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An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide

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An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide

Small intestinal bacterial overgrowth (SIBO) is an overgrowth of bacteria in the small intestine. SIBO is commonly misdiagnosed as irritable bowel syndrome (IBS), as they share many of the same symptoms. Studies indicate that up to 80% of patients with IBS have SIBO (6). Increased awareness and understanding of SIBO has led to the differentiation of SIBO subtypes: hydrogen-dominant, hydrogen sulfide-dominant, and intestinal methanogen overgrowth. Breath testing can diagnose and differentiate between the SIBO subtypes, helping to guide treatment recommendations. A functional approach to SIBO includes eradicating overgrowth and preventing recurrence.


What is Small Intestinal Bacterial Overgrowth (SIBO)?

In a healthy state, the small intestine is a relatively "clean" environment without bacterial colonization. Various protective mechanisms, like stomach acidity and intestinal motility, prevent the accumulation of bacteria in the small intestine. SIBO occurs when the body's innate protective mechanisms fail, or medical conditions predispose to the accumulation of bacteria in the small intestine. (1)

When SIBO occurs, bacteria interfere with normal digestion and absorption and cause inflammation to the small intestine's lining. The resulting maldigestion, malabsorption, and hyperpermeability of the small intestine cause the symptoms associated with SIBO. (2)

Different Types of SIBO

SIBO research, testing, and treatment developments have distinguished three distinct variations of bacterial overgrowth: Hydrogen-SIBO, Intestinal Methanogen Overgrowth (IMO), and Hydrogen Sulfide-SIBO. (3)

Hydrogen Dominant

Hydrogen-dominant SIBO (also called SIBO) is the overgrowth of bacteria in the small intestine that is diagnosed when excess levels of hydrogen are measured on a diagnostic breath test. Numerous bacteria have been associated with SIBO, including Enterococcus, Escherichia coli, and Klebsiella. Hydrogen-SIBO shares many symptoms with diarrhea-predominant IBS (IBS-D). (4)

Methane Dominant

IMO, previously referred to as methane-SIBO, is the overgrowth of methane-producing archaea in the digestive tract. Archaea are single-celled organisms similar to, but anatomically distinct from, bacteria. Methanobrevibacter smithii is the archaea linked to IMO when it overgrows in either the small or large intestines. Methane gas has been shown to slow intestinal transit and cause constipation directly. Because of this, IMO is most commonly known to cause constipation-predominant IBS (IBS-C) symptoms. (4)

Hydrogen Sulfide Dominant

The overgrowth of hydrogen sulfide-producing bacteria causes hydrogen sulfide-SIBO (or excess hydrogen sulfide). Among others, bacterial Citrobacter, Clostridium, Collinsella, Desulfovibrio, Escherichia, Enterobacter, Fusobacterium, Klebsiella, Prevotella, and Proteus species are known to produce hydrogen sulfide. Hydrogen sulfide can relax smooth muscle and be pro-inflammatory in excess. Hydrogen sulfide-SIBO is highly correlated with increased rates of diarrhea and IBS-D symptoms. (4)

SIBO Symptoms

The main symptoms of SIBO are those of IBS:

  • Abdominal pain
  • Gas, bloating, belching, and flatulence
  • Changes in bowel movements (constipation, diarrhea, or both): hydrogen and hydrogen sulfide gases are more likely to cause diarrhea, and methane gas is more likely to cause constipation.

SIBO can cause other symptoms related to and outside the gastrointestinal tract, including (5):

  • Heartburn and acid reflux
  • Nausea
  • Fatty stools
  • Food sensitivities and intolerances
  • Headaches
  • Joint pain
  • Fatigue and brain fog
  • Skin symptoms: eczema, rosacea, psoriasis, rashes
  • Depression and anxiety
  • Weight loss

You may see signs of malabsorption on labwork, like deficiencies in iron and vitamins A, B12, and D. Nutrient deficiencies can cause their own problems, like anemia, numbness and tingling, night blindness, and muscle twitching. (1)

What Causes SIBO?

SIBO can occur when any number of diseases, surgeries, medications, lifestyle factors, or genetics interrupt the body's innate defense mechanisms at preventing bacterial/methanogenic overgrowth.


The migrating motor complex (MMC) is a spontaneous burst of muscle contractions that occur in the stomach and small bowel during a fasting state. The MMC clears debris from the small intestine into the large intestine, including bacteria. Not only does a deficiency in the MMC allow small intestinal bacteria to accumulate, but it also allows bacteria from the large intestine to travel into the small intestine.

