Small Intestinal Bacterial Overgrowth (SIBO)

Okay, I am about to get all science-y on you.   Are you ready?  Thinking cap on? I attended a great conference last weekend, a SIBO symposium sponsored by the National College of Natural Medicine in Portland, Oregon.  Top SIBO specialists that presented most of the information  at the symposium included: Mark Pimentel, MD, FRCPC, Allison Siebecker, ND, MSOM, LAc, Leonard Weinstock, MD, FACG and Steven Sandberg-Lewis, ND, DNANP Having had SIBO myself back in 2003 and again in 2013….and having close to 65 % of my client test positive for SIBO–I have a vested interest in this disorder! {In fact, I wrote an article for Today’s Dietitian back in 2011 that you can access if you choose to check it out.   Click here for the article. } What is SIBO? SIBO is an acronym that stands for small intestinal bacterial overgrowth. Normally, the small intestine provides a home for  few bacteria but in SIBO, bacteria that normally reside in the colon, sneak up into the small intestine and wreak havoc.  Symptoms of SIBO mimic those seen in IBS but bloating is typically the most troubling complaint. How do you get SIBO? The researchers at the conference reviewed several factors that may contribute to or predispose  someone to developing SIBO:

  • Infection (such as post-infectious IBS)
  • Decrease in pancreatic enzymes
  • Decrease in bile acids (bile acids normally emulsify in the intestine and don’t allow bacteria to grow).
  • Stress-decreases motility of the intestine so bacteria can build up in the intestine.
  • Low stomach acid

Some diseases and syndromes are associated with SIBO include some well accepted in the medical community and some ‘new kids on the block’ disorders that are linked with SIBO but more research is necessary to provide a definite link. Disorders that are well accepted as associated with developing SIBO include:

  • Scleroderma
  • Small intestinal pseudo-obstruction
  • Adhesions (scar tissue) that may cause the intestine to kink like a garden house
  • Pancreatic insufficiency
  • Small intestinal diverticulosis (small pouches that develop in the small intestinal wall)
  • Low stomach acid (achlorhydria)
  • Diabetes
  • Radiation enteritis  (inflammation of the small intestine following radiation therapy)
  • Immunodeficiency (Ig A def, T-cell deficiency)
  • J-pouch, ileo-cecal valve resection

Dr. Weinstock mentioned several other disorders that may increase risk of SIBO but more research is needed, these include:

  • Crohn’s disease
  • Celiac disease
  • IBS
  • Liver disease
  • Restless leg syndrome
  • Rosacea
  • Parkinson’s disease
  • Chronic renal failure
  • Hypothyroidism
  • Post-chemotherapy
  • Fibromyalgia
  • Rheumatoid arthritis
  • Interstitial cystitis

Wow…right!? Testing:  The consensus at this conference was to undergo a lactulose breath test to evaluate for SIBO. The test should measure BOTH  hydrogen and methane gas.  Some GI doctors are not fully on board with this the breath test for diagnosing SIBO as it is not a validated test… but for now…it is the least invasive and most likely test to be used in clinical practice. Dr. Pimentel provided info on what he deems a positive test: A positive methane test is anything >3 PPM during the testing w/ in 90 minutes. A positive hydrogen test is >20 PPM (not necessarily 20 PPM rise above baseline but rather any reading 20 PPM would be a + test) w/in 90 minutes. Interesting to note:  hydrogen sulfide producing bacteria use up 5  hydrogens to produce this gas and methane gas uses up 4  hydrogens–so it is possible to have a flat line hydrogen gas reading during the breath testing but still have SIBO.  New testing is being explored to test for hydrogen sulfide gas but is not fully developed yet. Treatment: The consensus at this conference was first line treatment was antibiotics, followed by a prokinetic (a drug that enhances your intestinal tract’s motility) for 3 months and a repeat breath test and a diet low in fermentable carbohydrates. For a + hydrogen test the recommended antibiotic therapy included:  550 mg Rifaximin three times a day for 14 days.  Caution was made to ensure to stick with this course and do not miss a pill to keep therapy as effective as possible.  Dr. Pimentel did note that higher doses would not warrant better results. For a + methane test the recommended antibiotic therapy included:  550 mg Rifaximin three times per day in combination with neomycin 500 mg twice a day for 14 days OR Rifaximin 550 milligrams three times per day with Metronidazole 250 milligrams three times per day for 14 days. Prokinetic: Dr. Pimentel mentioned erythromycin 1/4 tablet or 50 mg at night.  He reiterated the importance of taking erythromycin on an EMPTY stomach.  Probiotics: There was a difference in opinion regarding the use of probiotics for this condition.  Dr. Pimentel does not recommend them at this time but some of the other physicians do.  Probiotics mentioned included Align and Culturelle (Nature Health and Wellness w/o inulin). Probiotic studies have revealed that they enhance motility–but more research in this area is needed to provide individual recommendations. Diet:  There is no evidenced based diet to use with SIBO.  There needs to be research in this area!!  Diets that were discussed and utilized by these practitioners includes: low FODMAP, specific carbohydrate diet (SDC), a combo SDC and low FODMAP and Cedar Sinai’s Dr. Pimentel’s protocol.  Again a difference in opinion from the speakers. Dr. Siebecker likes to use a combo of the SCD and low FODMAPs diet while an individual has SIBO with a transition to low FODMAP for prevention. For those interested in learning more about this, check out Dr. Siebecker’s site here.  She mentioned that in individuals that seem to tolerate sucrose (table sugar) and grains/starch/fiber or in the underweight client low FODMAPs may be a good starting point.  Dr. Pimentel feels sucrose (table sugar) is well absorbed and is okay on the diet for those with SIBO (of course, within reason!). And lastly some key take-aways for me from this symposium:

  • SIBO is not a diagnostic term–it is a condition that arises due to something else.  Work with your doctor to determine WHY you developed SIBO.  If you don’t determine the cause, it will likely just come back.  Dr. Pimentel feels the decrease in MMC (migrating motor complex or ‘cleansing waves’) is the primary cause of SIBO in seen in IBS.  Remember in order for the MMC to initiate a cleansing wave you must be in the FASTING state–so avoid grazing and try to space/snacks meals 3-4 hours apart. You can include water or coffee in between meals.
  • Methane + constipation is harder to treat and should be treated with rifaximin and neomycin together.  This combo drug therapy may be better than neomycin on its own in terms of minimizing risk of neomycin drug resistance.
  • Methane bugs tend to come back sooner.
  • Methane gas appears to come primarily from Methonobrevibacter smithii which is actually not a bacteria but rather a microorganism from the Archaea kingdom. These microorganisms do not have a cell nucleus. Methane bacteria are linked with higher body weight (>BMI)
  • Dr. Pimentel said he would like to frame IBS patients as non-methane IBS or methane + IBS vs. IBS-C and IBS-D: treatments differ for the two based on gases.
  • Use a prokinetic drug and diet to help minimize risk of re-occurance.
  • If you have a SIBO  relapse within 1 month, it is likely in 50% of individuals that another disease is causing it.  If no relapse, pull back on erythromycin or prokinetic after 3 months.
  • Diet for SIBO should be customized–work with a dietitian or health care practitioner with SIBO knowledge!
  • Dr. Pimentel’s theory in regard to diet during antibiotic treatment is to NOT be on a low fermentable carb diet while using antibiotics as the microbes go in a hibernation phase and are less likely to be eradicated….I  tell my clients that fermentable carbs are somewhat like cheese to a mouse–let those microbes come out to eat so you can get ’em with the antibiotic!!

Why rifaximin might not work for some?

  1. SIBO too severe for symptom relief in one course
  2. Methane bacteria benefit from dual treatment: rifaximin + neomycin
  3. Bacteria may not be sensitive to rifaximin
  •  NOTE: Rifaximin has two forms: the alpha form has the anti-microbial while the beta form is not anti-microbial  (some forms found outside US such as India may have a combo of beta and alpha which would be LESS effective).

Herbal therapies such as herbal antibiotics that may be helpful: berberine herbs, allicin for methane producers, oregano & neem were all mentioned.  Of course, if you choose to try herbal therapies do so with a knowledgable practitioner.  Just because a product is an herb doesn’t mean that it will not have side effects! Personally, I find a low FODMAP diet keeps my SIBO at bay with meal spacing a key component! I have worked with some clients that have needed a bit more of a strict diet including removal of some grains and leanings toward the SCD diet but I have found that has been more of an exception than a rule.  Prokinetic drugs to add a longer duration of therapeutic benefit for many but not all of my clients have tolerated them.  Trying alternatives to erythromycin might offer benefit such as trying prucalopride or cisapride. Congratulations if you made it this far with my ramblings! Is your brain full from this post? Ha! More to come in this exciting area of digestive health! Stay tuned!

147 replies on “Small Intestinal Bacterial Overgrowth (SIBO)

  • Alorie Parkhill

    I haven’t been tested yet, BUT I am concerned about taking too many antibiotics and developing resistance to them. What do we know about that?

    • Well Balanced - Food - Life - Travel

      Alorie, I completely understand where you are coming from…in fact, when I had SIBO back in 2003 I tried alternative treatments before deciding to finally give antibiotics a try. The message at this workshop was that rifaximin does not contribute to plasmid resistance. I am not an expert in pharmaceuticals but can only tell you that per Dr. Pimentel this would mean that it is less likely to lead to full resistance to the drug in contrary to drugs that do lead to plasmid resistance such as Ciprofloxacin and Doxycycline. And there was mention that rifaximin may actually lower incidence of resistance to neomycin when used as a combo treatment.

