Small intestinal bacterial overgrowth, known as SIBO, occurs when an excessive amount of certain microbes colonize your small intestine. This condition can cause a wide range of gastrointestinal symptoms, based on the type of gas produced by the microbial overgrowth. Three types of SIBO have been identified and are known as hydrogen-dominant SIBO, methane-dominant SIBO, and hydrogen-sulfide SIBO. It is possible to have multiple types of microbial overgrowth simultaneously, which can complicate treatment. (Source) 

In this article, we’ll review the 3 types of SIBO, associated risk factors and symptoms, treatment options, and holistic interventions to consider in tandem with medical care for long-term management. 

The Role of Your Small Intestine in Digestion

Your small intestine plays a key role in the digestive process, as it is the location of nutrient absorption. Approximately 90% of nutrients (including carbohydrates, fats, proteins, vitamins, minerals, and water) from the foods you eat are absorbed in your small intestine. To make this possible, the walls of your small intestine are densely packed with folds to increase its surface area and maximize absorption of nutrients into your bloodstream. Nutrients are then able to move to key areas of your body to be used or stored. (Source, Source) 

Following the breakdown of food and absorption of nutrients, remaining food byproducts are pushed from your small intestine into your large intestine by wave-like contractions known as peristalsis. Within your large intestine, trillions of microorganisms that make up your gut microbiome further break down remaining food, eventually forming stool. (Source, Source)  

In contrast to the immense collection of bacteria, yeast, viruses, and fungi found in your large intestine, your small intestine contains a limited amount of microbes. However, the minimal microbial population found in your small intestine can abnormally increase based on changes to your gastrointestinal motility (the speed with which food moves through your digestive system). (Source)

This change in motility can occur as a result of: 

• anatomical issues with your small intestine 
• injury to your small intestine 
• gastric surgery 
• abdominal radiation exposure 
• immune disorders 
• gastrointestinal disorders (such as Crohn’s disease, celiac disease) 
• diabetes 
• hypochlorhydria (low stomach acid) 
• metabolic disorders 

(Source, Source)  

Although SIBO can affect any population at any stage of life, women and the elderly are more likely to develop the medical condition. (Source) 

Symptoms of SIBO 

Symptoms of SIBO vary in intensity and frequency based on the type or types of overgrowth you have, microbial abundance, and other underlying conditions. These include: 

• abdominal bloating 
• abdominal pain
• gas
• diarrhea
• constipation
• belching 
• fatigue
• weight changes 
• nausea
• appetite loss

(Source, Source, Source) 

If left untreated, SIBO can be associated with a variety of other health conditions, including:

• malabsorption
• nutrient deficiencies 
• osteoporosis (thin and weak bones) 
• thyroid disorders 
• irritable bowel syndrome
• skin disorders

(Source, Source, Source)

Diagnosing The 3 Types of SIBO 

There are 3 main types of SIBO, named according to the gas the overgrown microbes in your small intestine produce. These are hydrogen-dominant SIBO, methane-dominant SIBO, and hydrogen sulfide SIBO. 

If your health care provider suspects you have SIBO, they will order laboratory testing to confirm your diagnosis. They may order a duodenal aspirate (collection of fluid from the small intestine), although this procedure is not commonly performed due to its invasive nature. Instead, health care providers typically opt for noninvasive breath tests that measure the type and amount of gas produced by any present microbial populations in your small intestine, specifically hydrogen gas and methane gas. (Source, Source) 

1. Hydrogen-Dominant SIBO 

Hydrogen-dominant SIBO is the most common type of small intestinal bacterial overgrowth. 

An abnormal level of hydrogen-producing bacteria in your small intestine is linked to excess serotonin in the gut. Serotonin is a neurotransmitter (chemical messenger) that affects your mood and emotions, but in the GI tract it helps regulate peristalsis, the contractions in your small intestine that push food through. Elevated levels of serotonin can increase peristalsis so that food passes through your digestive tract too quickly, causing episodes of diarrhea, cramping, and bloating. This decreased transit time can also result in poor nutrient absorption, leading to chronic malnutrition if left untreated. (Source, Source, Source) 

