A Functional Medicine Intestinal Methanogen Overgrowth Protocol (IMO): Testing, Nutrition, and Supplements

What if there were a solution to the chronic discomfort of constipation, bloating, and abdominal pain that plagues those diagnosed with irritable bowel syndrome with constipation (IBS-C)? For many patients, these symptoms are a persistent challenge, leading to frustration and a diminished quality of life.

However, emerging research suggests that a significant subset of IBS-C sufferers may be dealing with a condition known as intestinal methanogen overgrowth. This discovery opens the door to targeted treatments that go beyond managing symptoms to potentially offering a curative approach. 

By accurately diagnosing and treating IMO, healthcare providers can tailor interventions that address the root cause, bringing countless individuals lasting relief and a renewed sense of digestive freedom.

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What Is Intestinal Methanogen Overgrowth?

Intestinal methanogen overgrowth, or IMO, occurs when methane-producing archaea are found in excess numbers at any point along the digestive tract. Overgrowth of these bacteria-like microorganisms, predominantly Methanobrevibacter smithii, can cause digestive symptoms that often go undiagnosed or misdiagnosed as IBS-C.

IMO is a newer term that replaced methane-dominant SIBO (small intestinal bacterial overgrowth) to characterize the overgrowth of methanogens anywhere along the digestive tract. This newer terminology distinguishes two main differences between IMO and SIBO:

1. Methanogens called archaea, not bacteria, are responsible for causing IMO.
2. IMO can occur anywhere along the length of the digestive tract

Intestinal Methanogen Overgrowth Signs & Symptoms

IBS, SIBO, and IMO share many of the same symptoms, including:

• Abdominal pain
• Bloating and abdominal distension
• Gas
• Nausea
• Constipation and diarrhea
• Indigestion and heartburn

Distinct gut microtypes are linked to breath-gas patterns in patients with IBS-C. Driven by methanogens, such as M. smithii, methane gas has been shown to slow intestinal transit directly, causing constipation and strongly linking it to IBS-C. This differs from the other subtypes of SIBO (hydrogen- and hydrogen sulfide-predominant SIBO), which are more often associated with diarrheal presentations.

Malabsorption can result from IMO, causing unintentional weight loss, fatigue, and fatty stools. Deficiencies in iron and vitamins B12 and D are also commonly measured on labs. (12)

Extraintestinal symptoms are also common in the context of IMO, such as headaches, joint pain, brain fog, skin lesions, and changes in mood (12).

Root Causes of Intestinal Methanogen Overgrowth

A breakdown in the innate protective mechanisms against archaeal overgrowth predisposes an individual to IMO. Interruptions in normal digestive enzyme production, intestinal motility, and secretory IgA can cause IMO. (12)

Food poisoning increases the risk of IBS by four times, and it is estimated that 80% of patients with IBS have at least one of the three SIBO subtypes. When you get food poisoning, the body produces antibodies that attack the interstitial cells of Cajal, which help with intestinal motility. This disrupts the migrating motor complex (MMC), a vital housekeeping function that essentially acts to sweep out the bowels. An impaired MMC increases the risk for methanogens to overgrow in the intestines. (28)

Advanced age, abdominal surgery, intestinal anatomic variations, and chronic stress can interfere with normal gastrointestinal function and increase the risk of IMO (12).

Medical conditions that reduce mucosal immunity, slow intestinal motility, and create intestinal adhesions can contribute to methanogenic overgrowth. These may include diabetes mellitus, hypothyroidism, autoimmune diseases, colon cancer, and inflammatory bowel disease (IBD). (11, 12, 14)

The use of certain medications can also increase IMO risk. Chronic, frequent use of antibiotics can disrupt the normal balance of beneficial bacteria, allowing the opportunity for methanogens to overgrow. Opiates and smooth muscle relaxants contribute to dysmotility. Proton pump inhibitors and other acid-reducing medications reduce hydrochloric acid, a natural antimicrobial digestive secretion. (11, 12, 14)

How to Diagnose Intestinal Methanogen Overgrowth

Doctors can diagnose IMO and uncover its underlying causes using a step-wise approach.