  • Lauren

    I have severe bloating every day which progresses as the day goes on. I’ve been tested for a few things but have yet to find an answer. My doctor put me on a 10 day course of Xifaxin- if I had SIBO would this have been enough to get rid of it? If you have any other ideas of what could be causing the bloating please let me know!!

    • Well Balanced - Food - Life - Travel

      Hi Lauren,
      I don’t think a 10 day course would be enough. I would recommend a breath test to rule out methane producing gases which would provide a combo drug approach likely –rifaximin 550 mg three times a day with neomycin 500 mg twice a day for 14 days. There are many causes of bloating–dumping syndrome would be another potential cause. Fat malabsorption–maybe even yeast overgrowth. Have you checked stool for fat, stool elastase, yeast culture.

      • Lauren

        Thank you for your reply! I haven’t been checked for any of those, but have an EGD scheduled so I think that will check for malabsorption (?) I will ask about the other causes you suggested. I appreciate any help/suggestions I can get!!

  • dkaj

    Hi Kate,
    First of all, thanks for the notes and keeping everyone informed on your blog! Also, big applauds for being instrumental in getting FODMAPs some screen time on the Dr. OZ show. And, of course, I do have a question for you. I have the SIBO breath test sitting here for my 8 y/o dd just waiting to take the test. I was reading over your SIBO notes, and I have a concern. This has been my concern even before seeing the conference notes. One of the things mentioned for contributing to SIBO is stress. Thus, I need some advise on timing for taking this test. My dd is not having a good year stress wise at school that’s related to her teacher. I’ve requested a room change and it’s been denied. And, I don’t see this changing b/c a couple kids have already moved out, and it’s a number situation now. I know this stress is not helping her IBS at all, as she tells me her stomach is in knots every day until she gets in the car to come home. And her constipation has gotten worse since school year started. Thus, I’m wondering if I should just wait on doing this test more until later spring and if she comes back positive, treat over the summer. I just don’t know how the antibiotics will affect her stomach either while she’s in school and this makes me nervous. Her teacher has strict bathroom rules as to how often one can use their bathroom passes without loosing behavior points. Teacher is tenured and and I’m fighting an uphill battle in this area. Plus, I don’t want to treat, just to have it come back, because of this particular teacher and the “stress” issues. Just hoping for a better year next year and will make sure we don’t run into this situation again teacher wise. Any advise you might be able to give would be greatly appreciated. PS. Do you have any planned FODMAP educational seminars for the midwest coming soon?? No “formally” trained dieticians in our area either. Thanks for all you do Kate!!! Wish you lived in our area!

    • Well Balanced - Food - Life - Travel

      Personally I would go ahead and get the test. If treatment makes her better she’ll have less stress for the rest of the year. Most people do okay with rifaximin–and from my experience–if the person has been on low FODMAP first-there is a better tolerance to the antibiotic. But remember during treatment (antibiotics) you need to liberalize the diet a bit to make it most effective. Patsy and I did a training session last fall near Chicago for RD–so there are many RDs trained there! I am speaking at the Nebraska dietetic association in April so hope to teach a few RDs there….and will be speaking at U Michigan to even more RDs in May! All while trying to enjoy a well-balanced life of my own! Ha!

    • dkaj

      Thanks Kate for the advice. That helps a ton! We will go ahead and do the test then sooner than later. Will let you know how things turn out. And thanks for the info on the conferences! Yeah, you are coming to our state!!!

  • Erika

    I really wish that pelvic floor would have been brought up as a possible cause of the SIBO!! I received my diagnosis from Mayo Clinic and since starting treatment for the pelvic floor dysfunction my sibo has not been present! Mayo Clinic is one of the only facilities that seems to have this diagnosis and the treatment that is really needed to help fix the issue!! This needs to be a more discussed topic and doctors need to stress finding the underlying condition causing the sibo, because the antibiotics can only help for so long and so much!!

    • sally

      Erika, I am excited to see your post! I have SIBO and went to Mayo in Jacksonville in 2010. They only gave me antibiotics. I am a physical therapist and know about pelvic floor dysfunction and have treated it. Having the worst flare of SIBO ever and have been so ill since December that I have totally neglected my pelvic floor. Which Mayo and which MD did you see? I would really appreciate hearing from you! Is there any way that you can contact me?
      Thanks, Sally

  • Marcy

    Thanks for the update! Does Dr. Pimentel still suggest staying under 40 grams of sugar/day? I count my 2 fruit servings towards this amount. What recipes would be ok to add table sugar to my diet. I sometimes have 1 bar (instead of both) of the NatureValley Peanut butter Granola(bars) – so that is 6 grams. Otherwise that is my only sugar. I’m looking for other foods since dropping too much weight. I have started eating Smuckers Natural Peanut Butter for some added fat/calories. Also, what grains/starches do you feel are ok for post SIBO treated clients? I have tried 1/2 cup oatmeal, white potatoes with skin, Jasmine Rice, some frozen potatoes (steak fries – Alexa brand). Think ok to start adding starchy veggies (corn,peas, etc) or not wise for SIBO. Continuing to trying to figure it all out… Thanks for all of your previous advice and posts!

  • casey

    Hi Kate, thanks for this update on your conference! Hope you had a chance to check out Portland, its great here. I was wondering if you have ever heard that a history of bulimia can be a cause of IBS or SIBO? You mentioned the bile aspect and it made me think of that. Eating disorders are never listed as a cause to digestive orders but it seems like bulimia or binge eating really can cause lasting damage to the GI tract. Your thoughts?

    • Well Balanced - Food - Life - Travel

      Yes Casey…I do think eating disorders have a big impact on GI issues –and many IBS symptoms–and there is research that supports this link. Not sure specifically in regard to SIBO but time and research will tell.

  • David Knight

    Great Information! Having read Dr. Pimentel’s book, “A New IBS Solution” it’s clear he’s definitely an expert on SIBO– I also feel strongly that Probiotics play a major roll. Several studies have shown that certain strains of Probiotics have helped with Motility. This appears to be a key part–
    factor in the mix.

  • Joanna

    Hi Kate. This is very helpful – thank you! Two questions:
    1. Is it important to get re-tested to see if the SIBO is resolved? My GI said they don’t re-test, they just keep treating if symptoms don’t resolve (!). I think it’s resolved, but don’t know for sure. I have not taken a prokinetic.
    2. On meal spacing… I am petite and have fast metabolism and tend to get hungry 2-3 hours after eating. Do you recommend larger meals to try to avoid snacking when hungry?
    3. On antibiotics… Neither Rifaximin nor Flagyl (my GI’s second-round choice) seemed to work for me. Cipro seemed to work. What does this mean if I need another course at some point? Try Rifaximin again, or not? I don’t know if I had high methane or hydrogen (or both).

    • Well Balanced - Food - Life - Travel

      Well….I can only speak from my experience –as I am not a GI doctor–I am not really sure about the antibiotic choice-but Cipro use is linked with C. Diff infection so you need to know that risk. I would try to add a bit of fat and fiber to your meals which may help with satiety if you tolerate that–for instance adding some chia seeds or handful of walnuts to your morning cereal or adding a bit of olive oil and nuts to a salad to maybe provide a bit more staying power. If there is not fat or fiber or minimal at the meal–it tends to lead to quicker digestion and hunger. Do your best spacing your meals–but sometimes you just have to eat when you are hungry, right? There are varying opinions on whether to do a repeat breath test-the consensus at the symposium was to do a repeat but most practitioners I have worked with do not do this.

      • Joanna

        Thank you! I almost always have protein with my meals and snacks, and I still usually get hungry 2-3 hours later – perhaps I just need to eat bigger meals. I would love to know who Dr. Pimentel would recommend for a GI in Denver…

  • andy

    Fantastic info, thanks for reporting back from the symposium.

    I have been tested twice for SIBO, both positive. Rifaxamin didn’t work for me but I have constipation predominant SIBO. I was a little worried about the side effects of Neomycin (hearing loss specifically).

    Instead I have decided to follow the Vivonex Plus elemental diet. Do you know anything about this approach? Or was it discussed at all? It seems like it offers a good rate of success according to the literature.

    Again thanks so much for this blog post. I’d have loved to have been there!


    • Well Balanced - Food - Life - Travel

      Andy they did bring up the Vivonex approach but briefly. Dr. Pimentel said he doesn’t use it as much. Pricing has increased. Dr. Siebecker has created a homemade formula that she uses but I have not checked it out. The elemental diet approach can be effective but it is important to have a good support team while you undergo this restrictive plan as it can be very difficult. The formula doesn’t taste good. There was some discussion about neomycin’s side effects–and certainly I can appreciate your concern.

      • andy

        That’s interesting as to why Dr Pimentel doesn’t use it as much. The price is restrictive to a lot of people. I paid a fortune for the packs. The studies do show a very high rate of success however. My biggest fear with the anti-biotics is getting something like c.diff, which can be a lot worse than SIBO. Not that I’m averse to taking them. It’s just Rifaxamin didn’t work for me. I think because I have constipation type SIBO.

        I agree you need good support. It is revolting but hopefully it works! It does provide all the nutrition your body needs, provided you take enough packs.

        Thanks again Kate, It’s great you’re sharing such important information.


    • Steve


      I’m in the same boat-SIBO + constipation and no luck with rifaxamin. Did you have any success with the Vivonex Plus elemental diet?