Food poisoning, and the resulting production of antibodies to vinculin and CdtB, can cause autoimmune damage to the cells that generate the MMC, slowing the MMC. Other causes of dysmotility and impaired MMC function can include diabetes, hypothyroidism, Parkinson's disease, Ehlers-Danlos Syndrome, traumatic brain injury, medications (e.g., opioids, antibiotics, smooth muscle relaxants), and stress. (1, 6)

Digestive Enzyme Deficiencies

Digestive enzymes are important not only for healthy digestion and absorption of the food we eat but also for acting as natural antimicrobial substances to kill excessive bacteria and pathogens traveling down the digestive tract. Hydrochloric acid, bile, and pancreatic enzymes kill and arrest the growth of incoming bacteria. Enzymes deficiencies can occur from H. pylori infection, atrophic gastritis, cholecystitis, pancreatitis, surgery, and use of certain medications (e.g., proton pump inhibitors and H2 blockers for heartburn). (1, 6)

Structural Abnormalities

Abdominal and intestinal adhesions, strictures, obstructions, loops, diverticula, and fistulas can be caused by gastrointestinal diseases or complications of surgeries. These can inhibit motility and create niches for bacteria to accumulate. (6)

The ileocecal valve is the sphincter located at the junction of the last portion of the small intestine and the beginning of the colon. A "leaky" valve allows for the back-migration of bacteria from the large to the small intestine. Cancer, infections, diet, and stress may contribute to ileocecal valve dysfunction.

Functional Medicine Labs to Test for Root Cause of SIBO

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ran for patients suffering from SIBO.

SIBO Breath Test

The SIBO breath test is the most commonly utilized testing tool as a non-invasive diagnostic alternative to the gold standard of small intestinal (duodenal) aspiration. Bacteria and archaea in the gastrointestinal tract ferment carbohydrates and produce hydrogen, methane, and hydrogen sulfide gases. These gases diffuse into the bloodstream from the digestive tract and are exhaled through the lungs. SIBO breath tests take advantage of these bacterial digestive byproducts to diagnose SIBO.

Different types of SIBO breath tests are classified by the substrate administered (glucose and lactulose) and the duration of the testing period (2-hour and 3-hour). Until recently, breath tests could only measure hydrogen and methane levels. The trio-smart breath test is the newest development in SIBO testing and holds the capacity to measure all three SIBO-associated gases. There is no universal standard SIBO breath test. Elevations of gas levels measured on the breath test are diagnostic for SIBO and IMO. Per the North American Consensus, a test is positive if at least one of the following criteria is met (7):

  • Hydrogen-SIBO: hydrogen levels rise at least 20 ppm from baseline within the first 90 minutes of the test
  • IMO: methane level is at least 10 ppm at any time point during the test
  • Hydrogen sulfide-SIBO: hydrogen sulfide level is at least 3 ppm at any time point during the test

Comprehensive Stool Test

A comprehensive stool test cannot diagnose SIBO or IMO, but it can offer insight into potential underlying factors predisposing the patient to overgrowth. Large intestinal overgrowth of SIBO-associated bacteria, digestive enzyme deficiencies, and decreased immune function within the large intestine can contribute to SIBO and IMO development.

Nutritional Assessment

A comprehensive nutritional assessment screens for nutritional deficiencies that may occur secondary to SIBO. This may be more pertinent for patients with SIBO/IMO on restrictive diets to manage gastrointestinal symptoms or signs/symptoms of malabsorption.

Helpful Tests for Identifying the Underlying Cause of SIBO

Referral for antroduodenal manometry, endoscopy, or barium follow-through may be helpful to definitively diagnose MMC deficiency and structural anomalies causing SIBO and IMO.

Vinculin and CdtB antibodies can be measured in the blood to confirm post-infectious IBS and SIBO due to food poisoning.

Conventional Treatment for SIBO

Antibiotics are the standard treatment for SIBO and IMO to treat the overgrowth. Conventional treatment fails to address underlying mechanisms predisposing a person to an overgrowth in the first place, making SIBO recurrence after antibiotic therapy high. Some research estimates relapse rates as high as 43.7% nine months after treatment. (8)


How to Treat SIBO Naturally with Functional Medicine

A functional approach treats the overgrowth and addresses the underlying factors causing SIBO, increasing treatment success.

SIBO Diets

An elemental diet is a liquid formula of pre-digested nutrition that starves microorganisms in the gastrointestinal tract while providing essential nutrients to the patient. It is the only diet that can treat SIBO.

Other diets, while they cannot cure SIBO or IMO, can be helpful during SIBO/IMO eradication by reducing the intake of trigger foods that cause digestive symptoms commonly associated with eating. Typical therapeutic diets recommended to patients include the low-FODMAP, SIBO Bi-Phasic, Specific Carbohydrate, and GAPS.

Patients with hydrogen sulfide-SIBO may benefit from a low-sulfur diet, which reduces the consumption of dairy, meat, cruciferous vegetables, onion, garlic, and sulfites.

