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

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

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

This article will discuss what IMO is, what causes it, and functional medicine labs to help diagnose and treat it. It will then discuss allopathic and alternative options for an IMO eradication protocol.


What Is Intestinal Methanogen Overgrowth (IMO)?

IMO is a subtype of small intestinal bacterial overgrowth (SIBO). Previously called methane-predominant SIBO, its name has been changed to reflect that the causative microorganisms are archaea, not bacteria, and can be located throughout the digestive tract, not just isolated to the small intestine.

Symptoms of Intestinal Methanogen Overgrowth (IMO)

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. (1)

Extraintestinal symptoms are also common in the context of IMO, such as headaches, joint pain, brain fog, skin lesions, and changes in mood (1).

What Causes Intestinal Methanogen Overgrowth (IMO)?

A breakdown in the innate protective mechanisms against bacterial and archaeal overgrowth predisposes an individual to IMO. Interruptions in normal digestive enzyme production, intestinal motility, and secretory IgA can cause IMO. (1)

Food poisoning increases the risk of IBS by four times, and it is estimated that 80% of patients with IBS have some form of SIBO. When you get food poisoning, the body produces antibodies that attack the interstitial cells of Cajal, cells that 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. (4)

Advanced age, abdominal surgery, intestinal anatomic variations, and chronic stress can interfere with normal gastrointestinal function and increase the risk of IMO (1).

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). (1-3)

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. (1-3)

Functional Medicine Labs to Test for Root Cause of Intestinal Methanogen Overgrowth (IMO)

A SIBO/IMO lactulose breath test is an at-home test that measures gaseous byproducts of bacterial and methanogenic fermentation that are exhaled through the lungs. This is the most common test utilized in clinical practice to diagnose IMO due to cost and convenience. 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.

Your doctor may also recommend additional testing to provide further insight into the root cause of IMO, including:

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.

Thyroid Panel

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

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.


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

Functional Medicine Labs That Can Help Individualize Treatment for Intestinal Methanogen Overgrowth (IMO)

Additional functional medicine tests can be considered to help individualize treatment plans. These tests may not be indicated for every individual but are commonly recommended by functional medicine 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 the presence of IMO.

Food Sensitivities

IMO creates an inflammatory environment when present in the small intestine, leading to leaky gut. Increased intestinal permeability increases the risk of food sensitivities, which exacerbate mealtime digestive symptoms. A food sensitivity panel can help personalize a therapeutic dietary plan for patients with significant food-related symptoms while IMO is being treated.  

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.


Conventional Treatment for Intestinal Methanogen Overgrowth (IMO)

Standard allopathic treatment for IMO is a regime of antibiotics to kill the excessive methanogens in the gastrointestinal tract. A standard course of antibiotics to treat IMO is rifaximin with either neomycin or metronidazole for two weeks. It is important to note that multiple courses may be required for complete eradication.

Rifaximin Dose: 550 mg three times daily

Metronidazole Dose: 250 mg three times daily

Neomycin Dose: 500 mg twice daily

Functional Medicine Treatment Protocol for Intestinal Methanogen Overgrowth (IMO)

The predominant difference between a conventional and functional medicine approach to IMO treatment is the functional medicine provider's focus on treating the root cause of IMO,  understanding that IMO is a symptom of another gastrointestinal imbalance. If this is ignored, the IMO will likely recur after antibiotic therapy.

Given the complexity of SIBO pathogenesis, this article cannot discuss treatment protocols specific to every underlying cause of IMO; check out the  Rupa Health Magazine for more articles on integrative treatment strategies specific to your individual case. Dietary modifications and natural antimicrobial options for IMO eradication and symptom palliation will be discussed below.

Therapeutic Diet and Nutrition Considerations for Intestinal Methanogen Overgrowth (IMO)

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. Therefore, 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. (11)

Because the MMC is interrupted by feeding and its absence is associated with SIBO and IMO, meal spacing is encouraged to promote gastrointestinal motility. Patients should be advised to space meals during the day by 4-5 hours, eat their last meal two hours before bed, and fast overnight for 10-12 hours.

The elemental diet (ED) is the only current diet with data supporting its ability to eradicate SIBO. 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 home-make their elemental formula or buy commercially-made formulas, most commonly Physicians' Elemental Diet or Vivonex Plus. (11)

Supplements Protocol for Intestinal Methanogen Overgrowth (IMO)

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.

