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A Functional Medicine Protocol for Peptic Ulcers

Medically reviewed by 
A Functional Medicine Protocol for Peptic Ulcers

Living with peptic ulcer disease (PUD) can be incredibly challenging, with symptoms like abdominal pain and discomfort making everyday life difficult. It's estimated that over four million people in the United States are affected by PUD each year, highlighting the widespread impact of this condition. However, there is hope. 

A comprehensive PUD treatment protocol can provide relief and improve quality of life. This protocol involves various steps, including addressing the root causes, such as Helicobacter pylori infection, and making lifestyle changes to promote healing. By following these steps, individuals can better manage their symptoms and reduce the risk of complications associated with PUD.


What Is Peptic Ulcer Disease?

Peptic ulcer disease (PUD) refers to painful sores (ulcers) that form most commonly in the lining of the stomach or small intestine. These ulcers develop when the protective lining of these organs is eroded, exposing the underlying tissue to stomach acid and digestive enzymes.

Ulcers in the stomach lining are called gastric ulcers; those that occur in the lining of the upper portion of the small intestine (called the duodenum) are duodenal ulcers. Duodenal ulcers are four times more common than gastric ulcers. 

Signs & Symptoms of Peptic Ulcers

Having a peptic ulcer can feel like indigestion and cause symptoms like: 

  • Burning stomach pain: Gastric ulcers typically cause pain within 15-30 minutes of starting a meal. Pain associated with duodenal ulcers subsides at the beginning of meals and then increases 2-3 hours after mealtime. 
  • Bloating
  • Burping
  • Heartburn
  • Nausea and vomiting
  • Indigestion
  • Increased fullness/reduced appetite 
  • Unintentional changes in weight (loss or gain)
  • Black, tarry stool

Root Causes of Peptic Ulcer Disease

The most common causes of PUD are Helicobacter pylori infection and the use of nonsteroidal anti-inflammatory drugs.

Helicobacter pylori

H. pylori is a bacteria that infects up to 75% of the world's population and is responsible for 90% of duodenal ulcers and 70-90% of gastric ulcers. H. pylori is highly capable of evading the immune system, adhering to intestinal mucosa, inducing inflammation, and causing ulceration in the gastrointestinal (GI) mucosa. (5, 16)

Nonsteroidal Anti-Inflammatory Drugs (NSAIDs)

NSAIDs, including aspirin and ibuprofen, inhibit the COX-1 enzyme responsible for producing prostaglandins, which are molecules that protect the gastric mucosa. Taking high-dose or long-term NSAIDs decreases intestinal mucus secretion and mucosal blood flow, contributing to ulcer formation. (16)

Other Causes

Less common causes of PUD include:

  • Viral, fungal, and bacterial other than H. pylori
  • Loss of blood supply to the GI tract
  • Chemotherapy or radiation therapy
  • Zollinger-Ellison Syndrome: A condition characterized by tumors (called gastrinomas) that cause the stomach to make too much acid
  • Crohn's disease: an autoimmune disease that causes chronic inflammation in the GI tract
  • Stomach cancer


Other risk factors for PUD include:

  • Smoking
  • Drinking alcohol
  • Eating spicy foods
  • Stress

How to Diagnose Peptic Ulcer Disease

When a doctor is suspicious of a peptic ulcer causing clinical symptoms, they will follow these outlined steps to make a definitive diagnosis, find its cause, and rule out complications.

Step 1: Endoscopy

An upper endoscopy is a procedure that allows doctors to visualize the upper digestive tract, including the esophagus, stomach, and duodenum. It is the most accurate test for finding active ulcers. During the procedure, doctors can take tissue biopsies and treat bleeding ulcers that they find. 

Step 2: H. pylori Testing

H. pylori infection can be diagnosed with a:

  • Serum ELISA antibody test
  • Urea breath test
  • Stool antigen test
  • Endoscopic biopsy

Examples of H. pylori tests that can be ordered through Rupa Health include:


Step 3: Screen for Iron Deficiency Anemia

Upper GI bleeding occurs in 15-20% of patients with PUD. Chronic GI bleeding is a common cause of iron deficiency and iron deficiency anemia (IDA). To rule out IDA as a secondary complication of PUD, your doctor will assess red blood cell numbers and iron concentrations with complete blood count (CBC) and ferritin blood tests.

Treatment Plan for Peptic Ulcer Disease

A specific treatment plan for PUD will depend on the underlying cause of the ulcer, but the basic principles of healing an ulcer include killing H. pylori infection, avoiding NSAID use, and supporting mucosal healing.

1. Remove Inflammatory Triggers

Here's Why This Is Important: 

Healing an ulcer will be difficult if underlying inflammatory triggers are not removed. Trigger removal supports efficient mucosal healing and can provide the patient with symptom relief. 

How Do You Do This?