Step 1: Breath Test

A SIBO/IMO lactulose breath test is an at-home test that measures gaseous byproducts of bacterial and methanogenic fermentation exhaled through the lungs. Due to cost and convenience, this is the most common test utilized in clinical practice to diagnose IMO. According to the North American Consensus guidelines, a methane peak of at least 10 ppm at any time point during the test is diagnostic of IMO.

Any one of these three breath tests can diagnose IMO: 

• SIBO - 3 Hour by Genova Diagnostics
• SIBO/IMO Lactulose Breath Test by Commonwealth Diagnostics International, Inc.
• trio-smart SIBO Breath Test by Gemelli Biotech

Step 2: Tests to Investigate the Root Cause of IMO

Once a patient is diagnosed with IMO, a common question arises: "Why?" The following tests can help uncover IMO's underlying causes.

Vinculin & CdtB Antibodies

In addition to a positive SIBO breath test, positive vinculin and CdtB antibodies confirm a diagnosis of post-infectious IBS and food poisoning as the cause of IMO. The ibs-smart panel by Gemelli Biotech measures both of these antibodies.

Thyroid Panel

A comprehensive thyroid panel screens for hypothyroidism and thyroid autoimmunity, which can impair digestive enzyme secretions and intestinal motility. 

Examples of comprehensive thyroid panels that include TSH, free T3, free T4, and thyroid antibodies include: 

• Comprehensive Thyroid Assessment by Genova Diagnostics
• Comprehensive Thyroid Panel w/ Antibodies by Precision Point

Hemoglobin A1c (HbA1c)

HbA1c is a three-month average blood sugar diagnostic for diabetes. In advanced and untreated diabetes, damage to the nerves that innervate the intestines can cause gastroparesis (slowed stomach emptying) and impaired intestinal motility.

Imaging

Some patients may require endoscopy, colonoscopy, barium follow-through, and/or antroduodenal manometry to confirm inflammatory bowel disorders, intestinal structural anomalies, and MMC deficiencies.

Step 3: Tests to Customize IMO Treatment Plan

Additional functional medicine tests can help individualize treatment plans. Although these tests may not be indicated for every individual, they are commonly recommended by providers during a comprehensive gastrointestinal evaluation.

Comprehensive Stool Test

A comprehensive stool test cannot diagnose IMO, but it can detect digestive enzyme deficiencies, intestinal inflammation, and large intestinal dysbiotic patterns that contribute to or result from its presence.

These are popular comprehensive stool tests ordered through Rupa Health:

• GI-MAP + Zonulin by Diagnostic Solutions
• GI360 by Doctor's Data
• GI Effects Comprehensive Profile - 3 day by Genova Diagnostics

Food Sensitivities

When present in the small intestine, IMO causes inflammation and a leaky gut. Increased intestinal permeability increases the risk of food sensitivities, which exacerbate mealtime digestive symptoms. 

Any of these food sensitivity panels can help personalize a therapeutic dietary plan for patients with significant food-related symptoms while IMO is being treated:

• Basic Food Sensitivity Panel - 96 Foods by Ayumetrix
• 184 IgG Food Sensitivity Panel by Alletess Medical Laboratory
• P88-DIY Dietary Antigen Test by Precision Point

Cortisol Testing

A salivary cortisol test identifies maladaptive adrenal stress responses that can occur with chronic stress. Cortisol secretion imbalances can impair gastrointestinal digestive secretions and motility and often present as physical and mental fatigue and insomnia, further perpetuating the maladaptive stress cycle.

When trying to assess the stress response, any one of these panels is an excellent place to start:

• Adrenal Stress Profile by ZRT Laboratory
• Salivary Cortisol x 4 by Access Med Labs
• Adrenal Stress Panel by Ayumetrix

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Treatment Plan for Intestinal Methanogen Overgrowth

A successful treatment plan for IMO can be divided into three stages.

Step 1: Antimicrobial Therapy

Here's Why This Is Important:

The use of antibiotics is the cornerstone of IMO treatment. The goal is to reduce the intestinal methanogen population, which is directly responsible for causing the symptoms associated with this condition.