  • Timothy

    Hi Kate,

    Thanks for your info on SIBO. I have Dr. Pimentel’s book and had a positive breath test for it.

    1. I was also wondering about spacing meals apart, I’m also underweight and can get hypoglycemic if I don’t keep my blood sugar up. If I tried spacing my meals apart, should it be something like 600-700 calories, 3x a day? I don’t have a dietitian to help me.

    2. Would having glucose tablets or pure glucose in my tea/coffee be a good option to keep blood sugar up in-between meals?

    Thanks for any suggestions!

    • Well Balanced - Food - Life - Travel

      Timothy…From what was provided at the recent SIBO symposium via Dr. Pimentel: You need to have nothing with caloric value between meals to allow the cleansing waves to occur–so based on this, glucose (although well absorbed) would be caloric and interfere with this process. I find my patients do best when they eat a balanced meal with: carbs (rice/potato) plus protein (chicken, fish, lactose free yogurt) plus low FODMAP produce AND lastly a little healthy fat (olive oil, acceptable nuts, seeds) to help keep them satisfied and also to maintain a stable blood sugar. Calorie range needs are individual based on height, weight, gender, age and exercise-most men would need close to 2100-2500 per day. A snack can be incorporated as long as you space the timing with other meals in the 3-4 hour window.

  • Steve

    Hi Kate. This is VERY helpful as always.
    I just got done with a treatment of Xifaximin 1200mg per 8 days. I feel like my symptoms have improved but have not been completely dismissed. How long should I wait to get tested again and to start a new treatment following Dr. Pimentel’s directions?

    • Well Balanced - Food - Life - Travel

      HI Steve-not sure the dosing you received was optimal so you likely will need to be re-treated. I would discuss with your gastroenterologist or primary care doctor since I really can’t give out specific medical treatment guidelines in a blog format.

  • Stefanie

    Hi kate,
    I have been struggling with GI issues for over a year now and have tried every diet known to man including Low FODMAP, clean guy, low histamine, etc… Over the past month my stomach has gotten progressively worse with bouts of constipation, diarrhea, severe bloating and shooting pain. About 2 1/2 weeks ago I came down with the flu and was prescribe amoxicillin for 10 days. Since then my stomach has been 300 times better when normally antibiotics destroy my stomach and cause diarrhea. My first response was SIBO but I am unsure. I am supposed to go see a GI next week and want to be sure to cover everything. Any recommendations/thoughts would be greatly appreciated!
    Thank you,

    • Well Balanced - Food - Life - Travel

      Hi Stefanie–Certainly it might be that you had or have SIBO and the antibiotics improved your symptoms. I would discuss your response to the antibiotics with your GI doc and perhaps consider getting breath tested for SIBO in 8 weeks if your symptoms return or if you don’t have full resolution of your symptoms. Did you notice any symptom improvement on the low FODMAP diet–I find some of my clients with SIBO do get symptom improvement on the low FODMAP diet but only partial response. Just curious.

      • Stefanie

        Hi Kate,
        Thank you for getting back to me. Most restrictions I tried gave me no relief, or gave me relief only for 1 day, including the FODMAP (though I did only do it for 2 weeks with no relief and because I am vegan for the most part and 5’6″ and 115 lb I was losing weight so I got off it) Some diets gave me very negative effects, for example the Clean Gut which made me very ill to my stomach (though I partially attribute that to all the supplements you have to take). So all that being said I was completely lost and thus planned to go the GI doctor. It was a complete coincidence that I started the antibiotics. On a side note 3 days off the medications and the dull pain has started back up. best way to describe it is similar to period cramps.
        Thank you for all your help!

      • Dr Judy Warrington

        I have had SIBO for several years. Each time, my GI Doctor treated me with a course of Neomycin.Finally I switched Doctors and also went to see who I thought was a SIBO nutritionist at Beth Israel She put me on a FODMAP diet.Just prior to that I had purchased a book, titled Fast Tract Digestion, written by Norman Robillard, founder of The Digestive Health Institute, The two diets have similarities but also have some opposite recommendations . I am currently working on the Fodmap diet. However, I just read your comment to Stephanie where you say, ” I find some of my clients do get symptom improvement on the low Fodmap diet, but only partial response” I feel confused now as to which diet will be most suitable for my particular case.

      • katescarlata

        I think one of the most important points about SIBO is that it is not an end of the line diagnosis. It is a symptom of something else going on. Has your GI doctor determined the cause? Motility problem? Inflammation? Maldigestion? The low FODMAP diet does work for many with SIBO from my perspective but I do believe some patients also have colonic dysbiosis as well–which in this case may benefit from modifying the diet in a way the Norm Robillard outlines—BUT there is NO research on this to my knowledge. We do need more research to look at how diet impacts this condition (SIBO) so that we have evidenced based research to guide us in treating it more effectively. I find that meal spacing –eating every 3-4 hours rather than grazing, modifying FODMAPs and using a prokinetic such as iberogast –can be quite helpful in keeping SIBO at bay for most people.

  • Timothy


    Thanks for the reply earlier. By any chance, at the symposium, did Dr. Pimentel give any alternatives for prokenetic drugs like Domperidone? I took it in the past. It is prescribed a lot for gastroparesis. It can be better tolerated because it doesn’t cross the blood-brain barrier. Just curious. Thanks! I wish I could have attended that convention.

  • Snenny

    Hi Kate,

    Thanks so much for a clearly written and informative post!

    My doctor had told me that the severe stomach distension and pain I get is from IBS, and although it’s certainly possible that this is the case, I haven’t been checked for anything alternative such as SIBO or candida overgrowth.

    I’ve been trying the low fodmaps diet but am really struggling – not only am I not finding relief from it, it is triggering negative thoughts and patterns from a previous eating disorder. I’m starting to panic at the thought of eating, and haven’t been able to go out to eat or to a friend’s house because there’s so little I feel i can eat (I also have coeliac disease and am vegetarian – when I eat out on low fodmaps, it feels like I can only really eat boiled rice or a baked potato with no toppings… ).

    I was wondering whether you would recommend getting lactose and fructose intolerence tests, because if I test negatively for one of those, I might be able to have a slightly less restricted diet, and even if I test positively, I would then at least know that I’m doing the right thing in avoiding these foods rather than forging on but not knowing if it’s going to make a difference. I was also thinking of getting SIBO and candida overgrowth tests to make sure it’s really IBS I suffering from, as I haven’t had anything ruled out – I’ve just been told that if it’s stomach pains, it’s IBS. Reading this post has made me think that perhaps it is SIBO as my main symptom is severe bloating, and none of the constipation or diarrhea often associated with IBS.

    Sorry for such a long comment – I wouldn’t usually post something like this, but stomach issues are really getting me down and I’m terrified that I’m going to go back to having an eating disorder, which, especially if the fodmap diet is not actually the answer for me, would be just awful.

    • katescarlata

      I recommend you work with a dietitian and health professional that specializes in eating disorders. There is an overlap of GI issues and ED and I believe the ED needs to be addressed – as a relapse is obviously not the direction you want to go in. You may have SIBO so I certainly would start with that testing. I would not encourage a strict low FODMAP diet given your ED history…at this time. Especially since it doesn’t appear to be offering you much relief.

      • snenny

        Hi Kate,

        Thank you so much for your quick reply!

        I really appreciate your advice, and will book an appointment with my doctor to raise not only the SIBO but ED concerns. As you say, it may be that the GI pain is ED related, even though I have been in recovery for a few years now.

        Thank you for giving me hope that something can be done which might address both the GI pain and the ED anxiety.


  • Melissa

    Hi Kate,
    First, thank you so much for your blog, it is so informative and helpful! I had started FODMAP elimination when I tested positive for methane + SIBO. My GI had me stop the elimination phase while on antibiotics. I just finished 2 weeks of Rifaximin and already within 2 weeks I’m back to having symptoms. I unfortunately do not meet with my GI for another month, so I’m doing a lot of my own research to try to determine the next step for me. Do you think that your 21 day Tummy book would be helpful to read and follow or can you recommend another book that might be better? Thanks in advance!

  • Sky


    Is there anyone you can recommend on the east coast that treats SIBO effectively? Seems like who your provider is strongly correlates to a positive outcome. Would be nice not to have to fly to LA. I’m DC based so heading up to Bonston to see whoever helped you wouldn’t be an issue.

    • Well Balanced - Food - Life - Travel

      I am very happy with Susan Kelly at BIDMC. She is well versed in treating SIBO.

  • Christine

    Thank you so much for all of your information. I finished a round of antibiotics and retested with overgrowth still present. My naturopath recommended another round of antibiotics. We got to this diagnosis after about a year and a half of infertility. Have you seen any link in successful pregnancy after SIBO treatment?

    Thanks, Christine

    • Well Balanced - Food - Life - Travel

      Christine–this is a very interesting question and I am not sure I have the answer. I can say that I have had a few patients get pregnant after feeling better on the low FODMAP diet–not sure there is a cause and effect though. We do know that hormones can impact GI function/motility. Some people experience worsening of symptoms during menstruation for instance. I think I need to do a little research on this–but my guess is–there won’t be much.

  • Megan

    Hi Kate,

    This is my first comment in a blog. Here we go.

