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Myths and Mysteries of SIBO

Updated: Apr 12, 2022


I attended an integrative medicine conference last year that included major updates on the difficult to treat digestive issue known as SIBO. I am super excited to share the highlights of what I learned because the information was a GAME CHANGER.


What is SIBO?

SIBO is an acronym for Small Intestinal Bacterial Overgrowth. Humans are supposed to have a LOT of bacteria in our large intestines, but only very little bacteria in our small intestines. There is even a valve between the small intestine and large intestine that keeps those compartments separate. When bacteria from the large intestine migrates backward up into the small intestine, this creates a situation known as SIBO. To be clear, this is not necessarily an infection, the bacteria that move from the large intestine into the small intestine may be normal, healthy gut bacteria, they are just not supposed to be in the small intestine. The resulting symptoms are intense abdominal bloating after even small meals, along with diarrhea or constipation (or both). What is really frustrating is that bloating is often worse with healthy high fiber foods, brassicas (broccoli, kale), and probiotics - things that are often sited as beneficial for gut health.


Intestinal bacteria (and yeast) feed on the food that we eat and produce various gasses as a byproduct of their metabolism. We all have gut microbes that produce some gas. Why is it so much worse with SIBO? Gas is gas right?


The problem isn't the gas. The problem is the location of the gas. The large intestine walls are much thicker and stronger than the small intestine. The large intestine is built to withstand both solids and the pressure of gasses. The small intestine wall is very thin and flexible. It is not built to withstand the pressure of gas, and gasses are not supposed to be present in the small intestine (remember, those microbes are not supposed to be there). When microbes from the large intestine make their way up into the small intestine, gasses are produced and the small intestine inflates like a balloon. The muscles of the small intestine are also not designed to move gasses, so the gas tends to move very, very slowly. This leads to dramatic, very uncomfortable and prolonged bloating after eating, which is the main and defining symptom of SIBO.


What causes SIBO?

There are LOTS of things that can contribute to SIBO. Some are chronic underlying conditions, some are acute or short term situations. The common denominators for developing SIBO are:

  1. slow small intestine transit time and slowing of the migrating motor complex

  2. dysfunction of the ileocecal valve (the sphincter that keeps the small and large intestines mostly separated)

These two things can be caused by:

  • Acute gastrointestinal infection (dysentery)

  • Low HCL production in stomach

    • stress

    • acid blocking drugs (used for heartburn or ulcers)

  • Low bile production

  • Autonomic imbalance (chronic fight or flight response, weak parasymptathetic function)

  • Hypermobility disorders (ex: Ehler's Danlos) causing "stretched out" intestines

  • Adhesions from injuries, surgery, endometriosis causing restrictions in bowel motility

  • Many more

While in the short term, SIBO is in essence an infection that can be treated with antimicrobials, it also always has an underlying cause that must also be addressed.


Testing for SIBO

In addition to the classic symptom presentation, it is also possible to test the breath for the presence gasses produced in the small intesetine. Several companies offer this type of testing. Some versions are designed to be done at the doctor's office, some can be completed with home tests (though they are a bit complicated).

It is also worth mentioning here that the official diagnostic criteria for SIBO are a little strange, and can make getting a diagnosis difficut. Technically a SIBO breath test is negative if there is not a large enough increase in gas ppm from baseline levels. This criteria is a bit incomprehensible as it completely ignores the fact that baseline gas should be near zero if there is no bacteria in the small intestine. (which, as we noted above, there should not be)



New News about SIBO

SIBO is notoriously difficult to treat, and is well known for its high recurrence rate.

Based on what I learned, there are several (now obvious) reasons for this.

  1. Inadequate testing: only testing for one type of gas

  2. Misinterpreting testing

  3. Failing to treat all the classes of microbes present

  4. Failing to treat long enough

  5. Failing to support motility and overall health / underlying conditions

Traditionally SIBO testing covers one gas type (hydrogen). Likewise, classic treatment for SIBO often defaults to one particular antibiotic (Rifaxamin) for 2 weeks, plus a diet that restricts the types of fiber that feed gut bacteria. But, different types of microbes produce different types of gasses. So while this classic approach helps many cases, it does not help everyone, and even when it does help, symptoms often return quickly because not everything has been addressed.


Here are the new "little known facts" about SIBO that I learned at the conference:

  • There are three different types of SIBO based on the kind of gas produced.

    • Different species of organisms/ bacteria produce these different gas types.

    • These different bacteria cause different SIBO presentations (beyond the severe bloating common in all types of SIBO).

    • These different bacteria require different anti-microbial treatments. (key point)

    • The amount of gas present determines how many rounds of treatment will be required for resolution. Each round of antimicrobial treatment can clear about 30ppm of hydrogen gas, and many people have levels much, much higher than that. (another key point)

  • Gas types:

    • Hydrogen

      • Is produced by "healthy gut bacteria" that have migrated up from the large intestine

      • Hydrogen gas is associated with diarrhea.