Treating Hydrogen-Dominant SIBO

Hydrogen-dominant SIBO is typically treated with antibiotics, commonly rifaximin, which is considered to be effective and safe according to a limited number of studies. Depending on your unique health history and symptoms, your health care provider may also recommend herbal antimicrobials to further target bacterial overgrowth. A 2014 study published in Global Advances in Integrative Medicine and Health found that herbal therapies were as effective as rifaximin in the treatment of SIBO. (Source, Source) 

2. Methane-Dominant SIBO 

Methane-dominant SIBO is the second most common type of SIBO. Abnormal levels of single-celled organisms called methanogens produce methane gas in your small intestine, drawing from hydrogen gas and carbon dioxide already present. Given the need for hydrogen gas to produce methane gas, hydrogen-dominant SIBO and methane-dominant SIBO are likely to co-exist; however, each needs to be uniquely addressed. (Source, Source) 

Methanogens can colonize both your small and large intestine, prompting the American College of Gastroenterology to recommend that methane-dominant SIBO be renamed intestinal methanogen overgrowth (IMO). Unlike hydrogen-producing bacteria, methanogens slow the pace of food moving through your digestive tract, which can lead to constipation. As food sits and ferments for longer periods of time, your body absorbs additional calories, which can lead to weight gain. (Source, Source) 

Treating Methane-Dominant SIBO

Methanogens are not bacteria, so a standard antibiotic treatment like rifaximin will only target hydrogen-producing bacteria that fuel methane gas production. In cases of IMO, pairing rifaximin with other antibiotics such as neomycin or incorporating antimicrobial herbal protocols can be more successful at eliminating methanogens. (Source, Source)   

Pharmaceutical or natural prokinetics (agents that increase gut motility to counter constipation) such as ginger may help to prevent methane-dominant SIBO relapse by activating your migrating motor complex (MMC), which sweeps bacteria from your small intestine into your large intestine between meals. Fasting for at least 3-4 hours between meals can also support proper MMC stimulation, as can avoiding food before bedtime. (Source) 

3. Hydrogen Sulfide SIBO 

Hydrogen sulfide gas occurs naturally within your digestive tract, and in normal abundance it has numerous beneficial anti-inflammatory properties to help maintain GI tract integrity. (Source, Source) 

When overgrown bacteria produce hydrogen sulfide gas in excessive amounts, you may experience symptoms such as: 

• diarrhea
• constipation
• adverse cognitive changes
• abdominal pain 
• bloating
• sulfur-smelling gas 

(Source, Source, Source, Source) 

Excessive hydrogen sulfide gas can lead to a number of associated health problems, including: 

• increased risk of colon cancer 
• mitochondrial damage
• compromised immune system 
• inflammatory bowel disease (such as ulcerative colitis) 

(Source, Source, Source) 

As of now, standard breath tests administered in medical settings do not directly test for hydrogen sulfide gas. Still, these breath tests can be used as a diagnostic tool to measure excessive hydrogen gas levels that can contribute to the development of hydrogen sulfide SIBO. Alternatively, it is possible to obtain a test kit for home use that you can perform independently outside of a medical office that measures all 3 potential types of SIBO. (Source, Source, Source)

Treating Hydrogen Sulfide SIBO 

Unfortunately, evidence-based interventions for diagnosis and treatment of hydrogen sulfide SIBO remain limited at this time. However, while a low-sulfur diet is not recommended for everyone, your health care provider might recommend you temporarily restrict foods and supplements containing high amounts of sulfur, while monitoring any change in symptoms during your elimination trial diet. (Source)

The problem is that sulfur-rich foods include health-promoting animal and plant proteins, vegetables, dark leafy greens, nuts, and spices. Sulfur compounds are also found in drinking water and are used in medications for their antimicrobial, antiviral, and anti-inflammatory properties. Given the lack of evidence on the long-term efficacy of following a low-sulfur diet, additional research is needed before it can be recommended as a treatment for hydrogen sulfide SIBO. (Source, Source)

Evidence-Based Dietary Interventions for SIBO 

SIBO may recur if the root cause of your condition is not addressed. Up to 45% of people treated for SIBO with antibiotic therapy will relapse several months after treatment. This emphasizes the importance of pairing medical treatment with other evidence-based interventions to ensure long-term health and remission. Notably, therapeutic diets have been shown to reduce symptom severity and jumpstart healing. (Source) 

