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Irritable Bowel Syndrome (IBS) and Small Intestine Bacterial Overgrowth (SIBO)

As those who suffer from IBS know, IBS is a frustrating and chronic condition which can cause constipation, bloat and/or diarrhea, along with other bothersome symptoms and often-times varied food intolerances. Though basically we still don’t know what causes IBS, there are new ideas that are being studied and which may lead to new treatments. One such idea relates to small intestine bacterial overgrowth (SIBO).

What is SIBO?

We’ve long known that the small intestine (the fifteen feet or so beyond the stomach, where food is absorbed) stays fairly free of bacteria, compared especially to the colon (large intestine), which has enormous amounts of bacteria. We know that if large amounts of colon bacteria grow inside the small intestine that food digestion can be altered, abnormal amounts of gas and other chemicals can be released and that some individuals develop diarrhea. However, there is now good evidence that modest amounts of SIBO may occur in at least some—perhaps most—sufferers of IBS. Some cases follow a bad but acute “ stomach flu”; others for unknown reasons, but in either case, the small intestine may fail to do its normal “housekeeping,” in which strong contractions sweep all the way down from stomach to colon and push food debris and bacteria down into the colon. SIBO can then result, which may release gas (methane and hydrogen particularly) inside the small intestine, where gas doesn’t belong normally. The methane, in turn, seems to have a further slowing effect on intestine function. The result: bloat and constipation, even though the anatomy looks fine. Others may get diarrhea from the disturbances in nerve and bacterial balance. The intestine becomes excessively sensitive and irritable in its behavior. This theory is still controversial but there is good evidence supporting this. Researchers have even developed models in animals that support this theory, and more research is underway to understand why some people are susceptible, some not, and why different symptom patterns occur.

Is there a test for SIBO?

Yes, but not a test that is necessary in every case in order to try treatment. In fact, the most “specific” test, of quantitative cultures of bacteria deep within the small intestine, is not practical or sensible. When we feel it is very important to test for before treatment, we refer patients to our specialty lab for a “breath test”. After some diet preparation and attention to what medicines you might be taking, a drink of a precise dose of a sugar solution is taken (lactulose, sometimes glucose). If there is significant amounts of bacteria, or very abnormally fast transit through the small intestine, bacteria break down the non-absorbed sugar and release hydrogen and sometimes methane; the gas concentration is measured in samples of breath periodically over about 2 hours. An abnormal pattern of gas detected is evidence of SIBO. The test is NOT 100% accurate or specific, but a positive test helps confirm the idea SIBO is present; a negative test helps us know that SIBO is very unlikely. The test is harmless and easy to do, just takes time. We provide the SIBO breath testing through our inSite lab, preferably with a take-home kit for which we have an instructional video; there is a modest fee for the convenience of the home test kit. We do offer the option of going to our lab to have the test administered if you wish. HMO patients need to have prior authorization for the test.

What do I do about my IBS?

If we believe it may be useful to treat the possibility that SIBO is causing or contributing to symptoms, there are several steps we need to follow:

  1. Treat the bacterial overgrowth with an antibiotic that eliminates the abnormal bacteria in the small intestine while trying to leave alone the “healthy normal” bacteria in the colon. The best “traditional” antibiotic for this appears to be generics of the brand Augmentin (amoxicillin + clavulanate), taken 2 or 3 times daily for 7-14 days. However, some people are allergic to Penicillin/Ampicillin, some will get diarrhea as a side effect, and rarely a form of colitis (inflamed colon lining) that can become severe, though quite treatable. A newer antibiotic named rifaximin (Xifaxan) seems unique in type and is essentially not absorbed from the intestine, doesn’t disturb the “good bacteria” as much as Augmentin, but is unfortunately expensive (and seems to require a 550 mg dose three times a day for 14 days, at retail cost of $1,400!!). The FDA has OK’d rifaximin for IBS with diarrhea, but due to its expense, many health plans don’t want to pay for it. We’ll assist as best we can in getting treatment authorized, often by going through a specialty pharmacy good at working through these preauthorization issues. We have very limited samples, copay discount coupons may be available, or can steer you to the Xifaxan website of the Salix company to see if they have special programs. We encourage the use of the “GoodRx” app or website to compare pharmacy costs with online sources like In some cases, mainly with constipation the main symptom and positive methane breath test results, we give Neomycin antibiotic along with the rifaximin.
  2. We also need to try and get the small intestine to “keep clean” by stimulating the contractions that normally sweep the bacteria back down into the colon. We use a small dose of the antibiotic erythromycin for this purpose, usually ½ of a 250 mg tablet taken at bedtime. In small doses, it seems to reduce bloaty discomfort and at night seems to turn on the small intestine “housekeeping” function—we are not using it as an antibiotic but as a “pro-motility” drug. We don’t know how long we need to use erythromycin for—perhaps indefinitely if the results stay good.
  3. We know that SIBO may come back, particularly if the “housekeeping” stops happening! This means that some people may need repeated courses of antibiotic(s). The effectiveness and safety of repeated courses appears good, particularly for IBS with diarrhea.
  4. As always in IBS, we also need to address issues like stress, which can intensify symptoms of IBS; and address diet, which should be balanced, with regular meals consumed slowly, avoiding too much fat, and sometimes spicy food or lactose (milk sugar). Less “gas forming” foods (navy beans, cabbage, raw bran) is sometimes advised, along with restriction sometimes of a broad range of “FODMAP” foods (see our Low FODMAPS diet). Some people need to limit gluten (the main protein in wheat products).
  5. Sticking closely to the medications prescribed, and then following up after a few weeks time is extremely important. We need to see if the SIBO treatment seems to make a big impact on symptoms, then on whether the symptoms stay away long enough to be convinced the treatment was really effective, and that wasn’t just a random fluctuation in the amount of IBS symptoms. We’ll still use other approaches to IBS in many cases.

While we don’t yet have a “cure” for IBS, we hope that the theory of SIBO explains many cases of IBS, because this would make us optimistic that treatment described here can offer a new approach to an old stubborn problem.

Medication Information

  • Rifaximin (Xifaxan) 550 mg tablets three times a day for 14 days (we sometimes refer to Canadian pharmacies where the 200 mg form is available but daily cost lower).
  • Neomycin 500mg three times daily for 10-14 days
  • Erythromycin ½ of a 250 mg tablet at bedtime, or elixir compound (more expensive).

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