    I have been struggling with digestive problems (mostly constipation and bloating) for over a year now. I’ve never had any sort of health problem in my life, and the constant bloating makes me miserable. I am a college senior, 21 years old, 130lbs, overall healthy eater, and LOVE running, especially long distances. I started working with a GI doctor last March, but tested positive for SIBO just about a month ago. (before that I had tried the low-fodmap diet and others multiple times) I went on the Rifaximin/Neomycin plan for 10 days (Rifaximin 3x/day, neomycin 2x/day). The first couple days my symptoms improved, but not much. After the 10 days there wasn’t much of a change. It’s been almost 2 weeks since I finished the treatment, and I’m currently waiting to hear back from my doctor about the next step. My symptoms have completely returned.

    2 factors I figure I should mention:

    1. It is a huge battle for me to balance a low-carb/fodmap diet with my physical activity. I am currently training for a marathon and must eat a lot of carbs to maintain my energy. Could this be a huge factor holding me back in eradicating my sibo? I absolutely hate the idea of decreasing my physical activity so that I can eat less, but if you (and my doctor) strongly recommend it, I would highly consider it. Along those lines, I absolutely hate dieting and restricting my diet. It is so hard for me to come home from a 10-mile run and know that I can’t go have a big pancake breakfast with my friends. It affects my mood and overall well-being. But, I know this is just a part of SIBO, it’s no one’s fault, but I just wanted to mention that it is SO hard for me to do this. Sorry if this is too much whining, I know many people have it worse than me, I just want to be honest.

    2. When I was in middle school and high school, I had acne problems and worked a lot with my dermatologist to get rid of my acne. I went on MANY different antibiotics for fairly long periods of time (I don’t know them all, but I’m certain I have been on tetracycline, monocyclin, Doxycycline, etc.). During these times, could I have seriously disrupted my normal microbiota, and now am left with nothing but “super-resistant to antibiotics” bacteria? I am currently taking a microbiology course so that is just something I thought about while learning about our normal microbiota. 🙂 The main reason this thought doesn’t seem as relavant is because I haven’t been on an antibiotic for my acne in at least 5 years. I went on Accutane 2 years ago, and that cured my acne (yay), but again, I’ve been off that for years now.

    Do you have any thoughts for me? Especially regarding the last 2 points?


    • Well Balanced - Food - Life - Travel

      Hi Megan,
      I hear and feel your frustration. It’s not easy feeling lousy.
      You pose lots of great questions and I hope you have a good dietitian and gastro to guide you. I can’t provide individual health recommendations in a blog setting but I can provide a few thoughts for you.
      As a runner, I know exactly what you are saying about needing to keep up with your calories and carbs with the tremendous energy burning that occurs training for a marathon. Although I have run a marathon and a couple 1/2 marathons–I do worry about the effects of distance running on your gut and overall health…especially if SIBO is still present. There is some research that shows the gut has greater permeability when we engage in intense exercise. I would encourage you to pull back on the running and work on less intense workouts–walking, yoga and work with a dietitian to help provide a balanced low FODMAP diet to help potentially manage symptoms while working on healing your intestine. Adequate nutrients, perhaps even supplements such as L-glutamine as needed–but of course, discuss appropriateness of supplements with your doctor as well. It’s hard to say exactly what impact your past history of antibiotic use and accutane has had on your gut flora–

    • Lori

      Megan, you sound EXACTLY like me, been the route of all those antibiotics and accutane. I have exactly the same problems as you. If you find something that works, please post!

  • Shannon

    Hi Kate,

    I had a couple questions.

    I was diagnosed with SIBO (Methane +) back in August. I took the prescribed antibiotics in September and felt more or less symptom free for about three months. Prior to taking the antibiotics and during the 2 week course of treatment, I was gluten-free (mainly to help symptoms and due to Hashimoto’s Hypothyroidism). In December, I enjoyed the holidays without dietary restrictions. I didn’t notice many repercussions until January when I went back to my prior g-free/healthy diet. My stomach was back to where it had been prior to antibiotics. Based on my docs recommendations, I just started round two of the same antibiotics. This doc (different than the first to prescribe but within the same facility and both NDs) said I needed to adhere to a low carb, low sugar, no alcohol diet for the 2 weeks during antibiotic treatment and the month following. I know you mentioned doctors differed with their opinions on this. Do you have any recommendations based on what you have seen in your own treatment or with clients? Do you feel that by cheating I will set myself back or that I should have some of these foods so that my body can rid them from my system?

    Lastly, my doctor had indicated that by me eating “whatever I wanted” for the month of December I may have allowed the SIBO to come back. Does that mean that I should be regimented about this diet forever, or again, if the meds work, I should be able to eat things within reason?

    Any insight would be greatly appreciated. I understand everyone is different but I would love to know other thoughts/opinions.


    • Well Balanced - Food - Life - Travel

      Shannon-great questions. Let me speak from personal experience. I find that if I veer off the diet for TOO long, say on vacation,–I will develop symptoms but it is possible for me to pull out FODMAPs for a few days and calm things down. I think in some cases when individuals veer off for the diet for longer–perhaps the FODMAPs over feed the bacteria and the bacteria flourish too successfully. At this point, it becomes a bit impossible to get back in bacterial balance without antibiotics. Research has shown that the low FODMAP diet alters (decreases) healthy gut bacteria populations in the intestine–and so, is not designed as a long term diet. So perhaps you will tolerate some dietary alterations –but not for days on end. Additionally, you want to work with your doctor to determine what caused the SIBO. In other words, do you have a treatable cause such as a motility disorder that could benefit from meal spacing, an evening pro kinetic or other gut motility medications. During antibiotic treatment, Mark Pimentel recommends that the diet is not restricted as bacteria ‘hibernate’ and will not be eradicated as well. I tend to recommend to my clients–to eat some FODMAPs but not so much they are miserable during treatment.

      • Evelyn

        Hi – after years of going from doctor to doctor I’ve finally tested positive for SIBO, just yesterday.

        Don’t mean to prod- but since you keep mentioning that SIBO has underlying causes such as motility issues, MMC, etc; have you yourself worked through those causes? You mentioned many times that you seem to relapse after a vacation or such. It seems that addressing these underlying causes are just as important, if not more than, taking an antibiotic.

        Thank you!

      • katescarlata

        Hi Evelyn, When I say I have a little flare–I am not talking about SIBO returning–but rather my belly feeling a little off–and going low FODMAP for a day a two settles me back to my usual self. AND you are correct, SIBO is a symptom of something else–so determining the cause is key!

      • Evelyn

        Thanks! Would you mind sharing a bit about what your specific causes were? Maybe they are similar for others, or there is a process of elimination/ specific testing that can be done to look at those underlying issues.

      • katescarlata

        Evelyn–my SIBO is likely due to surgery –I don’t have an ileo-cecal valve the ‘door’ btw the small intestine and large intestine. There are many reasons individuals can be predisposed to SIBO–motility disorders such as IBS -with a decline in small intestinal cleansing waves, a bout of food poisoning, small intestinal diverticula, autoimmune disease such as scleroderma that alters motility, diabetes, to name a few.

      • Bill K

        Hi – this comment is for Evelyn. Evelyn – you mentioned going from one doctor to the next and finally getting a diagnosis of SIBO. Would you be willing to share your symptoms? The reason I ask is that I have a mystery disease (LPR) that I’m wondering if SIBO is playing a part in that…and I’m trying to network to see if anyone else with SIBO had/has throat symptoms (hoarseness, sore throat, excess mucous in throat)?

        Best Regards,
        Bill (Minnesota)

  • Vero

    Thank you so much for this detailed symposium report (and all the wonderful FODMAPs resources provided on the site).

    I was diagnosed with SIBO (methane+). Like Andy, I am reluctant to take neomycin due to side-effects, but am taking rifaximin (rolling the dice as *some* methane-producers have had relief with rifaximin – none for me so far though). I will do neomycin if push comes to shove, but want to try herbal antibiotics and FODMAPs first. I realize the symposium was several months ago, but hope maybe you can remember whether the following questions were answered there.
    Did the GI docs say anything about liberalizing FODMAPS with herbal antibiotics as they recommended with conventional antibiotics? In your own experience or your patients’, have you used herbal abx and FODMAPs concurrently or consecutively, and, if both, have you observed any differences in outcomes?

    Second, you mentioned that the naturopaths have used allicin for methane-producers. Are the fructans in garlic eliminated in the process of producing allicin? Also, did the docs at the symposium say whether there is a difference between the liquid and pill forms of allicin or any other herbals?

    Thank you again.

  • Marianne

    Hi Kate, I have not been tested for SIBO, but suspect I have it. I don’t have pain or cramping, but do have 3 bms every morning #6 on stool chart. I also getting bloating after meals and it is difficult to pass gas. Sometimes can’t pass gas until later in the day or evening. I get a discomfort below my left rib cage while eating sometimes and have some issues with burping as well. I don’t sleep well due to hot flashes and night sweats even though I am post menopause. I have lost 30 lbs and am underweight, with lose of muscle tone as well. Tests have ruled out c-diff, Candida and parasites but show I have an overgrowth or imbalance in my bacteria and low in some of my good ones. Also, had colonoscopy and the top down showing I had a little diverticulitis and gerd. This condition I am in now was brought on with antibiotics over a year ago. My life has been hell since then. With my symptoms do you think this is SIBO? I am currently on Rifaximin 550mg 3x a day. This is day two. Also I read I can eat pretty much anything while on the Rifaximin, and want to make sure that is true. Bring the bugs out as you say. Thank you, Marianne

  • Margaret

    This is my third go-around with SIBO. First was 2 years ago, 2nd this January. Rifaximin helped the first two times along with the SCD diet. The doctor does not want to prescribe antibiotics again. He wants to do more testing, beginning with a gastro-emptying test to see what may be causing the SIBO. In the meantime, I am miserable. Weight loss of a pound per day, all the standard symptoms associated with SIBO, plus no appetite and no energy. I have restricted my diet to a gut healing diet and it’s helping a little. It is hard for me to have patience in waiting for testing and answers, especially since I have a husband who need surgery and my help thereafter, plus a close family member I need to travel to visit who is dying from stomach cancer and has about 30 days left to live. Any advice is appreciated.

