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A Functional Medicine Protocol for Peptic Ulcers

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A Functional Medicine Protocol for Peptic Ulcers

Peptic ulcer disease (PUD) affects four million people worldwide yearly and has a 5-10% lifetime prevalence. The global prevalence of PUD has decreased in past decades, but the incidence of its complications has remained constant, making accurate diagnosis and effective treatment imperative. Conventional pharmacologic treatments for peptic ulcers have demonstrated side effects, relapses, and drug interactions. Fortunately, natural options exist with better safety profiles that can effectively be integrated into holistic protocols for treating and preventing peptic ulcers. (2, 3)


What are Peptic Ulcers?

A peptic ulcer is an ulceration, or open sore, of the mucosa in the stomach (gastric) or upper portion of the small intestine (duodenal). Duodenal ulcers are four times more common than gastric ulcers and more common in men than women. (1, 4)

Peptic Ulcer Signs & Symptoms

The most common symptom of peptic ulcers is burning stomach pain. The timing of upper abdominal pain helps to distinguish between gastric and duodenal ulcers. Gastric ulcers cause pain within 15-30 minutes of starting a meal, whereas pain usually subsides at the beginning of a meal and then surges 2-3 hours after mealtime with a duodenal ulcer. (1, 5)

Other symptoms commonly associated with PUD include (5):

  • Nausea and vomiting
  • Indigestion
  • Increased fullness
  • Bloating
  • Belching
  • Heartburn
  • Reduced appetite
  • Unintentional changes in weight

Left untreated, peptic ulcers can cause internal bleeding. When this occurs, vomit may appear red or black, and stools may appear black and tarry. Additionally, anemia and iron deficiency may appear on labs secondary to blood loss. (5)

What Causes Peptic Ulcers?

Peptic Ulcer Disease is predominantly caused by Helicobacter pylori (H. pylori) infection and the use of nonsteroidal anti-inflammatory drugs (NSAIDs).

H. pylori is a bacteria that infects up to 75% of the world's population, although most of this population will remain completely asymptomatic. H. pylori possesses many virulence factors (cellular structures and systems) that make it highly successful in evading the host's immune system, adhering to the gastrointestinal mucosa, and causing inflammation and ulceration. H. pylori is responsible for 90% of duodenal ulcers and 70-90% of gastric ulcers. (1, 4)

NSAIDs inhibit the COX-1 enzyme responsible for the production of prostaglandins. Normally, prostaglandins protect the gastric mucosa; however, chronic NSAID use can result in decreased gastric mucus, reduced mucosal blood flow, and ulcer formation. (4)

Other risk and lifestyle factors associated with PUD include smoking, alcohol, and stress (5).

Functional Medicine Labs to Test for Root Cause of Peptic Ulcers

An upper endoscopy is used for the definitive diagnosis of PUD but is not required in all patients. Endoscopy should be performed on all patients 50 years old or older with new-onset symptoms or patients with at least one of the following symptoms: unintended weight loss, early satiety, difficulty or pain with swallowing, gastrointestinal bleeding, iron deficiency anemia, persistent vomiting, a palpable upper abdominal mass, enlarged lymph nodes, or other abnormal imaging. Upper endoscopy should also be considered in patients with a family or personal history of upper gastrointestinal cancer.

H. pylori

H. pylori infection can be tested with either a urea breath test or stool antigen testing. Functional stool tests can also assess for H. pylori virulence factor and antibiotic-resistant genes, which help to quantify infection severity and guide treatment recommendations.

Complete Blood Count (CBC)

A CBC is a blood assessment of red blood cells, white blood cells, and platelets. Abnormal results can indicate anemia secondary to gastrointestinal bleeding or infection.

Food Allergies

Although food allergies and sensitivities are not known causes of PUD, they can exacerbate inflammation, swelling, and bleeding of ulcerations. A blood test can measure the concentrations of antibodies to food proteins, which, if present, can diagnose food allergy and sensitivity. Consider ordering an allergy panel, especially in patients with other allergic-type symptoms, like eczema, migraine, and nasal congestion.