Antibiotics for SIBO

Functional doctors may recommend antibiotic therapy for eradication of SIBO and IMO. Antibiotic recommendations are based on SIBO type, as research shows that different combinations are more effective at treating the various forms. Solo therapy with rifaximin provides optimal benefit for patients with hydrogen-SIBO. Eradication of IMO is best achieved when rifaximin is combined with another antibiotic, typically neomycin or metronidazole. Research specific to treating hydrogen sulfide-SIBO is limited, but rifaximin, combined with bismuth subsalicylate, appears effective at reducing hydrogen sulfide gas levels. A course of antibiotic therapy is usually two weeks; however, a single course is not always effective in eradication. A patient may require multiple courses for successful eradication. (8-11)

Herbs and Supplements for SIBO

Herbal antibiotics are just as effective as rifaximin for the resolution of SIBO and can also be effective for patients who are rifaximin non-responders (12). Antimicrobial herbs and botanical compounds commonly recommended for SIBO eradication protocols include oregano, berberine, neem, and allicin. Herbal antibiotics should be dosed for a minimum of 4-6 weeks before reassessment. Similar to antibiotics, multiple courses may be required for complete eradication.

Choices in herbal agents are generally dependent on the type of SIBO present. Herbal protocols should entail dosing a combination of two herbs at a time. Hydrogen-SIBO is usually most responsive to berberine, oregano, and neem (12). IMO protocols should entail dosing berberine, oregano, or neem with allicin or the herbal formula called Atrantil. General dosing recommendations for each herb are as follows:

  • Berberine: 1,500-5,000mg daily (split into three doses throughout the day)
  • Oregano (emulsified): 150-300mg daily (split into 2-3 doses throughout the day)
  • Neem: 900-1,800mg daily (split into three doses throughout the day)
  • Allicin: 1,350-2,700mg daily (split into three doses throughout the day)
  • Atrantil: 2 capsules three times daily

Alternatively, two capsules twice daily of one of the following herbal formula combinations for four weeks resulted in a 46% eradication rate compared to a 34% eradication rate in those treated with rifaximin.

  • Dysbiocide® and FC Cidal™ (Biotics Research)
  • Candibactin-AR® and Candibactin-BR® (Metagenics)

Supplements can be used as needed to manage SIBO/IMO symptoms. For example, magnesium acts as an osmotic laxative to treat constipation. Peppermint is an antispasmodic proven to improve abdominal pain in patients with IBS. Partially-hydrolyzed guar gum (PHGG) is a fiber most SIBO patients tolerate, which can firm loose stools and improve diarrhea.

Prevention Strategies for SIBO

SIBO and IMO often recur if underlying causes of SIBO aren't addressed after the discontinuation of pharmaceutical or herbal antibiotic therapy. Treating underlying medical conditions, if present, like diabetes and hypothyroidism, is an important aspect of this.

Promoting healthy upper intestinal motility is critical in any SIBO/IMO prevention plan. Natural prokinetics support the MMC without overstimulating the large intestine. Ginger and an herbal formula called Iberogast are two of the most researched natural prokinetics that successfully stimulate the MMC and reduce digestive symptoms. Spacing meals 4-5 hours apart, with a 12-hour overnight fast, will also promote a healthy MMC.

Visceral manipulation is a manual technique involving gentle forces to the abdomen to encourage normal mobility and tone of the internal organs, connective tissues, and ligaments. Visceral manipulation can be beneficial in treating gastrointestinal symptoms (e.g., acid reflux), encouraging healthy intestinal movement, and treating abdominal adhesions (scar tissue).

Digestive enzymes may be required with meals to replace deficient hydrochloric acid, bile, and pancreatic enzymes discovered through testing.

Practicing vagal nerve stimulation exercises, including cold plunges, carotid artery massage, and deep breathing, promotes digestive function and reduces stress.



Small intestinal bacterial overgrowth and intestinal methanogen overgrowth are conditions of overgrowth of bacteria and archaea that disrupt digestive function, promote intestinal inflammation, and cause disruptive digestive symptoms similar to IBS. Breath testing can identify the specific subtype of SIBO, which helps guide eradication recommendations. A functional approach to SIBO and IMO treatment goes one step further, understanding that the overgrowth is a symptom of underlying dysfunction and imbalances. Identifying and addressing these causative factors makes a functional approach to SIBO more effective than conventional treatment techniques.

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.
Learn More

Lab Tests in This Article

1. Wedro, B. (2022, August 8). SIBO (Gut Bacteria Problem) Symptoms, Causes, Treatment. MedicineNet.

2. Siebecker, A. SIBO - Small Intestinal Bacterial Overgrowth. SIBO Info.

3. SIBO and Other Forms of Intestinal Overgrowth. Trio-smart.

4. Takakura, W., & Pimentel, M. (2020c). Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome – An Update. Frontiers in Psychiatry, 11.

5. Siebecker, A. Symptoms. SIBO - Small Intestinal Bacterial Overgrowth.

6. SIBO (Small Intestinal Bacterial Overgrowth): Symptoms, Diet, Causes & What it Is. Cleveland Clinic.

7. Cloyd, J. (2023, March 14). SIBO Testing 101: A Complete Guide to The Top 3 SIBO Tests. Rupa Health.

8. Pimentel, M., Saad, R.J., Long, M.D., et al. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. The American Journal of Gastroenterology, 115(2), 165–178.

9. Cloyd, J. (2023, March 10). How to Use the trio-smart Test from Gemelli Biotech in Clinic. Rupa Health.

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