Rifaximin: Why It May or May Not Improve Your SIBO

Rifaximin: Why It May or May Not Improve Your SIBO

Rifaximin is one of the most common antibiotics prescribed for SIBO. It is a relatively safe antibiotic and can help reduce bacterial overgrowth in the small intestine. There are, however, some drawbacks associated with its use, of which, many people are sadly unaware. 1 2

Rifamycin Class of Antibiotics

The rifamycin class of antibiotics was discovered in the 1960s and is used currently in the treatment of MAP, tuberculosis, SIBO, and MRSA. It is synthesized from Streptomyces mediterranei. The antibiotic inhibits DNA-dependent RNA synthesis in prokaryotes and has a poor affinity for eukaryotes. Antibiotics in the rifamycin class have an average side effect profile (gastrointestinal upset, diarrhea, headache) but have also been associated with hepatotoxicity. 3

Rifaximin is very special compared to other antibiotics in its class. The pros of using rifaximin for SIBO over other antibiotics include:

Rifaximin Pros

  • Very poorly absorbed by the intestinal tract. Therefore, its antimicrobial effects occur only in the small intestine and not systemic circulation. This is important in treating conditions like SIBO because it makes it more effective in the small intestine without harming beneficial flora in other parts of the body. 4 5
  • Poor bioavailability greatly lowers the chance of liver toxicity. 6
  • Low bacterial chance of requiring antibiotic resistance due to the mechanism of action. 7
  • Rifaximin has a low serious side effect profile. 8
  • Can prevent traveler’s diarrhea if caused by ingestion of E. coli. 9

Rifaximin Cons

  • Rifaximin requires bile to become both soluble and activated. A lot of people with SIBO have issues with bile production and fat digestion. If your stool is not dark brown when you defecate, or you are having liver, gallbladder, or pancreatic issues causing you to not produce enough bile or digestive enzymes the antibiotic may not work properly. A possible alternative if you are having those issues is to take an ox bile supplement when you take Rifaximin so that it can be properly utilized in the small intestine to help combat your overgrowth. 10
  • Rifaximin will do very little to help combat overgrowth in the large intestine. Bile salts are largely reabsorbed by the body and by the stool by the time your stool reaches the ileocecal valve. Therefore, rifaximin will not work properly in the large intestine to eliminate overgrowth. Lack of bile salts in the large intestine might also explain why it is not systemically absorbed into the body. 11
  • Using an antibiotic like Rifaximin or even a natural antibacterial agent does not correct any of the direct causes of SIBO like damaged MMC (motility,) lack of stomach acid, yeast / parasite infection, damaged intestinal lining, or increased biofilm formation. This might explain the possible high recurrence rate of SIBO after treatment.

Rifaximin is an important treatment option in the fight against SIBO as long as its drawbacks are addressed in your wellness plan.

If you are taking Rifaximin, please work with your doctor to address these drawbacks to using the antibiotic by itself to help combat SIBO. If your doctor is too busy and you need additional help contact me, and I will see what I can do to improve your digestive health!

1 Comment
  1. Thank you for this. After many years, most of my adult life, dealing with a variety of gut issues I decided to take this antibiotic. I experienced, surprisingly, mood improvement and some relief of gas/bloating. I felt my gut to be more mine, if that sounds weird. I am working on relieving the original problem but feel confused about all the options. I’m going to take Interfase Plus, Motilpro, drink bone broth and supplement with collagen and other gut lining healing foods and herbs. Any other suggestions? I hope to get your book soon and possible ask for a consult. They only said bacterial overgrowth and am assuming I have SIBO-C type, definitely not D. Have history of candida too.

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