What is SIBO?

This blog post is a summary of our two-part video series on Small Intestinal Bacterial Overgrowth (SIBO). SIBO is defined by an overabundance of microbes in the small intestine greater than 103. [Leite et al] Our small intestine does contain microbes, but the quantity is less than that of the colon, and normally kept in check by our stomach acid, bile production, enzymes and migrating motor complex.

It is important to note that newer research identifies SIBO as an imbalance of pathogenic vs commensal microbes and lower microbial diversity in the small intestine. This also needs to be addressed within a treatment plan. [Banik et al] [Stefano et al] [Pimentel et al]

Common symptoms of SIBO include:

  • Gas and bloating
  • Diarrhea, constipation or both alternating
  • Skin issues, including eczema, rosacea or psoriasis
  • Weight loss or weight gain
  • Food intolerances
  • Vitamin and mineral deficiencies
  • Fat malabsorption
  • Heartburn, nausea or GERD
  • Mood related symptoms, such as depression or anxiety
  • Fatigue

SIBO Subtypes

SIBO has three subtypes, which we define by the type of gas being produced by the overgrown microbes. The three types are hydrogen, methane and hydrogen sulfide. It is not uncommon for clients to have more than one subtype. In fact, methane and hydrogen sulfide producing microbes both “steal” hydrogen in order to make their own gas.


Diagnosis is accomplished through a lactulose breath test. The client follows a week-long low fermentable foods diet until the night before the test. They will then fast until the test is complete. When taking the test the client will drink the lactulose solution and proceed to breath into 10 test tubes every 20 minutes, cap them off and send them to the lab for analysis. The lab will measure for hydrogen and methane gas. Hydrogen sulfide gas is not yet detectable by the breath test.

In the case of a client having diabetes, a fructose substrate breath test would be used in place of lactulose.

Skeptics of the breath test have emphasized the importance of microbiome testing for SIBO diagnosis, saying identification and targeted treatment of pathogenic microbes is essential. This is made evident by the third class of SIBO, hydrogen sulfide, for which diagnosis depends upon culture or PCR based testing and cross referencing of the client’s symptoms. As the paradigm has begun to shift, it appears that hydrogen-sulfide SIBO is much more common than previously thought. Additional studies have found that breath tests often produce a false negative in clients who have an overgrowth of hydrogen-sulfide producing microbes. [Banik et al] [Stefano et al]

For this reason I always use microbiome testing alongside breath testing with clients. This way we can reduce our chances of a false negative and can fine-tune the treatment plan according to the type of microbial overgrowth.

Addressing the Root Cause

Beyond a diagnosis and subsequent treatment to reduce SIBO microbes, experts agree that the cause of SIBO is generally multi-factorial and thus should be thoroughly investigated in order to prevent relapse. Relapse is unfortunately common in those treated solely according to breath test.

Top root causes of SIBO include:

  • Food poisoning
  • Ileocecal valve dysfunction
  • Structural issues, particularly post surgery, cholecystectomy, trauma to the abdomen or injuries involving the spinal cord
  • Low production of stomach acid
  • Irregular bile secretion
  • Low production of pancreatic enzymes
  • Deficiency of the migrating motor complex
  • Traumatic brain injury
  • Thyroid disorders
  • MS, Lyme, Ehlers Danlos Syndrome or Lupus
  • Lipopolysaccharide toxicity
  • Dysbiosis within the gut microbiome
  • Poor dental health
  • Hyperarousal of the parasympathetic nervous system
  • Mold toxicity
  • Heavy metal toxicity
  • Glyphosate toxicity
  • Celiac


Besides addressing the root cause, a treatment plan is typically made according to the dominant gas being produced. Options for treatment may include antibiotics, herbal antimicrobials or an elemental diet.

Antibiotic Treatment

Rifaximin is the primary antibiotic used for hydrogen dominant SIBO. It is usually combined with a Prokinetic such as low dose erythromycin, prucalopride or low dose naltrexone. Rifaximin can be made more effective by eating FODMAP rich foods or by supplementing with a prebiotic such as Partially Hydrolyzed Guar Gum.

Methane dominant SIBO is treated with a combination of Rifaximin and Neomycin. Dr. Pimentel is currently trialling a non-absorbable form of Lovastatin for methane dominant SIBO.

Hydrogen sulfide SIBO is treated according to the microbial overgrowth. Antibiotic options include ciprofloxacin, aminoglycosides, tetracyclins, ampicillin, gentamycin, or cephalosporins.

Treatment with Herbal Antimicrobials

The benefit of using a herbal protocol is that there is more opportunity to shift the quality of the intestinal terrain due to the multi-functional nature of herbs. The downside would be that clients with a lot of intolerances may not be able to tolerate the herbs.