  • Pam

    Hi Kate,

    I am looking for someone in the Ohio-Ky area knowledgable in treating SIBO. I had a positive HBT and took 10 Days of Xifaxin and feel worse than ever. I have many food intolerences also. Calling around the US has not gotten me anywhere with finding assistence.


  • Eric Kinman

    Can you speak a little more on potential issues of erythromycin? I’m scheduled to start taking it next week. A few years ago, metaclopramide didn’t sit well (brain-wise). Wondering if erythromycin may be similar.

    • katescarlata

      Hi Eric, the medication part of treatment is out of my scope of practice….but some of my clients have found erythromycin very helpful with no side effects. I gave it a trial personally –as I have a history of SIBO due to intestinal surgery–and my GI tract was not happy. So…it’s very individual.

  • dkaj

    Hi Kate, it’s me again. This time I have a question relying to myself but a little off topic. I myself have what I would call a milder case of IBS, but have Figured out my triggers over many years. I’m in a different predicament now though and need some suggestions. I have a large herniated disc in my neck and in a waiting state while Doctors are thing to get me scheduled for my epidural steroid injection and most likely surgery. This is my question. I AM NOW ON hydrocodone and Motrin around the clock as I AM in excruciating pain. I HELD OFF as long as I could trying to avoid any narcotic meds, but had one night sleeping wrong and my pain levels are unbearable. Anyways, it’s not a choice anymore. Any tip on how to protect my gut while taking these meds as I know they can damage the gut? I’m eating food overtime I take more meds, but anything else that might help? Not sure if I should start taking probiotics daily, haven.t needed to in past unless I was on an antibiotic, but wondering if this might be advisable or anything else that might coat or protect my gut. Not sure how long I’ll be needing meds prior to getting this all resolved? Any advise would be appreciated as I can already feel the effects of all the meds slowly starting after 5 days of having to resort to the hydrocodone and then the higher dose of Motrin. And unfortunately, even with this combo, I’m getting only minimal relief.

    • katescarlata

      Hi Deborah-
      Great question. Off the top of my head, L-glutamine powder and zinc carnosine may offer some help minimizing gut permeability. Here is an interesting article on zinc carnosine.
      Dosing would be 30 mg zinc l-carnosine daily per Gerry Mullin’s book, Inside Tract . L-glutamine is typically recommended in 1,000-3,000 dose but is contra-indicated in bi-polar disorder. SO….as always discuss supplement use with your health care provider to ensure dosage or application is appropriate for your individual case.

      • dkaj

        Thanks Kate!!! I knew you’d have good advise. I’ll talk to my spine doctors about the zinc. PS. I have Gerry Mullin’s book at home. It’s a great book and his story about his road to recovery is great. What an inspirational story… Unfortunately, my mind isn’t working too well with the pain and meds, I forgot about all about his book I have upstairs. Lol!!!

  • Marilyn Freeman

    I’ve read through many, many posts here and don’t see anyone complaining about the cost of Rifaximin. If I were to take the suggested 14 day dose, done twice by my naturopath, here in VT , it would cost me over $1,800. My insurance won’t cover it ( we have a $5,000 ) deductible . I have a severe case of SIBO, diagnosed by the breath test. I suffer from IBS-D symptoms, have pretty much my adult life ( close to 30 years ). I’m gluten-free, sugar-free, dairy-free, carb-free….my eating choices are a HUGE challenge in my life. Anyone have natural treatment successes ? ? ?

  • Amelia

    Hi Kate, I just stumbled across your blog and it is really great, thank you. I had a hydrogen breath test done for SIBO a couple of weeks ago and it came back as completely negative ie zero hydrogen or methane gas was produced during the test. I have read that according to Dr Pimentel a flat lining of both hydrogen and methane gas like this is indicative of hydrogen sulfide gas. Do you recall if they discussed how you would treat this type of bacterial overgrowth at the SIBO symposium? Both my gastroenterologist and nutritionist thought my test result was strange but didn’t know anything about hydrogen sulfide producing bacteria. We all agree that despite the negative test result i most likely have SIBO but I am unsure as to how best to go about treating it.

    • katescarlata

      Amelia, Great question…and I don’t have the answer unfortunately. Hydrogen sulfide seems to have both inflammatory and anti-inflammatory effects–this gut microbiome research is very fascinating–but we are still in the beginnings of understanding it! It seems from animal studies that a antibiotic combined with bismuth might be a potential option–but not sure.

      • Amelia

        Hi Kate, thought I would let you know that I was retested for SIBO about a month after the negative test result and I tested positive for both hydrogen and methane gas. Do you know which antibiotic, or combination of antibiotics, works best when both hydrogen and methane gases are present?

  • Patty

    Hi Kate, can you talk a bit about the meal spacing? How long between meals and why is this important?

    • katescarlata

      Hi Patty, the rationale for meal spacing is that your MMC (migrating motor complex) or small intestinal cleansing waves only occur in the fasting state, on average every 90-120 minutes BUT even less frequently in many of those with IBS. Having too few MMC cleansing waves are a risk for developing SIBO. So I encourage meal spacing of 3-4 hours (you need to be fasting in order for these waves to occur)…and this seems to help people.

      • Patty

        Kate, would you say that the size of the meal determines whether 3 or 4 hours is needed before eating again? Or is this determined by my tendency to be IBS-c vs. IBS-d? I believe that my system is, in general, slow-moving.

      • katescarlata

        Patty the timing of meals for SIBO is to encourage the MMC–migrating complex to initiate a cleansing wave of the small intestine–this would not be determined by the type of IBS you present with but rather is encouraged for anyone presenting w/ SIBO. Inadequate cleansing waves are one of the reasons people develop SIBO.

  • Frank McLeod

    Under your notes’ topic “Why rifaximin might not work for some “, (#2) methane bacteria benefit from dual treatment rifax/neomycin, I’m a little confused. Could you go into a little more detail ? Are you saying that although for many methane producing people the rifax/neomycin combo works but for others the combo may in fact benefit the methane bugs ??

    Thanks !!

  • Margarita

    Thank you, thank you for this wonderful and informative website. I’m mom to a 4-year-old who was recently diagnosed with SIBO (although has probably suffered from it since birth, based on symptoms). She has extreme constipation (unresponsive to medication), many food sensitivities (including many that go beyond high FODMAP foods, complicating efforts to eradicate high FODMAPs), and her breath test was positive for both hydrogen and methane. She was treated once, ineffectively, with a course of Augmentin, and now I’m hoping that a prescription for Rifaximin will come through. It sounds, though, like she might need to take Neomycin as well — is that possible with a child this young? I would also love to know from you how you might go about trying to do cleansing waves with a child of this age, who is prone to low blood sugar. Most of all, I would be grateful for any recommendations for dietitians or MDs who might be able to help us (we live in Northern California, near Oakland).

  • Bill K

    Kate – Your take away notes are awesome! I’ve had LPR for 3.5 years and spent much of my time getting worked over by ignorant, arrogant doctors (not saying this rudely or in a condescending tone…rather matter of fact). Recently I discovered that antibiotics have a direct correlation to symptom improvement for me. Since learning this, I’ve been reading and Googling…and all things point to SIBO (time will tell if this is true). I’m so exicted, I finally have something to work with. All that being said, your post on the SIBO conference in Portland is excellent, to-the-point and jammed packed with key take-aways! I really enjoy your site as well! Thanks for sharing your notes from the conference.

    Bill K
    Monticello, MN
    “For God so loved the world, he gave his only begotten Son, that whosoever believeth on him should not perish, but have everlasting life.” John 3:16

    • katescarlata

      Thanks Bill K! My notes were a bit exhaustive and maybe not compiled as nice as I would like–but I think there are some key points about SIBO that people who suffer with it–need to know! I am glad you found this post helpful!! And thanks for sharing!

  • Chelsea H

    Hi Kate-
    While living in Thailand (2012-2013), I got a nasty case of viral gastroenteritis causing me to loose 10 lbs, leaving me bed ridden and nauseated for over a week. I did not return to the US for a year. Throughout that year I had an incredible amount of bloating, abdominal distension and burping. Upon returning home to the US, Celiac and Chrons were ruled out with endoscopy/colonoscopy. I do not meet IBS ROME criteria. Since being home I would go a few months with minimal discomfort, and the excessive bloating/flatulence would “flare up” for 2 uncomfortable months. During these flare ups I would have dry eyes/bad breath/increased urination/fatigue. But my autoimmune markers are negative. I have been on the FODMAP diet for 5 weeks.

    However, I just received results for a positive SIBO breath test, and have started a course of Rifixamin. I would love some guidance with a good diet to complement the antibiotics. I have been ovo-lacto vegetarian my whole life (recently, no liquid milk, I just eat minimal amts of cheese). Most of the diets I have read seem to be Paleo style. Do I need to switch to eating meat and Paleo? I will if necessary to keep this thing at bay! I have also read some articles about garlic and peppermint oil to keep relapses from returning? Also, what are the effects of coffee with SIBO?

    Thank you for your great blog!

