Rifaximin (Xifaxan): Why It May or May Not Improve Your SIBO

Rifaximin (Xifaxan): Why It May or May Not Improve Your SIBO

Rifaximin (Xifaxan): Why It May or May Not Improve Your SIBO

Rifaximin (Xifaxan) is one of the most common antibiotics prescribed for SIBO (small intestine bacterial overgrowth). It is a relatively safe antibiotic and can help reduce hydrogen dominant bacterial overgrowth in the small intestine. There are, however, some drawbacks associated with its use, of which, many people are sadly unaware. There are however ways to try to insure that the antibiotic works properly to alleviate your SIBO and improve your digestive health!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 was initially synthesized from Streptomyces mediterranei which is now known as Amycolatopsis rifamycinica. The antibiotic inhibits bacterial DNA-dependent RNA synthesis. Antibiotics in the rifamycin class have an average side effect profile (gastrointestinal upset, diarrhea, headache) but have also been associated with hepatotoxicity, because they increase liver mitochondrial oxidative stress, and decreased white blood cell counts. Antibiotics that are used from this class include rifampin, rifabutin, rifapentine, and rifaximin.3

Rifaximin is very special compared to other antibiotics in its class. So what are the pros and cons for using rifaximin in the treatment of SIBO over other antibiotics?

Rifaximin (Xifaxan) Pros

  • Very poorly absorbed by the intestinal tract. Therefore, its antimicrobial effects only occur within the small intestine and not in other parts of the digestive system or systemically. Working only in the small intestine helps to protect your microbiome outside of the small intestine.4 5
  • Poor systemic bioavailability dramatically lowers the chance of liver toxicity associated with the rifamycin class of antibiotics, including rifaximin. Since it is not absorbed very well if at all by the intestinal tract it is not metabolized by the liver.6
  • Rifaximin has a lower serious side effect profile. Like with most antibiotics it can still cause gastrointestinal upset, headache, rash, and causing rare allergic reactions.7
  • Lower chance of bacteria acquiring antibiotic resistance due to it only being effective in the small intestine and not affecting the microbiome of the entire body. It works well against most hydrogen dominant bacteria which is the main cause of SIBO-D.8
  • Can prevent traveler’s diarrhea if it is caused from opportunistic E. coli.9
  • May be effective against Clostridioides difficile dysbiosis of the jejunum and ileum of the small intestine if there is enough bile (C. diff may interfere with bile) to make it effective.10 11

Rifaximin (Xifaxan) 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 problems causing you not to produce enough bile or digestive enzymes the antibiotic may not work correctly. 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 appropriately 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.12
  • Rifaximin will do very little to help combat upper gut (upper part of the duodenum, stomach, esophagus, larynx, and oral cavity) dysbiosis. Bile is generally not found in this area of the digestive tract unless you are suffering from bile reflux. Therefore, rifaximin will not be activated and work properly to reduce dysbiosis in these areas.13
  • Rifaximin will also do very little to help combat large intestinal dysbiosis. 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 correctly in the large intestine to alleviate dysbiosis. Lack of bile salts in the large intestine might also explain why it is not systemically absorbed into the body.14
  • 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 even though it is better than other antibiotics used in the treatment of SIBO in many aspects, it still reduces the probiotic microbiome of the small intestine. Supplementation of prebiotics to feed your probiotic microbiome during its use and after may help change the microbiome in someone with SIBO to hopefully a more favorable microbiome. I recommend asking your medical professional about trying the prebiotics 2-FL, GOS, arabinogalactan, or partially hydrolyzed guar gum to see if it improves your digestive health and help to keep your SIBO in remission.15
  • Rifaximin by itself is ineffective against methane dominant Archaea that cause SIBO-C (constipation) or upper gut 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 (Xifaxan) 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!

7 Comments
  1. Hello,

    after few courses antibiotics last year , inlcuding 1 week of quinolones I am experiencing adverse reactions at my tendons, muscles, brain, and gut. Few months ago I ate sauerkraut around a bowl and then my allergies and constipation started. I think sauerkraut maed me SIBO. SIBO was seen from my microbiome test also. Doctor prescribed me rifaximin but I could not yet use it since I am afraid of side effects. I used oregano oil also, but it caused big allergy on me. So, I am little out of solution. Probiotics I tried (Klaire labs for ex.) did not help me. Can you please suggest me what to do? Can rifaximin be safe in my case you think? Also, do you think sauerkraut amount may cause SIBO?

  2. 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?)

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

  4. 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.

  5. 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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