Nutrition protocols for SIBO are often similar to those recommended for irritable bowel syndrome (IBS), a gut disorder that causes changes in bowel function and mirrors SIBO symptoms. Research suggests that about 80% of people with IBS will test positive for SIBO, supporting the case for treatment overlap. (Source) 

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The Elemental Diet 

The elemental diet, a liquid meal replacement that contains nutrients broken down into their most digestible form, may be temporarily recommended by your health care provider if you test positive for hydrogen-dominant or methane-dominant SIBO. This diet allows your digestive system to rest while starving bacterial populations and curbing their ability to multiply in excess. The elemental diet has been shown to improve symptoms of IBS and assist in normalizing SIBO breath tests. (Source, Source)  

The Low FODMAP Diet 

The low FODMAP diet is commonly recommended for people with IBS, and therefore also SIBO. FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) are short-chain sugars found in certain foods, such as garlic, onions, and apples (among others), that are poorly absorbed in your small intestine and easily ferment in your large intestine, causing gastrointestinal distress for some people. By temporarily eliminating and then slowly reintroducing foods high in FODMAPs, specific trigger foods can be identified and restricted long term. Most recently, a 2022 meta-analysis published in Gut found that following the low FODMAP diet was effective in curbing common symptoms associated with IBS. (Source, Source)  

The Specific Carbohydrate Diet 

The specific carbohydrate diet (SCD) eliminates grains, reduces dairy products high in lactose, certain sugars, and other carbohydrates rich in fiber. Because of its clinical success in lowering inflammatory lab markers, this diet is often recommended for people with celiac or Crohn’s disease. The SCD is more restrictive than the low FODMAP diet, so it’s important to work with your health care provider to determine which dietary pattern might be right for you. The diet can be personalized to fit your unique needs and ensure you are consuming sufficient nutrients, given the removal of certain food groups. (Source, Source, Source, Source) 

Whole-Body Interventions for SIBO 

In addition to medical treatment plans and dietary interventions, supportive lifestyle practices can have a positive effect on your overall gastrointestinal health and can be used in tandem with treatment provided by your care team. 

Manage Stress 

The gut–brain axis describes the communication signaling that occurs between your central and enteric (intestinal) nervous systems, which influences your emotional state. This relationship is also affected by your microbiome (the trillions of microorganisms that populate your gastrointestinal tract). Dysbiosis, or gut microbiota imbalance, can negatively affect your immune response, is linked to mood disorders, and can increase your susceptibility toward developing IBS. (Source) 

Chronic psychological stress can also influence gut motility, slowing the speed of food moving through your digestive system, and increasing SIBO risk long term. Research suggests that mindfulness-based calming activities and psychotherapy (including hypnotherapy) can reduce both emotional and gastrointestinal distress, notably decreasing IBS severity. (Source, Source, Source) 

Prioritize Sleep 

Poor sleep can negatively affect anyone, but especially those with IBS and related gastrointestinal disorders like SIBO. A 2015 review article published in Gastroenterology and Hepatology on sleep dysfunction and gastrointestinal diseases found that people with IBS or SIBO reported increased sleep disturbances, incidents of restless leg syndrome, increased abdominal pain, and anxiety. A 2018 meta-analysis published in the Saudi Journal of Gastroenterology assessing over 63,000 people with IBS found that 37.6% had sleep disorders. (Source, Source) 

Regardless of your health history, practicing good sleep hygiene is important for maintaining overall health. A number of supportive techniques to consider before bedtime include: 

• reducing evening light exposure
• limiting screen time 
• maintaining a consistent bedtime 
• avoiding heavy meals  
• limiting alcohol and caffeine 

(Source) 

The Bottom Line

The 3 types of SIBO can cause a wide range of uncomfortable GI symptoms and if left untreated can exacerbate existing health issues and increase your susceptibility to developing long-term chronic conditions. Your prescribed treatment plan, recommended dietary interventions, and lifestyle modifications depend on the severity and nature of your SIBO. Moreover, without identifying the root cause of your SIBO, relapse is likely to occur. Ultimately, understanding the type of SIBO you have can help you reclaim your health. 

Given the complexities of SIBO diagnosis and treatment, working with a qualified nutrition practitioner who can support your unique recovery through dietary and gut-healing protocols is essential. Our WellTheory membership can help clarify your SIBO recovery process and provide community connection to support your mental and physical well-being.