The SIBO Saga: Part 1

Disclaimer:  As I have said in the past, I’m not a research blogger.  I’m here to mix “data with soul” and give you useful info, but only in the context of my real, human experience.  That is not to say that citation on my part and proper follow-up on your part are not important.  Everything I wrote about in this blog was presented by Dr. Mark Pimentel and Dr. Alison Siebecker at the SIBO Symposium during January 2014 and you can pay to have access to those presentations through the National College of Natural Medicine’s website.  

Friends . . . for real . . . the SIBO Symposium hosted through the National College of Natural Medicine in Portland, Oregan this past January was mind blowing.  I have been promising to write about it for almost two months.  Why so long, Angie?  Get on it already!

Honestly, there was so, so much information, most of which I had never learned before (and I have spent a ton of time learning about SIBO, so this is saying something), that I just simply could not distill it all and competently write about it.  I’ve decided the best way to handle that is to go back and slowly rewatch each video from the two days of presentations, reread all my notes (and take more) and re-review all the handouts and THEN write a series about each topic within the broader SIBO subject.  Today I’m going to write about Methane-Dominant SIBO.  (Also, weird topics I never expected to be interested in during my lifetime:  Methane-Dominant SIBO.  So just want to mention that!)

Okay, so I have posted on my Facebook page before about the two kinds of organisms that lead to SIBO (btw, if you are reading this & still don’t know, SIBO stands for Small Intestine Bacterial Overgrowth):  hydrogen producers and methane producers.  Hydrogen producers lead to SIBO with diarrhea and methane producers lead to SIBO with constipation.  The dominance of either gas is detected during a Lactulose Breath Test, where a patient drinks a sugary solution that the organisms ferment.  The patient then blows these gases out into a small baggy and that captured air is measured by a machine.  This is why it is so important for you to learn about the gas measurement results from your breath test, should you have one performed to detect SIBO.

Notice that in the past I have always referred to these organisms as bacteria & the name SIBO itself implies bacteria only, but according to one of the presenters at the symposium, Dr. Mark Pimentel, the pre-dominant methane producing organism in humans is NOT a bacteria.  It is called Methanobrevibacter smithii or M. smithii and is an archaea.  This organism, M. smithii, is responsible for the constipation associated with Methane-Dominant SIBO, because methane changes our intestinal muscle motor function.

As you might have guessed, treatment for SIBO changes depending on whether or not you have diarrhea or constipation.  Unfortunately, treatment for SIBO with constipation is tougher, this is because there are not specific drugs developed to deal with the methane producing M. smithii.  The absolute best, hands down most effective antibiotic for SIBO is called Rifaximin (also called Xifaxan).  It knocks out the overgrowth, but it is also mostly absorbed in the intestine so it is not as damaging system wide as other antibiotics.  However, Rifaximin alone will not work on the methane organisms.  It is best to combine Rifaximin with another antibiotic, called Metronidazole, when treating SIBO with constipation.

This was a very interesting piece of information for me, because my personal experience with SIBO with constipation definitely confirms this to be true.  The first time I was treated for SIBO, I was given Metronidazole.  It was very hard on me emotionally, with each dose reducing me to tears (gut-brain connection, people!), but it worked very well.  I had relief right away and despite not being on a low FODMAP diet, I didn’t have any trouble with SIBO again for nearly a year.  Then I had retesting and the lactulose solution sparked a resurgence in the SIBO (I am actually not a fan of retesting for this reason).  This time, my doctor only prescribed Rifaximin (after an herbal antibiotic attempt, more on that later) and it didn’t work as well.  I had symptoms again within a short period of ending the treatment.  Thankfully they were mild enough that I brought them under control with a low FODMAP approach.

Another good option, according to Dr. Pimentel, is an antibiotic called Neomycin combined with Rifaximin.  Occasionally, insurance providers will not cover Rifaximin for SIBO treatment.  This is because Rifaximin is normally used to treat people with Hepatic Encephalopathy, which is a liver disease that is effecting the brain.  In those cases, a combination of Metronidazole and Neomycin may be the best option for treating either kind of SIBO, diarrhea or constipation.

There is also another situation that can sometimes occur with SIBO.  A patient comes back with a breath test that does not show high levels of methane, but they are reporting constipation.  Remember, constipation goes with high methane.  Based on Dr. Pimentel’s presentation, this is because occasionally there is enough methane being produced by M. smithii to slow motor function, but not enough to be detected in the breath test.  The breath test is not sensitive enough to detect parts per billion, only parts per million.  If this is the case, the patient might be treated with Rifaximin, but it does not work since Rifaximin alone can’t deal with methane producing organisms.  Again, I think this means you need to be aware of your exact breath test results, but you should also be forward with your doctor about your symptoms.

Another reason that Methane-Dominant SIBO (SIBO with constipation) is so tough to treat, is that these organisms come back more quickly following a course of antibiotics.  This is where following a low FODMAP diet comes into play.  It is very important with this kind of SIBO to remain low FODMAP for a period of time following medication, in order to starve any of the remaining organisms that did not die off during antibiotic treatment.

Since we are talking about diet, I think it is also important to note here that according to one of the other presenters (and my SIBO heroine), Dr. Alison Siebecker, diet alone will NOT treat SIBO in adults.  In the Autoimmune Paleo community we tend to be very, very careful about antibiotic use and even approach it with alot of skepticism.  That is a good attitude, since for many of us, overuse of antibiotics may be in part to blame for our predicament, but there are appropriate times to use them.  I believe SIBO is one of those times.

