been used as an anti-ulcer drug for decades. Because of its anti-inflammatory, antioxidant, and mucosal-healing properties, its use has been extended to treating H. pylori, GERD, oral mucositis, esophagitis, ulcerative colitis, and hemorrhoids.

Berberine is a botanical extract found in various plants, including Oregon grape root (Berberis aquifolium), barberry (Berberis vulgaris), and goldenseal (Hydrastis canadensis). It has potent antimicrobial and anti-inflammatory properties and is effective in treating H. pylori when used to replace bismuth in a conventional quadruple therapy regimen.

Dose: 2 capsules twice daily

Duration: 8 weeks


A probiotic supplement can reduce the side effects of antibiotic therapy and increase infection eradication rates. Many probiotic strains have been studied successfully as part of a treatment protocol, including species of Lactobacillus, Bifidobacterium, Saccharomyces boulardii, and spore-based probiotics. (6, 7)

Dose: per label instructions

Duration: 8 weeks


Lactoferrin is a protein found in mammalian milk that enhances immunity and has been shown to improve the efficacy of H. pylori eradication therapy.

Dose: 300mg once daily

Duration: 8 weeks

When to Retest Labs

Natural H. pylori protocols should be performed for eight weeks before retesting with either breath or stool testing to confirm H. pylori eradication.



This article discussed the frequency and consequences of H. pylori infection. Because conventional therapy involves multiple pharmacologic agents for extended periods, many people seek functional and integrative medical care to alternative means to eradicate infection. The dietary and supplemental measures discussed in this article can be used to guide practitioners in creating effective natural treatment regimens for H. pylori infection.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


1. Cloyd, J. (2023, March 16). A Functional Medicine H. Pylori Treatment Protocol. Rupa Health.

2. Sweetnich, J. (2023, June 1). Integrative Treatment Options for Common Stomach Disorders: Specialty Testing, Nutrition, Supplements. Rupa Health.

3. Sankararaman, S., & Moosavi, L. (2019, June). Urea Breath Test. National Library of Medicine; StatPearls Publishing.

4. Fashner, J., & Gitu, A.C. (2015). Diagnosis and Treatment of Peptic Ulcer Disease and H. pylori Infection. American Family Physician, 91(4), 236–242.

5. Chey, W.D., Leontiadis, G.I., Howden, C.W., et al. (2017). ACG Clinical Guideline: Treatment of Helicobacter pylori Infection. American Journal of Gastroenterology, 112(2), 212–239.

6. Feng, J.-R., Wang, F., Qiu, X., et al. (2017). Efficacy and safety of probiotic-supplemented triple therapy for eradication of Helicobacter pylori in children: a systematic review and network meta-analysis. European Journal of Clinical Pharmacology, 73(10), 1199–1208.

7. Wang, F., Feng, J., & Chen, P., et al. (2017). Probiotics in Helicobacter pylori eradication therapy: Systematic review and network meta-analysis. Clinics and Research in Hepatology and Gastroenterology, 41(4), 466–475.

8. Weinberg, J.L. (2022, September 23). An Integrative Medicine Approach to Gastritis. Rupa Health.

9. Cloyd, J. (2023, April 13). A Functional Medicine Protocol for Peptic Ulcers. Rupa Health.

10. Parikh, N.S., & Ahlawat, R. (2022, August 8). Helicobacter Pylori. PubMed; StatPearls Publishing.

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