SIBO – Cause, Testing and Treatment

February 18, 2016

What is SIBO?

Irritable Bowel Syndrome (IBS) afflicts an estimated 15% of Americans. Small intestine bacterial overgrowth (SIBO) is responsible for more than 50% of (IBS) cases. Gas or bloating 30 minutes after a meal, abdominal pain or altered bowel movements are telltale signs that you could have SIBO. Generally you should have at least one daily bowel movement. The stool should be well formed;bristol_stool_chart a type 3 or 4 on the Bristol stool chart shown on the right. Types 1 and 2 indicate constipation. Types 5 to 7 are on the diarrhea side of the spectrum. Some people can experience a mixture of both constipation and diarrhea. Here is a complete list of SIBO symptoms:

•    bloating/ abdominal gas
•    flatulence, belching
•    abdominal pain, discomfort, or cramps
•    constipation, diarrhea or a mixture of the two
•    heartburn
•    nausea
•    malabsorption: steatorrhea, anemia
•    systemic symptoms: headache, joint/muscle pain, fatigue, rosacea

SIBO occurs when bacteria that should be in the large intestine creep up into the small intestine because something called the migratory motor complex (MMC) is not keeping the bacteria down in the large intestine. Having these bacteria in the small intestine means that fermentation of food is occurring in the small intestine instead of the colon. The small intestine is not designed for this. It hampers the digestion and absorption of nutrients and often damages the intestinal lining. The gases and other by-products of these microorganisms creates symptoms in the digestive tract, and even in the nervous system and other organs.

When a practitioner first suggested that I had IBS and possibly SIBO I resisted. I didn’t think anything was wrong with my digestion because I didn’t experience pain, nausea or diarrhea. After researching and talking to other practitioners I realized that the amount of flatulence, constipation and burping I had was excessive. Testing showed that I did have elevated methane. It was foundational to other health issues I was having.  A food-borne illness, including traveller’s diarrhea, is the #1 culprit. Here’s a list of what could cause SIBO.

Potential Causes:

  • Infection (food borne pathogens can lead to partial small-bowel paralysis). This is the #1 cause.hand on tummy
  • Decrease in pancreatic enzymes
  • Pancreatitis
  • Hypothryoidism
  • Diabetes
  • Untreated celiac disease
  • Decrease in bile acids (bile acids normally emulsify in the intestine and don’t allow bacteria to grow).
  • Decreased motility of the intestine – enables bacteria to build up in the intestine. Can be stress induced.
  • GERD treated with proton pump inhibitors
  • Low stomach acid
  • Decrease in the migrating motor complex (MMC). Can be caused by infection.

SIBO Testing

sibo breath test

Monash University, Australia

It’s a good idea to test for SIBO to ensure you’ve accurately diagnosed your IBS issues. Treatments will vary depending on whether your SIBO results show a predominance of hydrogen or methane gases. The best test methodology is a breath test. After a day on a special diet you drink lactulose solution and then breath into a series of tubes over a 2 or 3-hour span depending on which test.  Both methane and hydrogen can be detected.  More than 3 parts per million (ppm) of methane is associated with constipation while elevated hydrogen numbers are associated with diarrhea. There are several good tests in the lab market. Three-hour tests are preferred (Commonwealth Labs) over 2-hour tests but a 2-hour test is adequate (Genova Diagnostics) if it’s your only choice.

How Do I Get Rid of SIBO?

The good news for many IBS sufferers is that SIBO is a clear-cut diagnosis with high success-rate treatments. Finally there’s something tangible to focus on and eradicate. It usually takes between 2 and 18 months to overcome SIBO depending on the type, severity, how aggressively you comply with dietary changes and whether you go the herbal or prescription antibiotic route. The bad news is that despite good compliance to an appropriate SIBO diet, SIBO will relapse for many people. The type of SIBO manifesting as constipation, and associated with methane-producing bacteria, is the most difficult one to eradicate.

In cases caused by food poisoning, including traveler’s diarrhea, the work of Dr. Mark Pimentel shows that SIBO is caused by an autoimmune mechanism. The food poisoning exposes you to Cytolethal Distending Toxin B (Cdt-B). Some people produce antibodies to this toxin. These antibodies not only attack the Cdt-B but also attack a protein in the gut called vinculin that is nearly molecularly identical to Cdt-B. Vinculin is needed to trigger the peristaltic-like waves for the migratory motor complex to maintain gut motility. And it keeps the large intestine bacteria in the large intestine. For people with this condition, you need to get the SIBO into remission through diet and anti-microbials (or antibiotics) and then take prokinetics for life to keep the MMC working.