Conventional Treatment for Peptic Ulcers

Treatment of uncomplicated peptic ulcers includes the cessation of NSAID use, antibiotic eradication of H. pylori infection, and proton pump inhibitor (PPI) therapy for up to eight weeks.

Functional Medicine Treatment Protocol for Peptic Ulcers

A functional medicine doctor will prescribe a personalized treatment plan based on an extensive intake and lab results. Below is an example of a typical treatment protocol prescribed for patients suffering from PUD.

Therapeutic Diet and Nutrition Considerations for Peptic Ulcers

Identified food allergens (IgE reactions on blood testing) should be eliminated from the diet to reduce histamine-mediated worsening of symptoms and inflammation (6, 7). A trial elimination of identified food sensitivities can also be considered, as long as this does not cause over-restriction of nutrient-dense foods, potentially contributing to additional unwanted weight loss and anemia. During an elimination diet, identified food triggers should be removed from the diet for 4-6 weeks. After the elimination period, the patient should reintroduce foods into the diet one at a time. Each reintroduction should be done over three days as follows:

  • Day 1: eat an average-sized serving of food in its purest form three times
  • Days 2-3: re-eliminate food from the diet and observe for any symptoms that would indicate a poor immunological response to the food (i.e., PUD symptom recurrence)
  • If the patient does not experience any adverse symptoms from the food rechallenge by the end of the third day, they can reintroduce the food into the diet. If they experience symptoms, they should continue to eliminate the food trigger and wait until symptoms resolve before beginning the next food rechallenge.

Patients should be counseled to chew their food thoroughly before swallowing. Chewing increases salivary secretions containing buffering agents and prostaglandin E2, which protect the gastric mucosa against ulceration.

A fiber-rich diet can reduce the risk of developing peptic ulcers by increasing the need for chewing and decreasing bile reflux into the stomach. In one study, patients eating a high-fiber diet had significantly lower ulcer recurrence rates than patients eating a low-fiber diet. Per the research, patients should consume 20-30 grams of dietary fiber daily. (8)

Supplements Protocol for Peptic Ulcers

Supplements should be prescribed to heal inflamed gastrointestinal tissues and eradicate H. pylori infection (if present).

Demulcent Herbs

Demulcent herbs are rich in carbohydrate polysaccharides that form a mucilage when they come into contact with water and stimulate natural mucous digestive secretions. Herbs like deglycyrrhizinated licorice (DGL), marshmallow, slippery elm, and aloe are commonly used independently or together to reduce irritation and promote healing through the length of the digestive tract. DGL has the additional benefit of possessing anti-H. pylori effects (10). Thorne's GI Relief is a popular gut-soothing and healing formula because it contains all four of these herbs.

Dose: two capsules three times daily

Duration: 6-8 weeks


L-glutamine is the most abundant amino acid in the body and is the small intestinal cells' primary fuel source. Glutamine deficiency is associated with increased intestinal permeability, decreased mucosal function, and increased incidence of ulceration. L-glutamine supplementation is indicated for many intestinal diseases and is associated with improved patient outcomes (9). Preliminary research suggests its utility specifically for the treatment of gastric ulcers.

Dose: 5 g twice daily

Duration: 6-8 weeks


H. pylori must be eradicated in infected patients with PUD. Conventional therapy entails triple or quadruple-antibiotic treatment and is not always effective. Pyloricil is an evidence-based natural formula containing zinc carnosine, mastic gum, berberine, and bismuth that effectively eradicates H. pylori (11-14).

Dose: two capsules twice daily

Duration: 6-8 weeks


Probiotics exhibit numerous health benefits for those with peptic ulcers. Probiotics are known to protect the mucosal barrier by upregulating prostaglandins, mucus, growth factors, and anti-inflammatory cytokines; increase cell proliferation and blood vessel formation to expedite healing of ulcerations; and provide significant benefits in treating H. pylori infection. Not only can probiotics mediate side effects from conventional antibiotic therapy, but their use also appears to make eradication protocols more effective. (15-17)

Dose: 10 billion CFU twice daily

Duration: 6-8 weeks

When to Retest Labs

Functional medicine treatment PUD protocols generally last a minimum of six weeks. Patients should be informed to follow up 6-8 weeks after initiating a treatment protocol. At this point, reviewing clinical symptoms and/or repeat labs can determine whether the treatment has been sufficient or needs to be continued.