How Do You Do This?

Prescription or herbal antibiotics effectively treat methanogen overgrowth in the gastrointestinal tract.

A standard course of antibiotic therapy involves two weeks of rifaximin with either neomycin or metronidazole. Multiple courses may be required for complete eradication. (33) 

Herbal therapy is equally as effective as rifaximin for treating SIBO. A course of herbal antimicrobial treatment for IMO involves dosing two herbs together for six weeks. Dosing more than two herbs at once does not usually provide additional benefits. As with prescription antibiotics, multiple courses may be required for complete IMO eradication. Combinations of the following botanical products can be considered for herbal IMO eradication protocols: 

• Allicin: 450-900 mg three times daily
• Berberine: 500-1,500 mg three times daily
• Emulsified Oregano Oil: 50-100 mg three times daily
• Neem: 600 mg three times daily

The elemental diet (ED) is the only current diet with data supporting its ability to eradicate SIBO/IMO. The ED is the most effective treatment option for SIBO and IMO, with an 80% eradication rate after two weeks of treatment. However, the ED is unpalatable to most, and commercial formulas are expensive. Additionally, as it is a liquid-only diet, many experience emotional challenges during the treatment protocol. Patients can make their elemental formula at home or buy commercially made formulas. (13)

Step 2: Palliate Symptoms

Here's Why This Is Important:

Many patients with IMO experience digestive symptoms related to mealtimes, as methanogens ferment dietary carbohydrates, resulting in increased methane production and associated symptoms like gas, bloating, abdominal pain, and constipation. 

How Do You Do This?

Nutritional modifications that limit fermentable carbohydrates can be helpful in palliating digestive symptoms but are usually not effective on their own in IMO eradication. Therapeutic elimination diets used for symptom relief during IMO treatment include the low FODMAP, Specific Carbohydrate (SCD), Bi-Phasic, GAPS, and Cedars-Sinai diets. (13)

In addition, a prokinetic agent can be added to either herbal or pharmaceutical antimicrobial therapy to support intestinal motility. Prokinetics can assist in relieving gas and bloating symptoms. Ginger, for example, is a popular natural prokinetic that has been shown to stimulate gastric emptying when administered to patients in a dose of 1.2 grams.

Step 3: Prevention

Why Is This Important?

Approximately 45% of patients experience recurrent IMO after completing antibiotic therapy. Implementing strategies to prevent recurrence can help reduce the likelihood of rapid IMO relapse.

How Do You Do This?

IMO should be viewed as a symptom of another gastrointestinal imbalance. If the root cause of IMO is ignored, it will likely recur after antibiotic therapy. Given the complexity of IMO pathogenesis, this article cannot outline specific treatment protocols for every possible underlying cause of IMO. Using patient history and specialty labs can help determine likely causes of IMO. Check out the Rupa Health Magazine for more articles on integrative treatment strategies and protocols relevant to your patient's case.

The Risks of Untreated Intestinal Methanogen Overgrowth

The persistent overgrowth of methanogenic archaea leads to continuous methane production in the gut. Elevated methane levels are closely associated with chronic gastrointestinal symptoms that can significantly impair a patient's quality of life.

Chronic constipation can lead to complications such as hemorrhoids, anal fissures, and rectal prolapse due to prolonged straining. 

Untreated IMO can exacerbate or contribute to the development of other functional gastrointestinal disorders, such as IBS or leaky gut syndrome. Once leaky gut has developed, toxins and undigested food particles can enter the bloodstream, potentially triggering systemic immune responses and inflammation linked to various conditions, including metabolic disorders, autoimmune diseases, rosacea, restless legs syndrome, and interstitial cystitis.

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Key Takeaways:

• Intestinal methanogen overgrowth is a common digestive problem often misdiagnosed as IBS-C. Diagnosing and treating IMO helps provide long-term solutions for otherwise chronic and untreatable digestive symptoms. 
• IMO treatment can be complex, given the many factors contributing to its development. Working with a trained medicine provider who is knowledgeable about proper root-cause treatment approaches, long-term eradication and prevention of IMO is possible.