That was the meat of the presentation relating to Methane-Dominant SIBO.  I will be writing about Hydrogen-Dominant SIBO, Herbal Antibiotics, Diet for SIBO, and also hopefully other health issues that are connected with SIBO in the coming weeks, so stay tuned.  There is alot to cover, but I think it is worth it, since SIBO & AI often seem to go hand-in-hand.  I’m going to do my best to provide great deets for you guys!

You can find Part 2 of the SIBO series here.

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.


  • […] SIBO Saga:  Part 1 can now be found HERE, at Autoimmune Paleo, where I and my blog partner, Mickey Trescott, now blog.  Thanks for […]

  • […] Linehan: I say guru because you have an excellent series called the “SIBO Saga” series and for those who haven’t checked it out, I highly encourage you to go to Angie’s blog. It has […]

  • Heather Burkhardt says

    Thank you for sharing your knowledge in a clear and concise way. Very helpful.

  • […] You can start at the beginning of the SIBO series here. […]

  • Robyn says

    Thank you for your series, Angie. I have been suffering for a very long time and am currently undergoing a 10-day treatment of Rifaximin and Neomycin for SIBO. According to my breath test I have hydrogen-dominant SIBO but my issue is with severe constipation, not diarrhea. Was there any mention of this case at the SIBO symposium? I am looking for any resources that can help as I don’t ever seem to be getting any better. Thank you.

    • Robyn says

      Also, my doctor said I should eat some carbs/sugar while undergoing treatment so that the antibiotics could kill the bacteria, but now I’m worried that I’ve over done it and the antibiotics won’t have enough time to eradicate the SIBO bacteria. (I’ve also been taking fiber-flow capsules I was prescribed and now realize are contributing to my constipation.) Do you know of the diet protocol recommended while using antibiotics?

      How long after completing a round of antibiotics should one re-take the SBIO breath test? My doc wants me to do the breath test when I complete my 10-day treatment (I just finished day 4), but I’ve heard of SIBO recurring as a result of drinking the testing solution too soon.

    • Angie Alt says

      Hi Robyn-
      Yes, I have heard of this situation w/ SIBO. If I understood all the materials at the Symposium, it occurs when the bacteria are converting methane to hydrogen. You have symptoms that appear like methane-dominant (constipation), but the breath test results show hydrogen. In this case you would treat it like a methane case, rather than a hydrogen case. I would not ever take fiber caps. I have heard of docs suggesting a moderate intake of high FODMAP foods during antibiotic treatment, for just what you mentioned, basically coax the bacteria out to “eat” & then kill it w/ the drugs. However, following treatment, I would eat strictly low FODMAP for about three months, per Dr. Siebecker’s advice. Retesting can be important, but if you find that the testing solution continually flares symptoms, I would ask your doctor to allow you time & only retest if symptoms appear on their own.

    • Michael says

      Robin, I was reading a study that said best results of Riflaximin are at least 4weeks -12 weeks. So what do most people recommend?

  • […] Health with Real Food, indicates that diet is a viable options for treatment of SIBO. Angie Alt of Autoimmune Paleo suggests that SIBO cannot be treated with diet alone. She references Dr. Alison Siebecker’s […]

  • […] And find Angie’s excellent ‘SIBO Saga’ series of posts here. […]

  • […] are suffering from Small Intestine Bacterial Overgrowth (more info on SIBO, testing, and treatment here!), fructose malabsorption, Candida, or another type of overgrowth. While not everyone with […]

  • […] parasite causing those symptoms. “Test, don’t guess” is the recommendation. Both Angie and Mickey had digestive symptoms that led to diagnosing and treating infections that boosted their […]

  • […] If you’d like to read my original SIBO series, starting with the 2014 Symposium, you can start here. […]

  • […] kept popping up.  At first it sounded a little far fetched, but eventually I came across a series of posts that broke down the topic in a way that made sense to me.  At last I had a plausible explanation […]

  • Elli says

    Hi Angie! I’m reaching out to you with a few questions I have about constipation dominant SIBO. Life has been a whirlwind of misdiagnoses and pain ever since I can remember and I might finally be heading in the right direction of treatment but I need some additional insight. I have a great doctor but being able to speak to someone that has directly dealt with and done specific research on this kind of SIBO would be very very helpful to me. My name is Elli and my e-mail is [email protected] if you would rather communicate that way. Thank you for this article! xo

    • Angie Alt says

      Hi Elli-
      I can’t work with you in a medical capacity, as I am not a doctor. I would suggest reaching out to Dr. Alison Siebecker if you’d like to work with a doctor and researcher in the SIBO arena. Her website is Thanks for reading here!

  • Gabriel says

    Hi Angie, My name is Gabriel im from Argentina and thank you for sharing all the good info you know. In my country, there is poor study about IBS and SIBO, because of that i’ve to investigate by my own and i absolutly agree with all that you explained above. I hope you can answer me this doubt: Low fodmaps + antibiotics (Rifaximin + Neomycin ) Should be do it at the same time or it’s recommended to eat anything during the antibiotic curse? Thanks again. Regards.

    • Angie Alt says

      Gabriel, there is some difference among the professionals in the SIBO field on that. Some say avoid FODMAPs during treatment & following. Others say eat FODMAPs during treatment to “trick the bacteria to come up & feed” making it easier to kill them w/ the antibiotics, then avoid FODMAPs following treatment to “starve” any remaining bacteria. I would take a look at Dr. Alison Siebecker’s site for additional guidance:

  • rob says

    Hi Angie,

    I have just diagnosed with Sibo and I will get flagyl for 10 days. My question would be the following. Do I need to be on diet during the treatment? Honestly, I tried several stuffs, but right now I want to “finish it” forever and I would do anything to support the antibiotics 🙂

    Any suggestion, what would help, diet, lots of water whatever would be very appreciated!

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