Healing peptic ulcers involves addressing H. pylori infection, chronic NSAID use, and dietary modifications. An integrative and functional medicine approach that includes dietary changes and supplements can effectively reverse PUD and prevent serious health complications that can occur secondary to disease.

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1. Cloyd, J. (2023, February 17). A Functional Medicine Peptic Ulcer Treatment Protocol. Rupa Health.

2. Abbasi-Kangevari, M., Ahmadi, N., Fattahi, N., et al. (2022). Quality of care of peptic ulcer disease worldwide: A systematic analysis for the global burden of disease study 1990–2019. PLOS ONE, 17(8), e0271284.

3. Kuna, L., Jakab, J., Smolić, R., et al. (2019). Peptic Ulcer Disease: A Brief Review of Conventional Therapy and Herbal Treatment Options. Journal of Clinical Medicine, 8(2), 179.

4. Malik, T., Gnanapandithan, K., & Singh, K. (2022). Peptic Ulcer Disease. StatPearls Publishing.

5. Peptic ulcer - Symptoms and causes. (2022, June 11). Mayo Clinic.

6. Raithel, M., Hahn, M., Donhuijsen, K., et al. (2014). Eosinophilic gastroenteritis with refractory ulcer disease and gastrointestinal bleeding as a rare manifestation of seronegative gastrointestinal food allergy. Nutrition Journal, 13(1).

7. Kern, R., & Stewart, S.G. (1931). Allergy in duodenal ulcer: Incidence and significance of food hypersensitiveness as observed in 32 patients. Journal of Allergy, 3(1), 51–57.

8. Vomero, N.D., & Colpo, E. (2014). Nutritional care in peptic ulcer. ABCD, 27(4), 298–302.

9. McRae, M.P. (2017). Therapeutic benefits of glutamine: An umbrella review of meta-analyses. Biomedical Reports, 6(5), 576–584.

10. Wang, Q., Feng, P., Li, Y., et al. (2023). Effect of polyphenol compounds on Helicobacter pylori eradication: a systematic review with meta-analysis. BMJ Open, 13(1), e062932.

11. Al-Habbal, M. J., Al-Habbal, Z., & Huwez, F. (1984). A double-blind controlled clinical trial of mastic and placebo in the treatment of duodenal ulcer. Clinical and Experimental Pharmacology and Physiology, 11(5), 541–544.

12. Cammarota, G., Cannizzaro, O., Ojetti, V., et al. (2000). Five-day regimens containing ranitidine bismuth citrate plus high-dose clarithromycin and either amoxycillin or tinidazole for Helicobacter pylori infection. Alimentary Pharmacology & Therapeutics.

13. Mahmood, A., Fitzgerald, A.P., Marchbank, T., et al. (2007). Zinc carnosine, a health food supplement that stabilises small bowel integrity and stimulates gut repair processes. Gut, 56(2), 168–175.

14. Berberine. (2007). Altern Med Rev, 5(2), 175–177.

15. Khoder, G., Menhali, A.A., Al‑Yassir, F., et al. (2016). Potential role of probiotics in the management of gastric ulcer. Experimental and Therapeutic Medicine, 12(1), 3–17.

16. Armuzzi, A., Cremonini, F., Ojetti, V., et al. (2001). Effect of Lactobacillus GG Supplementation on Antibiotic-Associated Gastrointestinal Side Effects during Helicobacter pylori Eradication Therapy: A Pilot Study. Digestion, 63(1), 1–7.

17. Canducci, F., Armuzzi, A., Cremonini, F., et al. (2000). A lyophilized and inactivated culture of Lactobacillus acidophilus increases Helicobacter pylori eradication rates. Alimentary Pharmacology & Therapeutics, 14(12), 1625–1629.

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