    • katescarlata

      Lots of great questions. Typically when on the antibiotic you want to liberalize the diet a bit to get the bacteria active and out of hibernating…then get ’em with the antibiotic. After the antibiotics I have my clients go on a strict low FODMAP diet–for 2-4 weeks. This is not an evidenced based researched diet for SIBO –in fact, there is no diet that has been studied for SIBO outside of a liquid elemental diet. But, I find it works for many of my SIBO clients. When you test + for SIBO…it is essential to find out why you got SIBO–otherwise if you don’t correct the issue (if it’s correctable) then it will likely come back! I think you can maintain a lacto-ovo veg diet maybe with some fish and have a balanced diet post treatment. Consider following up the antibiotic with a prokinetic drug info here: Try to work with a digestive health dietitian….truly it is so worth it to get guidance and find a diet that fits your nutrition goals BUT also nourishes your sensitive gut!

      • Chelsea H

        Thank you for your response, I will set up an app with a dietician and contact my doctor about Prokinetic agents to follow up. As per his direction and yours, I will liberate my FODMAP diet while on Rifaxmin.

        Have you noticed coffee/lattes influencing SIBO at all?

      • Kristina

        Hi there! Reading through all this, such great info! I have a question. I came down with what I thought was something I ate bad 5 months ago. I have not been the same since. I have had almost every test you can have done except a colonoscopy (my GI docs do not think necessary?) I did come back positive for Gastritis (mild) and am currently taking Carafate for this.

        My symptoms include gas (major), stomach pain (higher up) but sometimes move through the whole track and will feel lower. Belching (like crazy) and frequent bowel movements (which are normal). I tested negative for H Pylori and SIBO. Is there any way that I could have tested negative for SIBO and actually have it? I’m working with a natural person and waiting on a stool test as well as a saliva test. Any advice or suggestions would be so helpful!

  • Nancy Heaps

    Hi, I am a 58 yo female. I was positive for SIBO about 20 months ago. I was given a course of Rifaximin. When completed the symptoms came back and I have been on antibiotics since then (Flagyl alternating weekly with cipro). I want to get off the antibiotics (I have decreased dose from 2x to once daily). My GI doctor wants me to do another breath test while on the antibiotics to see if they are working. I have many medical problems including colnic inertia, rheumatoid arthritis, thyroid cancer and multiple upper and lower GI issues. Recently, my upper GI problems have been minimal. In what I have been reading and consults with another GI this does not appear to be normal management. I also don’t think I should be on antibiotics for this long. I would appreciate any feedback. Thank you.


    • katescarlata

      Hi Nancy, It’s so difficult to provide individualized health advice in a blog setting and really would not be good healthcare. I can say that for my patients that have recurrent SIBO –that is they test positive and get better on antibiotics but then it comes back==it is often helpful to do a trial of prokinetic drugs. These medications help with the cleansing waves of the small intestine. There is some great info here:
      Low dose erythro (50 mg) and prucalopride are the 2 that my clients are often prescribed…for some clients it really does keep them in good shape and away from chronic antibiotics–which of course, has health risks, such as C. Diff infection.

  • Sam

    My breath test came back positive for SIBO.

    My doctor gave me 200mg of Rifixamen tid x10 days. He did not give me a prokinetic. I am on day 8 and I have not noticed a change. Is there anything else I can do? Is a low dose causing any bacterial resistance?

  • Randy


    Your post of the symposium is probably the best post I have ever read in regards to the treatment of SIBO. There is so much misinformation out there, and you’ve managed to write a clear and concise article on the latest up-to-date treatments.

    Last year I took Xifaxan and it did wonders. The best I had ever felt. But two to three months later the symptoms returned. I then took another dose of Xifaxan but this time it did not do the trick, which I have read does happen. In your circles, have you heard what to do in a situation like this?

    Lastly, it’s tough finding a gastroenterologist who is willing to prescribe xifaxan/neomycin as a treatment because they’re hesitant on prescribing antibiotics and they just aren’t up on the latest research (like you are!). Is there some kind of directory of doctors out there who do this? I live in the Atlanta area.

    Thanks again for all you have done.


    • katescarlata

      Hi Randy, Treatment for small intestinal bacterial overgrowth is a bit tricky and treatments are individual–especially w/ relapse. I think the key for many people is to treat with the antibiotic and then follow up with a trial of a prokinetic. But, there is also the notion of whether some people have colonic dysbiosis (alterations of bacteria in the large intestine) vs. small intestinal bacterial overgrowth. And in this case, I wonder if another antibiotic may be more suitable. Satish Rao is a GI doctor in Augusta, Georgia–I might call his office and see if they can provide a colleague in Atlanta.

  • Brad

    I was tested for sibo a year ago treated with Rifaximin neomycin and never tested again. Never felt any better either. I insisted on retest last week and came up 32. My gasto has no idea how to treat. Can you recommend a Dr in Charlotte NC?

  • Mary

    Hi Kate,
    I just wanted to share my story in case it might help someone else. About 10 years ago I started eating gluten free because of stomach pain and diarrhea which resolved quickly once I started the diet. My tests for celiac prior to starting the diet were negative but I went gluten free anyway and was very pleased to see my symptoms resolve. Through the years my stomach seemed to become “more sensitive” and the stomach pain and diarrhea returned despite a strict GF diet. I also was diagnosed with SIBO X3 over the last 3-4 years, treated with first Cipro and then Xifaxim only to have symptoms return. Instead of going on antibiotics again, I have been finding success with a grain free diet. My diarrhea and stomach pain have resolved, my energy has returned and my weight has now stabilized at least rather than continued weight loss. It has not been a pleasant process to go through but I am now feeling like I am “in control”. A grain free diet is doable and there are some good websites out there providing recipes.

  • lauren

    Hi there,

    I am in Canada. I am positive that I have Methane producing SIBO bugs. I am on a loooong waiting list to get the breath test. Is there any way I can just buy the rifaximin and neomycin that you know of? Thanks!

  • Meghan O'Rourke

    Hi Kate!
    Suffering from SIBO… My doctors are all terrible . I need someone really good who can actually treat this condition. I’m in the DC area. Can you help me, please?!

  • Andy

    Hi Kate,
    Your article is very informative on the SIBO symposium 2014. I was wondering if you can help with some clarification about what Dr Pimentel recommended during this symposium. I had a lactulose test and it was positive and high for Hydrogen. I also produced Methane but it hovered around 7 PPM. My doctor has prescribed Rifaximin alone. I am of the BIS-diarrhea persuasion and not constipation. Did Pimentel recommend the Rifaximin+Neomycin regiment for all methane producers (>3ppm) or for methane producers that are of constipation persuasion? Thanks!


  • Andy

    Hi Kate,
    This is just a followup to my post. I felt perhaps I should clarify my question as follow:

    Did Dr Pimentel recommend the Rifaximin+Neomycin regiment for all methane producers (>3ppm) regardless if they have constipation, or is the Rifaximin+Neomycin regiment only for methane producers (>3ppm) that are of constipation persuasion? I am of the diarrhea camp.

    Thank You.

    San Francisco

    • katescarlata

      Hi Andy, Great question that we did not review—I believe it is + methane =dual therapy regardless of presentation….but can’t say for sure. Some patients trial rifaximin alone–and evaluate benefit. If the SIBO re-occurs then trial the dual therapy. This is really a relatively new treatment modality–and more research is needed.

  • Pam

    I have tested positive for SIBO and was wondering if you could tell me why my symptom is nausea. I never hear anyone talk about this, everyone always talks about IBS. I just finished a second round of antibiotics and feel better, but not 100%. I am following the FODMAP diet, but find this very hard. They think what triggered the SIBO was being on strong antibiotics for an appendicitis along with stress. Do you have any thoughts?

    • katescarlata

      Hi Pam, I think some people have slowed digestion due to methane producing microbes that live in some people’s intestines–and this might create nausea…as the stomach empties slower (just my thoughts!) OR ….that the distention from the gas in the intestine pushes on the diaphragm and stomach which could contribute to nausea. Have you had a gastric emptying study done? You could have delayed emptying or gastroparesis which is causing nausea too.

      • Jerry

        I also had nausea as my primary symptom of SIBO. Now feeling great after second round of Riflaxin. My primary cause of nausea was pressure on my diaphragm from bloating. Now easing off PPI which Dr had erroneously prescribed for nausea, and which I think may have caused my first recurrence. The nausea was unrelenting every night from 8:30-11:30 pm every night til my stomach emptied out. Very dibilitating.

      • Pam

        I just had my second dose, too, along with neomycin. I fell better, but not 100%. Have you ever tried taking lactase to help reduce the gas in the small intestine? I haven’t, but I am thinking about it. This is really hard to deal with…I’ve been this way for 3 months! Does anyone know if I could have some other issue?

  • Venus

    I have suffered for many years from IBS. Recently very bad symptoms. My doctor put me on Rifaximin for 2 weeks. It didnt work. The second doctor did breath test. I have both gases, extreme amount of methane. He put me on Rifaximin and Neomycin for 10 days. I also followed the low fermentation diet while on antibiotics. I felt good for two weeks, and then symptoms started even worse than before. I have so much gas and very sensitive mucus membrane. I even feel burning in my mouth.Very frustrating. He wants to do an MRI of the GI tract. Any suggestion? Please help.

  • Jean

    Hi Kate,

    I have had IBS and GERD for years. IBS (or perhaps food intolerance) for at least 16 years and the GERD started in 2007, I think. Hashimoto’s came along in 2010 and now I have muscle aches and fatigue that I don’t have an explanation for.

