SIBO Treatment Part 1: Antibiotics

Small Intestine Bacterial Overgrowth affects 84% of people with IBS.  84%!!   If you’ve been struggling with chronic gas, bloating, constipation or diarrhea it’s worth talking to your Doctor about SIBO testing.  (A SIBO overview, including testing information can be found here).  Once you determine that SIBO is an issue, a treatment plan can be put into place.

A treatment plan should be multifaceted and should, at a minimum, include dietary changes and antibiotic treatment (either herbal or prescription).  Some cases require further measures to reduce inflammation and improve the integrity of the gut lining, which can be compromised in SIBO.  Once SIBO is eradicated, measures should be taken to prevent relapse.

Sounds like a lot, right?  I will admit that when handed the outline for SIBO treatment I felt pretty overwhelmed.  It makes it easier to focus on one area at a time, which is how I will break down the treatment protocol through a series of posts.

But first, a disclaimer.  While this information was obtained through doctors, including the highly regarded and immensely valuable Dr. Alison Siebecker, you should always work with a health professional when diagnosing and treating SIBO.  Trust me, it makes it MUCH easier when trying to figure out what is and isn’t working.

The first part of treatment we will cover is the antibiotic protocol.  I know taking antibiotics seems counterintuitive when trying to fix gut issues, but hear me out: SIBO occurs when there is an overgrowth of bacteria.  We need to reduce the numbers through the use of antibiotics.  The good news for those who are reluctant to take prescription antibiotics is that there is also an herbal option.  Dr. Alison Siebecker refers to these as herbal antibiotics.

There are pros and cons to both prescription and herbal antibiotics.

Prescription antibiotics are strong and the prescribed duration is 10 – 14 days.  Successive rounds of antibiotics may be needed if your gas levels from your SIBO tests are more than 35-45 ppm.  Each round of antibiotics decreases gas levels about 25 – 35 ppm.

Rifaximin (Zaxine, in Canada) is often touted as the most effective antibiotic for SIBO as it is almost completely non-absorbable which means it stays in the intestines and don’t cause systemic side effects, like bladder infections.  The downside of Rifaximin is that it is very expensive and is often not covered by insurance.

Cephalexin is often used as an alternative to Rifaximin.  It is inexpensive and usually covered by insurance.

For constipation (methane) dominant cases, a second antibiotic, either Neomycin or Metronidazole, must also be used at the same time.

Exact dosing protocols can be found here.

There are side effects to prescription antibiotics, of course.  If you are prone to fungal issues, they may flare up during treatment.  I personally experienced diarrhea, mood swings, poor digestion and yeast issues (including on my scalp and tongue) after having to do four rounds of antibiotics to get my gas levels down.

Herbal antibiotics take longer to bring down gas levels; however, that does not mean they are less effective.  Studies have shown that SIBO can be eradicated solely using herbal antibiotics, not prescription.

“Numerous herbs demonstrate antibiotic activity, but as with any condition that antibiotics are used for, finding the right match and dose is crucial.  Because there have only been two studies, the best herbal antibiotics for SIBO have not been as well defined as the pharmaceutical antibiotics.” – Dr. Alison Siebecker

Dr. Alison Siebecker’s clinic uses a combination of berberine, neem, cinnamon, and oregano with the addition of allicin (garlic) for constipation dominant cases.  Doses are the highest levels that the product labels suggest.

There is another clinic (The Multi-Center) that uses Biotics FC Cidal with Biotics Dysbiocide, or
Metagenics Candibactin-AR with Metagenics Candibactin-BR.

Each round of herbal antibiotics is four weeks. You can alternate rounds of herbal and prescription antibiotics.

Get at me below if you want to hear anymore about my own experience with this part of SIBO treatment.





  1. Nat April 11, 2017 at 6:08 am - Reply

    I have many questions. So you used Zaxine in Canada. My doctor has prescribed it based on 8 years of symptoms after an parasite infection. I am on day 4 but so worried about c. Diff as I am using a generic canadian form and also the fact I am killing everything. So what did you do during your treatment and after that helped as far as diet and supplements? Thanks so much for the article.

    • Jessica Mosiuk April 11, 2017 at 5:33 pm - Reply

      Hi Nat! I went through four rounds of antibiotics (ahh!) due to my high methane number. I was also using herbal antibiotics (berberine, oregano, neem and garlic) between each round. Now that I know SIBO through and through, four rounds of prescription antibiotics PLUS herbals was overkill but we were going by symptoms rather than retesting. I used a lot of supplements throughout my treatment: Amino NAC for liver support and inflammation (it is also used as a biofilm disruptor), the herbal antibiotics that I previously mentioned, HCL & digestive enzymes, zinc carnosine & glutamine to heal the small intestine lining, probiotics and lastly, Resotran to restore the Migrating Motor Complex. Because I like to use myself as a guinea pig, I tested out some other supplements that are commonly recommended: ginger, Motil-pro, Sacro B, other herbal antimicrobials but at the time I didn’t feel them necessary in my treatment. Not to say they aren’t helpful in certain scenarios…

      For diet I used the SIBO Specific diet by Dr. Siebecker which is a combination of the Low FODMAP diet and the SCD diet. I then progressed to a Low FODMAP diet. I avoided my food sensitivities as per my sensitivity test results. It is generally recommended to keep some fermentable foods in the diet while taking antibiotics. This made me bloated during the antibiotics so don’t feel frustrated if you don’t feel better right away. It took a couple weeks for my symptoms to go away even after the antibiotics- my gut just needed time to adjust. I had been bloated consistently for 7+ years so it wasn’t an overnight success story, hah!

      SIBO treatment has changed a bit since I was treated. Sometimes the diet is less strict to accommodate the needs of the patient. I need to get an update on this blog ASAP! Stay tuned…SIBO is on my mind a lot lately because I’m seeing so many cases in my practice.

      I’d love to hear what you’re currently doing along with the antibiotics. Feel free to shoot me an email at

      Thanks for reading!

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