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 (small intestine bacterial overgrowth). 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 (Methicillin-resistant Staphylococcus aureus). 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 in systemic circulation or the colon. This is important in treating conditions like SIBO because it makes it more effective in the small intestine without reducing beneficial flora in other parts of the body. 4 5
  • Poor systemic bioavailability greatly lowers the chance of liver toxicity associated with the rifamycin class of antibiotics, rifaximin is one. 6
  • Low chance of bacteria acquiring 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. The only drawback in taking an ox bile supplement with the antibiotic is that it may activate it in the stomach and the duodenum as well and affect their microbiomes. 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 a damaged MMC (motility), elevated stomach pH, diet, dysbiosis, leaky gut, malfunctioning ileocecal valve, or opportunistic biofilm formation. This might explain the possible high recurrence rate of SIBO after treatment.
  • Rifaximin does not work well by itself with SIBO-C (constipation) or hydrogen sulfide dysbiosis. If you are dealing with SIBO-C then the rifaximin has to be combined with other antibiotics like Flagyl, Cipro, Neomycin, or Alinia (the only one I recommend for SIBO-C) for it to be sufficient.

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!

6 Comments
  1. Thanks for this!
    Any advice on what to take after the course of rifaximin to keep SIBO at bay? GOS? Probiotics? (if so, which ones?)

  2. If rifaximin doesn’t work well for hydrogen-sulfide SIBO, what does?

  3. I’ve finally broken down and will be doing a vourse of Rifaximin for my SIBO-D. What you said about light colored stool and not producing enough bile really hit me. I’m thinking that part of my problem is a lack of bile. Do I take the Ox bile pill with the antibiotic though or with my meals? I feel like I’m taking so many pills it’s hard to keep them all straight and to know when to take what. Thanks for your website, the last few days it’s been all I’ve been reading.

    • You could consider trying a low FODMAP diet first. Add in foods slowly after a period of this and see if you can tolerate prebiotic fiber. Just a thought. I don’t know your exact current situation but low FODMAP has seemed to help me so far at least keep diarrhea at bay, while being on SCD for 2 years prior didn’t help.

      I’d imagine if you do happen to remedy SIBO with Rifaximin, you may want to stick to a strict diet like FODMAP or SCD at least initially to try to ensure that you don’t get SIBO again. It seems to have a high recurrence rate.

  4. 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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