    Regarding the stomach issues. The main symptoms are pain, bloating and heartburn. Funny thing is, I thought EVERY ONE had pain at night. In 2008 I can remember wondering how Hillary Clinton could campaign all the time.. Doesn’t she feel crappy at night, like me?

    Along the way I have given up dairy, which was the first food intolerance I found, then decided that all things “white” are bad for you. Then I discovered wheat fiber (or any high fiber) made me REALLY sick, so I gave that up. I’ve tried gluten free, low histamine, dairy free, less meat yada, yada. I have given up alcohol, coffee, tea chocolate, all the things I love. I’ve had reactions (bloating) to some juices, gave up all fruit juice. I have not done any research at all for years. Just tried to keep things in check and thought I had a handle on things until my daughter just arrived home from college and my diet went a little haywire. So did my stomach. Once again I started researching and discovered FODMAP. OMG, this sounded like me! So I gave up all FODMAP. NO help. I kept a log for 3 weeks. I had 3 good days out of 3 weeks. I couldn’t see the pattern at all! I went to Europe 2 weeks ago and I felt pretty good! Strange. I had a few theories. 1) They don’t put a bunch of junk in their food 2) I was walking a lot. 3) I wasn’t eating much fruit.

    Fast forward two more weeks, still struggling and I came upon this article. I think I have made myself sick because I graze ALL the time. I looked back on my log and sure enough, the days I ate only 3 meals were my good days and in Europe I was eating 3 meals.

    Oh, I also didn’t mention that I was on antibiotics at least 5 times in the last 3 years. (maybe more – lost count). Also saw a DO (Integrative Physician and she put me on Berberine – which I think made me sicker – I need to try it again)

    So I guess my question is. How do I keep from feeling hungry between meals? If I don’t eat a lot of carbs I seem to get really hungry. I have tried low carb, high protein and it makes my stomach feel very queasy. I am so frustrated but so grateful that I found your website. Thanks so much for what you do.

    • lauren


      I think I have SIBO too, and you mentioned an interesting thing in your comment;

      I too think that Berberine makes my symptoms worse. I just had it prescribed to me by an ND and I decided not to take it because of my previous 2 tries with it.

      Now the REALLY interesting thing (if you are a giant nerd about this like me) is that I have recently put it together that when I took Primal Defence probiotic last year, that is when things got SUPER bad. I think I had mild SIBO before; now I have full blown IBS. SO this weekend I was researching what kills bacillus subtilis, which is the SBO (soil based organism) in Primal Defence which seems to make some people with weak immune systems worse (me). Basically it seems to kill the same way an antibiotic does, and then turns into a biolfilm of spores. Low and behold I find that Berberine in certain doses makes it WORSE! Very very interesting right? So, have you ever taken a probiotic that contained soil based organisms, like Threelac or Primal Defence?

      • Jean


        I had another moment of clarity as well. I think the FODMAP diet hasn’t worked because I already was following it pretty much.. after years of experience I kind of knew what set me off. So now I don’t feel so bad about the lack of help of FODMAP. The probiotic I was taking is Farrow’s IPS. It is a broad spectrum probiotic. I also didn’t mention, some of the reaction that I was having to the berberine was an itchy throat. I have some pretty severe allergies. So it was either that or the multivitamin supplement I had started taking around the same time. I will start taking it again and see if it does the same thing (without the other supplement).

        Good Luck!

  • Steve

    Hi Kate,

    I have SIBO + constipation. I have taken two rounds of rifaximin with no success. My GI doc seems stumped. Do you know of a SIBO specialist in the Louisville KY area?

    Also, SIBO symptoms started after I took 3 rounds of amoxicillin for a gum infection. Is it common for anti-biotics to cause SIBO? My GI doc has yet to find another cause.


    • katescarlata

      Steve–Did you measure positive for methane gas in your breath test? Sometimes methane + patients do better w/ dual therapy: rifaxmin and neomycin. Also, dosing of rifaximin can impact its efficacy. In my practice, I find the 550 mg rifaximin 3 times per day dose is better than 2 times per day. I have seen SIBO occur post antibiotics –must disrupt the gut flora balance or environment and make SIBO more possible

      • Steve


        Yes, for + methane. I have read other places about this dual therapy but my doc doesn’t seem to know about that. So I am looking for a doc that has more experience with SIBO. I would be willing to travel some. He also had me on 550 mg 2 x per day for 20 days on the second round. I took it on myself to take it for 3 x per day for 13 days after reading same advice elsewhere. Still wasn’t effective.


  • April Ogden

    I have been prescribed Neomycin 1 tab 2 x day and xifaxan 2 tab 4 times a day for 1600. I had c-deficle before and am extremely worried, is there any suggestions to avoid this? How about taking probiotics orally or through an enema? Fermented foods? I am causing myself much anxiety about this, but I know I need to do it. I have been following the scd diet for 8 mo and have been sick for year. Losing too much weight.



  • Joey Thomas

    Hi, The herbal antibiotics never get much attention on these blogs so I just wanted to add a comment here. I took herbal antibiotics to treat SIBO and although I haven’t been retested my symptoms have improved drastically and it is about 18 months now since I completed treatment. Low stomach acid was also a real issue for me and a believe contributed to the development of SIBO in the first place. The product I took contained a combination of things but he main ingredient was oregano oil. I took it for about 6 weeks. It zonked me out completly during the first week I took it but since completing treatment my fructose malabsorption issues are almost non existent and my energy levels are through the roof!

  • Vart

    Hi Kate,
    Did they say anything about Interfase plus (or other biofilm disrupters) during the symposium? Also, does Dr. Pimentel not want us to take probiotics during the antibiotic treatment only or in general? Great info on the website, by the way -Thanks!

    • katescarlata

      I gathered the avoidance of probiotics was while small intestinal bacterial overgrowth was an active issue. There was no mention that I recall about biofilm disrupters. I find this concept intriguing–but have not found them to be helpful with my clients that have tried them.

  • Barbara

    Hi Kate,

    Following a routine colonoscopy in March (everything OK), my bowels have never returned to normal. Spasms, pain, altered BMs, episodes of lightheadedness, etc – saw alternative dr who did stool testing, organic acid tests, food sensitivities. Showed bacterial “imbalances” including some pseudomonas aeruginosa but stopped short of labelling it actual dysbiosis in colon. Some few yeast.

    Continued to get worse – now nausea, burping, upper GI dyspepsia and pain, burning in throat – ENT saw inflamed esophagus. Still cannot pass gas. Been trying to take probiotics (which I always have for years) and viitamins, supplements but symptoms make it very difficult. Have been taking L-glutamine, Vitamin C, D and B2 (which I learned I was deficient in).

    I’m ready to do upper endoscopy because of such painful upper symptoms too but traditional gastro doc thinks everything is coming from “below” and that the colonoscopy prep caused my system to have a major IBS flare up and I need to take an antispasmodic (Librax) – which should calm things down. It has helped a lot in the past week, but tends to cause slow motility and sending me toward constipation. I’ve been limiting foods, eliminating dairy, trying to go gluten free and avoiding FODMAPS – have lost considerable weight in these past few months- am petite but now under 90 lbs. Getting freaked out about that.
    Of course, the antispasmodic is not a cure – I need to eradicate the bacteria that’s causing all this trapped gas, I guess.

    In the midst of all this, a cousin of mine thought I might have SIBO and through his lab, I did the lactulose breath test. Although technically negative, I had a high baseline methane (64) and it rose to 77 at one hour. Hydrogen levels were OK. So it did not meet the standard of rising 20 ppm, but they did discuss the possibilities that some might still diagnose me with SIBO due to high methane. They said there is little research to support that position, though. They suggested that I could still be having the major overgrowth from the colon as opposed to the small intestine. How would I know from where?

    At this point, I am at a loss as to how to proceed. This is very different than any previous IBS symptoms I may have had 20 years ago. I had not been really symptomatic up until the colonoscopy. My life has been turned upside down.

    My gastro doc admitted he does not know much about SIBO and in particular methane and would not know how to treat. I have read your wonderfully informative blogs and much of the research of Dr Siebecker and Pimentel and know that I need to find someone who can help me. Even if I wanted to try the antibiotics, I would need to have a doctor who is knowledgeable in this.

    What are your thoughts on whether this is just IBS (colon) or developed into SIBO? Or am I just a “methane producer” as the lab doctor suggested? Is there such a thing?

    Might you be able to recommend any dr in the Northern NJ area who can guide me? I would be so grateful.

    • katescarlata

      Barbara–I think it’s the methane producing microbes that are troubling you and contributing to all of your GI issues. Since your baseline methane was high I suspect it is most definitely in the upper GI tract–and perhaps you are overrun in the colon too! I don’t know of any GI docs in NJ well versed in SIBO. Can you travel to Boston? I know some great GI docs here.

  • Barbara

    Thanks, Kate for your response and your thoughts – I wish I could travel, but that is not possible at this time. I am seeing an integrative medicine dr (who was a traditional MD, but now practices integrative) and he’s the one who sent me for most of the other tests, unfortunately he does not know too much about SIBO – I’ll be seeing him again next week and perhaps we can figure some things out. I can bring along printouts of some of the information I have gathered from your posts and other web info.

    I understand that Dr. Siebecker recommends allicin (as an herbal antibiotic) for methane producers and since I am afraid of regular antibiotcs at this time, I thought I might try that along with some of the other things I have been taking, to see if I can make even a little headway in my condition.