Treatment Options

A combination of a SIBO diet and either herbal antimicrobials or antibiotics are the typical paths to at least temporary eradication. Several scientific studies have shown that the herbal antimicrobials are just as effective as antibiotics but take longer to work. For the SIBO diet Dr. Alison Siebecker, a renowned SIBO expert, has had the most success combining the Specific-Carbohydrate Diet (SCD) diet and low FODMAP diets while someone has SIBO and then transitioning to a low FODMAPs diet to prevent relapses.

  1. There are several dietary options for a SIBO diet:
    1. Low FODMAPs
    2. Low FODMAPs/SCD (Dr. Siebecker)
    3. Elemental Diet. This is a very strict diet of processed food packets that taste bad. You cannot eat regular food for 2 weeks. But it is very effective.
  2. Herbal antimicrobials
    1. Allicin (Allimed or Allimax Pro) and Neem are the gentlest protocol
    2. FC Cidal and Dysbiocide (from Biotics)
    3. Candibactin AR and BR (from Metagenics)
    4. Other herbal antimicrobials that can be used in combination with the above include: berberine, golden seal and oregano oil.
  3.  Antibiotics. While I generally advise against antibiotics, Rifaxamin may be appropriate for severe cases.
    1. Rifaxamin is commonly prescribed for serious cases of SIBO or those whose breath test numbers are in the hundreds.  For people testing high in hydrogen, Rifaximin alone is effective. For high methane numbers Rifaxamin plus Neomycin or Metronidazole works well. Rifaximin is one of the few antibiotics that stays local to the small intestine and does not affect the the whole body system.

Prevent Relapses

SIBO is a disorder that relapses because initial eradication does not often correct the underlying cause: a sub-optimal migrating motor complex (MMC).  The MMC moves bacteria down into the large intestine during fasting at night and between meals, clearing them from the small intestine (SI) everyday.  Without prevention bacteria can repopulate the SI within 2 weeks of finishing antibiotics or herbal antibiotics although it can take longer. As mentioned above, if antibodies are attacking Vinculin, the best you can do is stay on a SIBO diet and take a prokinetic that works well enough to keep the  MMC working.

In 2006 Dr. Mark Pimentel, MD, shared his prevention protocol: 1) a prokinetic drug (motility agent) and 2) a lower carb diet.  The key prevention areas are as follows:

  1. Stimulate the migrating motor complex (MMC), the bacterial cleansing wave of the SI, with a prokinetic drug (see below).
  2. Follow a low FODMAPs diet indefinitely.
  3. Supplement with Hydrochloric Acid (HCl), the antibacterial acid of the stomach, if deficient.
  4. Remove proton pump inhibiting drugs (PPI’s), and antacids, a cause of reduced HCl and risk factor for SIBO.
  5. Correct Ileocecal Valve Syndrome (IVC), the physical barrier to bacterial back-flow from the large intestine.
  6. Correct neurological deficits and dysfunctions, including sympathetic dominance.
  7. Treat any concomitant diseases that contribute to SIBO (see above under potential causes).

A prokinetic helps stimulate the MMC (cleansing waves) so that the colonic bacteria stay in the colon and don’t creep up into the small intestine. Here are examples of prokinetics:

  • Iberogast (herbal), 20 drops, 3x/day and before bed
  • MotilPro (high-dose ginger), 3 caps before bed and 3 caps 1-2 times a day between meals.
  • Low-Dose Naltrexone (prescription), 2.5 mg if you tend toward diarrhea, 4.5 mg if you tend toward constipation
  • Very Low-Dose Erythromycin (prescription), 50 mg

In order for the MMC to initiate a cleansing wave you need to be in a fasting state. This means not snacking for 3 to 4 hours between meals. Water or tea between meals is fine.


The low FODMAPs and SCD combined diets is the gold standard diet for treating and preventing SIBO relapses. This is true for during and after herbal antimicrobials or pharmaceutical antiobiotic treatment. Unless you’re comfortable doing your own research on how to customize your diet it’s best to work with a nutritionist or a health practitioner who has experience treating SIBO. There are subtleties in implementing the diet.  It’s easy to overlook things and cost yourself recovery time.


  1. Townsend Letter, Feb/Mar 2013
  2. Dr. Alison Siebecker’s web site,
  3. Consultation with Dr. Alison Siebecker, ND, MSOM, LAc; Feb. 11, 2016
  4. Monash University, Australia,