      • The prescription Rifaximin/ xifaxan works to lower the levels of this type of bacteria (but can only lower it 20-30ppm per 2 week round).

      • Herbal treatments may also be effective, but require a minimum of 4 weeks to clear 20ppm.

    • Methane

      • Is produced by ancient microbes caled archaea (not exactly bacteria)

      • Methane gas is associated with constipation

      • Archaea use hydrogen produced by the other bacteria to make methane.

      • There are 4 hydrogens in every molecule of methane

      • Because archaea use up the hydrogen, it can cause the hydrogen score to be low in spite of hydrogen being produced.

      • If methane is present on a breath test, then the presence of hydrogen producing bacteria is implied (multiply the methane score by 4 to estmate how much hydrogen is actually being made)

      • Archaea does NOT respond to Rifaxamin. Lowering archaea requires use of anti-parasite medications such as Neomycin, Flagyl or Alinia, AND Rifaxamin or herbs to address hydrogen producers.

      • Herbal treatments may also be effective but require a minimum of 4 weeks per round, and should always be combined with treatment for hydrogen producers.

    • Hydrogen Sulfide

      • Is produced by many different types of bacteria, some examples are:

        • Salmonella, Klebsiella, Campylobacter, Prevotella and many more

      • Hydrogen sulfide gas is associated with neurological symptoms

      • These bacteria are reduced by Rifaxamin

      • Hydrogen sulfide producing bacteria use hydrogen produced by the other bacteria.

      • There are 2 hydrogens in every molecule of hydrogen sulfide.

      • Because the hydrogen gets used up, it can cause the hydrogen score to be low in spite of hydrogen being produced.

      • Hydrogen sulfide absorbs quickly into the bloodstream, so is very difficult to identify on a breath test, most tests do not screen for it.

    • Carbon Dioxide

      • This gas is produced by Candida and other yeast.

      • Techinically this would be referred to as SIFO (small intestinal fungal overgrowth)

      • None of the SIBO breath tests screen for this gas

      • This frequently occurs with the various forms of SIBO above, especially since SIBO symptoms are often worse when eating a healthy, high fiber, high vegetable diet. That makes it more comfortable to eat a higher sugar diet, which then feeds yeast.


Mistakes I see often

Case 1: Patient with mixed constipation and diarrhea that is only tested for hydrogen. Test results show that hydrogen is low or absent. They are told they don't have SIBO and they are not treated for SIBO - even thought they have dramatic, persistent bloating.

Mistake: if you don't look for the methane, you definitely won't find it. If methane is present, then it can use up all the hydrogen, which makes the hydrogen portion of the test negative. Many of these people have mixed hydrogenic and methanogenic SIBO, but are not being tested properly, and never receive a correct assessment.


Case 1: Same scenario, but the patient is tested for both methane and hydrogen. Methane levels are positive at 10ppm, hyroden levels are considered negative at 10ppm. They are treated with 1 round of Flagyl, they feel a little better for a few weeks, but then their symptoms come right back. Further treatment is refused due to "failure" of previous treatment.

Mistake: The presence of the methane is hiding much higher levels of hydrogen production.

In order to make 10ppm of methane, 40ppm of hydrogen are used. This "implied" hydrogen must be added to the already 10ppm present on the test. So the actual hydrogen production is closer to 50ppm, which is quite high, and would require 2-3 rounds of treatment with Rifaxamin (or herbs) to clear completely, in addition to treatment for the archaea with anti-parasite medication or herbs. The original treatment did not fail, it just was not complete.



In Conculsion

The chances of treating SIBO successfully are dramatically increased by having a better understanding of what caused it, what gasses are present, and how much of each is present. Successful treatment plans will address all types of "gas formers", will include enough rounds of treatment to get through the infection, and will also have a plan in place to address the underlying causes of the SIBO. SIBO can have complex causes, and in some cases, chronic underlying issues are difficult or impossible to truly resolve. In these instances, it may be difficult to fully resolve SIBO symptoms and may be impossible to prevent all reapses of SIBO.

Cases that began with acute stress or infections and do not have chronic underlying conditions may be able to find full resolution if all of the infectious patterns are successfully addressed.


There are several other important aspects of SIBO that were not addressed in this article. I want to give them a brief mention so that they are on your radar for further study, but these topics were beyond the scope of my intent today.

  • Dietary management: symptoms can be improved by following modifications of the lowFODmap diet - this diet is not known to resolve SIBO, but it can help control symptoms.

  • Motility management: sometimes requires pharamaceutical intervention. Herbs and supplements that address constipation are NOT the same as increasing small bowel motility.

  • The Elemental Diet: this is a medical food replacement drink that provides calories and nutrients for the body, but does not provide any food for the bacteria. It is considered the most effective anti-microbial "kill off" procedure available for SIBO. It is difficult to complete (2 weeks with no solid food), but is very effective for people who are able to tolerate the process.



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