  • em

    hi Kate, I’ve been following strict low fodmaps for too long I know – over 2 years now & all my attempts at re-introducing fodmaps have failed. I have pretty good relief from all symptoms except wind and bloating. So I suspected SIBO and sent off for a test. Result is high+ for both Hydrogen and Methane.

    Have I somehow “caused” or exacerbated SIBO because of being on low-fodmaps too long? Where do I go from here? I don’t hold out any hope of getting the suggested antibiotics regime here in the UK where my GP & Gastroenterologist have not even heard of Fodmaps. Fed up!

    Thanks for all of this invaluable help.

  • Deborah

    Aug 4, 2014 breath test came up positive for SIBO, both positive for hydrogen and methane. My symptoms were extreme constipation, extreme flatulence, extreme fatigue, and chills (no fever). From Dec. 2010 until Aug. 2012, I was chronic C.Diff. (only cure was a fecal transplant by the University of New Mexico gastreonoligist). For the SIBO, I was put on the antibiotic Doxycycline Hyclate 100 mg for 10 days. After 3 days, I felt a difference in how I felt and the symptoms. On the 4th day after the last pill, the symptoms seem to be coming back. I should mention, I also have Epilepsy, and am on Primidone and Keppra, and I’m diabetic. The pharmacist told me that the Primidone would most likely keep the antibiotic from being “absorbed”, therefore, would not do what it is supposed to do. On the 1st day I started the antibiotic, I quit taking Primidone, and upped my Keppra the whole 10 days I was on the doxycyline hyclate. Rifaximin cost is too much for me to pay, and the UNM gastro doctor is aware of this. Because I had C.Diff in the past, my gastro doctor said that options for antibiotics are very limited. I go back to my UNM gastro doctor on Oct. 29th. Is there anything you could suggest that I ask on “where to go from here” when I see him, since I think the SIBO has not yet been controlled? Thank you for the wonderful info on SIBO, it’s the best info on the internet I have found.

    • katescarlata

      You might consider elemental formula, Vivonex, as a SIBO therapy–though it does taste awful. Or perhaps, your GI doctor can get rifaximin samples from Salix?? Meal spacing seems to be a key element of SIBO treatment–grazing doesn’t allow for adequate cleasing waves of the small intestine….in my practice, I have noticed this seems to really help.

  • Amelia

    Hi Kate, how long would you suggest waiting to retest for SIBO with the breath test after finishing a course of pharmaceutical/herbal antibiotics? My lab is saying i need to wait one month.

    • katescarlata

      You could opt for the glucose breath test and order the kit on your own through Commonwealth laboratories in Massachusetts. In order to do the lactulose test–you need to have an MD order. The glucose breath test is a bit more specific for SIBO–but misses cases that are in the lower part of the small intestine.

    • Steve


      You might try contacting QuinTron Instrument Company:
      Phone: 1-800-542-4448 / 1-414-645-4222

      They manufacturer the analyzers and can tell you what hospitals/practices in your area have their machines. You should then be able to find a doc to order one for you.

  • Mike

    Hi Kate,

    I emailed Commonwealth labs, and they were able to provide a doctor in my area who had ordered the SIBO tests recently. Finally met with her today, and it was great to discuss with a doctor who is well versed in these topics!

    Thanks for beating the fodmap/sibo drum…

  • Phil Paroian

    Hi Kate;
    I live on Olympia WA, about half-way between Seattle and Portland OR. I was diagnosed with probably SIBO, did a course of Xifaxcin, and just got the results of a breath test done 3-4 weeks after the antibiotics finished. That showed results that even more strongly confirmed SIBO. My local GI doc and I are trying to sort out treatment options, and with his full support, I was wondering if you knew of any SIBO experts in either Portland or Seattle that you’d recommend for a second opinion/consult? Thanks!


    • katescarlata

      Hey Phil,
      I would check out Alison Siebecker on–in Portland, Oregon or Adam Rinde at–outside of Seattle– both are naturopaths with great background in SIBO care. Meal spacing is very important and modifying diet too. Proper antibiotic therapy and follow up with a prokinetic such as low dose erythromycin -50 mg at night can help reduce reoccurrence. And remember SIBO is not an end of the road diagnosis–it is a SYMPTOM of something else going on. Try to get a good work up to determine why bacteria are growing in your small bowel.

      • April Ogden

        I’m in the same boat and my doc is working with me but is not real knowledgable on Sibo. What would be included in a good work up to determine why the bacteria are growing in the small intestine. He will order any tests I want but I need to know what to ask for. Thanks April

  • suzanne

    Hi Kate,
    I had a LACTULOSE breath test which showed a classic sharp rise within 20 mins. I then had a course of Doxycycline.
    Since then Ive had another Lactulose breath test and even though I strictly followed the preparation diet, my baseline for the test was a high reading with a slow gradual incline.
    Because of this my holistic doc has suggested i may still have SIBO.
    Is there another reson i may have had the high baseline? Many Thanks Suzanne.

  • Colette Binger

    Hi Kate- Thank you for this site and be dedicated to SIBO research. I was diagnosed in July with SIBO, am currently on my 4th course of antibiotic first however of Xifaxan and Neomycin (high in methane- and unfortunately, don’t have a dr/gi here that knew to treat with both earlier). First course, Flagyl, then two of xifaxin alone- now this. Dropped 40 pounds since April, when this all began and have been terribly ill. Have done 100’s of hours of research, phone consult with Dr. Keller (one of A. Siebecker’s partner’s in crime from Oregon), and have an appt with Weinstock in St Louis in 6 weeks. Here is my question and issue. This dose of meds is making me have explosive diarrhea, and feel worse, I have heard this can be common- thoughts? I am feeding the bacteria, do you have suggestions of how (I am lactose intolerant for sure). Protocol suggests doing a repeat breath test 5-14 days after meds (Pimentel/Siebecker)…do you know have suggestions after this if my levels are still higher than they should be? Vivonex? Which I hear makes people vomit? HELP? Frustrated and weak- feeling this week may be another weight loss week and just not up for that. :/

  • Tammy

    I have been tested positive for SIBO. I am being seen at Cedar Sinai with a doctor working with Mark Pimentel. The physician did not really discuss diet treatment with me. I have been on a low FODMAP diet for over a year. I have been prescribed a 10 day treatment of rifaxim and neomycin (which I am taking now day 4). Following, I will take 3 months of a prokinetic called prucalopride. I noticed in your article that Dr. Pimentel recommends eating a high fermentable diet while taking the antibiotics. I have been doing this, but my stomach has been so bloated. How high FODMAP do you recommend to eat? Do you know long it takes for some type of symptom relief to come? You stated that you had SIBO in the past. Did you follow a high fermentable eating protocol while you were on antibiotics?

    • katescarlata

      Tammy, typically I recommend small amounts of FODMAPs during antibiotics–perhaps 1/2 apple and some garlic–I don’t typically push fermentable carbs to induce terrible symptoms. Some people feel lousy during the antibiotic phase and then start to feel better with in the week of stopping the antibiotic–but I find it varies person to person.

  • Ashley

    Hi Kate,
    My GI just prescribed xifaxan 550mg twice a day for fourteen days, after months of sudden ibs and acid reflux problems.Ive been trying to educate myself on the subject of bacteria overgrowth and to be honest I’m overwhelmed. I have a few questions that I was hoping you could share your thoughts on…probiotics seem to be up in the air, to use or not to use.I think the basis behind not doing so have some merit, what do you think? My GI doesn’t seem to eager to help me get best possible outcome, when I asked about prokinetics she said there is nothing to do after taking the xifaxan except probiotics and yogurt. If she won’t prescribe one, is there some otc or natural prokinetic to keep things moving? One last question, I was reading about glutamine and how it repairs, should I take this?

    I know you can’t give medical direction, but I’m young, 28, and feel like I’m going into this blind.any thoughts would be greatly appreciated.Thank you for your time .

    • katescarlata

      Ashley–You might want to find another GI doctor that has better knowledge of SIBO. The majority of my SIBO clients have been helped with use of the pro kinetics post antibiotic therapy. I have mixed feelings about using a probiotic in a patient that is likely not cleansing their small bowel efficiently…which led to their developing SIBO. Most SIBO patients have less cleansing waves–due to the SIBO or due to having a motility disorder that contributed to the advent of SIBO. I often recommend l-glutamine in powdered form for patients with low grade inflammation or long term GI issues to help heal the gut. But l-glutamine is contraindicated in patient’s with bi-polar disorder. It is so important to find a dietitian that is well versed in digestive health and a GI doctor that enjoys working with SIBO and functional gut disordered patients.

      • Ashley

        Thank you so much for responding! After so many doctors with no real help, it’s so comforting to talk to someone with knowledge about this subject.
        If you don’t mind, I have just a couple follow up questions from your reply.
        I can’t get into a new GI for months and the only real help the current one has done is to prescribe the xifaxan. I am planning on :
        – xifaxan for two weeks, with a balanced diet ( should I take the Gluatmine while on antibiotic or start after? )
        -GI said probiotic only option for after, so discouraging her lack of knowledge or help. I was trying to find a non prescription prokinetic and Iberogast sounds promising.Have you ever heard of this herbal alternative? Again, start after antibiotic.
        -my only other question upon starting treatment is the use of HCL for low stoamch acid, do you have any opinions?

        Again I understand that you can’t give medical direction, but being able to ask questions to someone who understands this is helpful and comforting beyond words. Thank you again for your thoughts.

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