Hydrogen dominant SIBO can be treated with Berberine containing herbs alongside prokinetics.

Methane dominant SIBO should respond to allicin, the medicinal component of garlic.

Hydrogen-sulfide dominant SIBO is trickier to treat. Depending on the type of microbial overgrowth present, it may respond to emulsified oregano, cinnamon bark extract, lemongrass, or zinc acetate. Reduction of circulating hydrogen sulfide gas may be accomplished with zinc acetate, bismuth, B12 or binders, such as activated charcoal.

Treatment during Pregnancy

SIBO can be treated during pregnancy, but you will need to make sure you are working with a practitioner who knows which compounds are safe for you and your baby.

Elemental Diet Treatment

The elemental diet involves taking a specially formulated meal replacement powder for 14-21 days. Most of them are unfortunately foul tasting and the process of not eating real food for that long can be mentally challenging. That being said, it does work well in the right cases.

Our preferred formula is the Physician’s Elemental Dextrose Free. Other options include Elemental Heal by Dr. Ruscio or a home-made version for which the recipe is shared by Dr. Siebecker.


The main diet for reducing SIBO is the Low Fodmap or Low Fermentable diet. FODMAP stands for Fermentable Oligo-, Di-, Mono-saccharides And Polyols. These are short-chain carbohydrates that are poorly absorbed. In people with SIBO, a diet high in FODMAPs can induce diarrhoea and/or constipation, bloating, gas and abdominal pain.

That being said, the Low FODMAP diet will not work for every SIBO case. Depending on the client, they may actually respond to a higher-fibre diet. This is particularly true where the client is Hydrogen Sulfide dominant.

You can visit Monash Fodmap for a low FODMAP diet list.

It is important to understand that diet alone will not treat your SIBO. You will still need to treat for the microbial overgrowth and any other underlying causes.

Additional Information for SIBO Root Causes


If your SIBO developed after experiencing food poisoning, you have SIBO-D, or you’ve done testing to reveal that Campylobacter or Toxigenic E-Coli are present in your gut, you may wish to be tested for autoimmune antibodies. These microbes produce a toxin called Cytolethal distending toxin-B (CdtB) which cross-reacts with components of the migrating motor complex to slow things down. The test for this is “IBS-Chek” and is currently available in the US and Australia. Canada does not yet have access to this test.

Traumatic Brain Injury

If you have SIBO and have a history of concussion or brain injury I strongly suggest you and your practitioner curate a treatment plan that involves healing your brain. My top suggestion for this would be hyperbaric oxygen (HBOT), second to this would be photobiomodulation (PBL) delivered by helmet and/or cranial sacral therapy. These should be used in conjunction with nutrition and lifestyle adjustments.

Thyroid Disorders

Thyroid disorders often go hand in hand with SIBO. If you or your practitioner suspects that you have a thyroid disorder you will need to have them test your free T4, free T3, thyroid antibodies and reverse T3. TSH alone is not adequate for diagnosing nor monitoring thyroid disorders. For more information on this read the thyroid section in “Solving the Brain Puzzle”.


Diabetes can slow down your migrating motor complex and even cause gastroparesis; a slowing of the emptying of the stomach. If you suspect Diabetes ask your practitioner to test your fasting blood glucose, your hemoglobin A1C and run an oral glucose tolerance test.


Viral infections, such as reactivated Epstein Barr, or stealth infections, such as Lyme, can contribute to SIBO. If this is the case for you, make sure you work with a practitioner literate on these subjects.

Mold Toxicity

Maybe it isn’t just you who is sick, perhaps your home, car or work environment are too. The petri-dish test is not accurate enough to test for the presence of mold, make sure you work with a practitioner who can run mold panels for your body and recommend the most appropriate testing for your environment.

Structural Issues

You have 5 valves throughout your digestive tract that may need support throughout your SIBO treatment. I often recommend that our SIBO clients see someone trained in Visceral Manipulation to ensure the valves are working properly. To find a practitioner visit the practitioner directory at www.barralinstitute.com.

If you have a history of migraines or chronic headaches, pain or neck pain, spinal cord or neck injury, you may benefit from seeing a Chiropractor, Upper Cervical Chiropractor or other specialist to ensure an injury hasn’t infringed upon your vagal nerve function.


Endometriosis can both be the cause and occur downstream of SIBO. See a specialist to help you navigate this if it is an issue.


There are a number of medications that can give rise to SIBO including PPI’s or antacids, SSRI’s or anti-depressants, anti-diarrheal medications and opiate medications. If you wish to come off of these medications please do so under the care of a healthcare provider. There is a method to to make sure clients can reduce their medication safely and comfortably.


These are simply the highlights for successful management or treatment of SIBO. For more information please watch our video series on SIBO or contact us at info@taymountcanada.com

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