IMO treatment differs slightly from SIBO treatment because evidence suggests that allicin tends to be more efficacious at killing methanogens than other herbal options. Because of this, allicin should be the primary herb dosed during treatment, in conjunction with one of the following: berberine, oregano, or neem.

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 and can help in the prevention of IMO recurrence.


Allicin is an active constituent in garlic with potent broad-spectrum antibacterial, antifungal, antiparasitic, and antiviral properties. Allicin extracts have been shown effective in reducing methanogenesis, making it an important aspect of an herbal IMO antimicrobial protocol.

Dose: 450-900 mg three times daily

Duration: 6 weeks


Berberine is a potent, broad-spectrum antimicrobial commonly recommended by functional medicine doctors to treat bacterial, fungal, viral, and parasitic infections. Berberine has additional benefits in treating IMO because it exerts antioxidant and anti-inflammatory effects, healing intestinal mucosa and reducing intestinal permeability. (5, 6)

Dose: 500-1,500 mg three times daily

Duration: 6 weeks

Emulsified Oregano Oil

Oregano is another broad-spectrum antimicrobial that can specifically target pathogenic microbes without negatively impacting the microbiome's beneficial Lactobacillus and Bifidobacterium bacteria. Oregano oil is also anti-inflammatory and antispasmodic, so it can help relieve digestive symptoms like abdominal pain and cramping. (7, 8)

Dose: 50-100 mg three times daily

Duration: 6 weeks


Neem leaf has been used in traditional Indian medicine as a natural antacid, antiparasitic, antibacterial, antiviral, antifungal, antidiabetic, and anti-inflammatory agent.

Dose: 600 mg three times daily

Duration: 6 weeks

Motility Activator™

Integrative Therapeutics' Motility Activator™ is a patented formula containing ginger and artichoke that supports intestinal motility. Ginger and artichoke are commonly utilized in gut-supportive treatment protocols as they have been shown to help digestive processes, possess anti-inflammatory properties, and reduce digestive symptoms like nausea, gas, abdominal pain, and bloating. (9, 10)

Dose: 2-3 capsules before bed

Duration: start during or immediately after antimicrobial therapy, and continue for up to four months after IMO eradication

When to Retest Labs

Repeating a SIBO/IMO breath test is not required after a course of antimicrobial therapy, but it can help to confirm patient response to treatment, monitor treatment progress, and confirm IMO eradication. If repeating the breath test, it is recommended to do so as soon as possible after completing a course of antimicrobial therapy.



Intestinal methanogen overgrowth is a common digestive problem often misdiagnosed as IBS-C. Diagnosing and treating IMO aids in providing 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 functional medicine provider knowledgeable about proper root-cause treatment approaches, long-term eradication and prevention of IMO is possible.

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, April 3). 5 Health Conditions That Are Associated with Small Intestinal Bacterial Overgrowth (SIBO). Rupa Health.

2. Cloyd, J. (2023, March 30). An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide. Rupa Health.

3. Cloyd, J. (2023, May 4). A Functional Medicine SIBO Protocol: Testing and Treatment. Rupa Health.

4. Kim, J.H., Nam, S.J., Park, S.C., et al. (2020). Association between interstitial cells of Cajal and anti-vinculin antibody in human stomach. The Korean Journal of Physiology & Pharmacology, 24(2), 185.

5. Clinical Applications for Berberine. (2022). Natural Medicine Journal.

6. Habtemariam, S. (2016). Berberine and inflammatory bowel disease: A concise review. Pharmacological Research, 113, 592–599.

7. Oniga, I., Pușcaș, C., Silaghi-Dumitrescu, R., et al. (2018). Origanum vulgare ssp. vulgare: Chemical Composition and Biological Studies. Molecules, 23(8), 2077.

8. Si, W., Gong, J., Tsao, R., et al. (2006). Antimicrobial activity of essential oils and structurally related synthetic food additives towards selected pathogenic and beneficial gut bacteria. Journal of Applied Microbiology, 100(2), 296–305.

9. Bodagh, M.N., Maleki, I., & Hekmatdoost, A. (2018). Ginger in Gastrointestinal disorders: a Systematic Review of Clinical Trials. Food Science & Nutrition, 7(1), 96–108.

10. Artichoke: Uses, Side Effects, Interactions, Dosage, and Warning. WebMD.

11. Cloyd, J. (2023, April 26). Dietary Modifications for a Successful SIBO Treatment Plan. Rupa Health.

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