Doctors should take a comprehensive patient history to determine possible triggers contributing to PUD. Trigger elimination should be tailored to each patient's risk factors, but may include:

  • Discontinuing NSAID use
  • Avoidance of alcohol
  • Elimination diet to avoid triggering foods, such as spicy foods
  • Smoking cessation
  • Stress management

2. Support Mucosal Healing

Here's Why This Is Important:

This helps to restore the integrity of the mucous membrane lining the stomach or small intestine, which the ulcer has damaged. Promoting mucosal healing reduces the risk of ulcer recurrence, prevents ulcer-related complications, and alleviates symptoms such as pain and discomfort.

How Do You Do This?

The administration of a histamine 2 (H2) blocker or proton pump inhibitor (PPI) for four weeks induces healing in most ulcers. PPIs are recommended as first-line therapy for most patients because they are better at controlling pain and healing ulcers than H2 blockers. (20

There are many natural supplemental options with anti-inflammatory and healing properties. Evidence suggests that the following dietary and herbal supplements can be used to treat the symptoms of PUD and induce healing of GI ulcers:

3. Eradicate H. pylori Infection

Here's Why This Is Important:

Since H. pylori bacteria are a leading cause of ulcers, eradicating infection is essential for effectively managing PUD and improving the long-term outcomes for affected individuals.

How Do You Do This?

The American College of Gastroenterology (ACG) recommends antibiotic therapy as a first-line treatment for all patients who test positive for H. pylori infection. Standard antibiotic protocols include: 

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

4. Correct Iron Deficiency Anemia

Here's Why This Is Important:

Complications associated with untreated IDA include chronic fatigue, restless legs syndrome, heart problems, pregnancy complications, hypothyroidism, and hair loss (4, 8). 

How Do You Do This?

Patients with IDA secondary to a bleeding ulcer should be treated with iron to restore iron and red blood cell levels to an optimal range. The recommended oral dose of iron for treating IDA in adults is 120 mg of elemental iron daily, divided into multiple doses. However, newer evidence suggests that every-other-day dosing can improve the absorption rate of oral iron and restore serum iron levels faster. (8

The Risks of Untreated Peptic Ulcer Disease

Left untreated, PUD can result in:

  • Chronic GI bleeding, leading to severe blood loss, iron deficiency, and anemia
  • Perforation (hole) of the stomach or small intestinal wall
  • Obstruction of the upper GI tract
  • Increased risk of gastric cancer in those with H. pylori (17)

Alarm symptoms that warrant the need for prompt medical evaluation include: 

  • Anemia
  • Vomiting of blood
  • Blood in stool 
  • Loss of appetite
  • Unintentional weight loss
  • Persistent, severe upper abdominal pain radiating to the back


Key Takeaways:

  • Peptic ulcer disease is most commonly caused by H. pylori infection and chronic NSAID use. 
  • Healing peptic ulcers involves removing underlying triggers and supporting the healing of the intestinal mucosa. 
  • Comprehensive testing allows doctors to identify the specific causes of PUD so that an individualized and effective treatment protocol can be implemented to expedite healing, relieve PUD symptoms, and prevent ulcer recurrence.
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

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  2. Christie, J. (2022, March 8). Weakness, Pale Skin, And Headache Are Signs Of This Mineral Deficiency. Rupa Health.
  3. Cloyd, J. (2023, February 1). 6 anemia types you need to know about. Rupa Health.
  4. Cloyd, J. (2023, February 2). Top Lab Test to Run on Your Iron Deficiency Anemia Patients. Rupa Health.
  5. Cloyd, J. (2023, February 17). A Functional Medicine Peptic Ulcer Treatment Protocol. Rupa Health.
  6. Cloyd, J. (2023, March 16). A Functional Medicine H. Pylori Treatment Protocol. Rupa Health.
  7. Cloyd, J. (2023, May 26). A Functional Medicine Crohn’s Disease Protocol: Specialty Testing, Nutrition, and Supplements. Rupa Health.
  8. Cloyd, J. (2023, July 26). A Functional Medicine Iron Deficiency Anemia Protocol: Comprehensive Testing, Therapeutic Diet, and Supplements. Rupa Health.
  9. Cloyd, J. (2023, December 1). How to Interpret CBC Results: A Comprehensive Guide. Rupa Health.
  10. Cloyd, J. (2023, December 29). How to Use An H Pylori Test to Diagnose and Treat. Rupa Health.
  11. Cloyd, J. (2024, February 28). Clinical Applications of Zinc Carnosine - Evidence Review. Rupa Health.
  12. Ferritin. Rupa Health.
  13. Khakham, C. (2023, May 16). Natural Anti-Inflammatory Agents for Gut Health: An Evidence-Based Review. Rupa Health.
  14. Khakham, C. (2023, September 27). Top Causes of Iron Deficiency Anemia in Adults: How To Test and Diagnose. Rupa Health.
  15. Khoder, G., Al-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.
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  21. Sweetnich, J. (2023, February 21). Top Gut Healing Supplements Used By Integrative Medicine Practitioners. Rupa Health.
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  23. Zollinger-Ellison Syndrome. (2019, December 5). National Institute of Diabetes and Digestive and Kidney Diseases.
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