Just diagnosed with SIBO, what next…

Just got diagnosed with small intestinal bacterial overgrowth (SIBO) and not sure what advice to follow?

You are not alone.

For those of you that are not familiar with SIBO, it is a condition in which abnormal amounts of bacteria invade the small intestine. Symptoms of SIBO mimic those of IBS. I often say, it might feel like “IBS on steroids”.  For more info. on this topic, I have another comprehensive post on SIBO here.

The Internet offers a myriad of options of treatments for SIBO but in my humble opinion diet and medication recommendations should be tailored to the individual. The varying microbes that can overgrow in the small intestine may preferentially enjoy certain food substrates over others (making diet needs variable). Additionally, in severe cases, SIBO may lead to villous atrophy, (Greenson, 2015) which may impact the production of digestive enzymes that are produced on the villi, finger-like projections, that line the small intestine. A reduction of digestive enzymes, can impair your ability to digest carbohydrates that rely on these enzymes to break the carbs into absorbable one chain sugars. The unabsorbed sugars then can become fast food for small bowel bacteria. I highly recommend you work with a registered dietitian with digestive health expertise to help personalize nutrition modifications for you. The goal is to minimize symptoms with the least restrictive diet as possible. Restrictive diets can lead to malnutrition and reduce your quality of life. 

Treatment of SIBO should involve a comprehensive nutritional and diagnostic plan, which should include the following:

  1. Identify and treat the underlying cause of SIBO when possible, such as untreated or inadequately treated thyroid condition, severe constipation, small intestinal diverticula, untreated or under-controlled celiac or inflammatory bowel disease, pancreatic insufficiency, scleroderma, diabetes, and potentially IBS, or other motility related disorders. (Ref: Magge 2012 )
  2. Reduce microbes in the small intestine via antibiotics (herbal or traditional) or via a special liquid diet (elemental diet) made up of nutrients ready for absorption.
  3. Attempt to maintain remission with diet modification such as the low FODMAP diet or a diet reduced in fermentable carbohydrates, the preferred food source for microbes living in our small intestine, along with meal spacing to allow the migrating motor complexes to clean out food and excess microbes between eating cycles. (More on this later.)
  4. Assess for nutrient deficiencies and supplement diet to replenish nutrients at needed. Fat soluble vitamins, Vitamin A, D and E may be deficient as fat malabsorption can occur in SIBO. (Vitamin K, another fat soluble vitamin, typically remains normal.)  Vitamin B-12 may also be reduced due microbial consumption of this vitamin.
  5. Trial medications that promote motility of the intestine, called prokinetics (such as low dose-50 mg erythromycin at night, or perhaps resolor) Update December 18, 2018: I no longer recommend Iberogast due to case report linking it to potential liver problems. 
  6. In some cases where the underlying cause of SIBO is not treatable,  periodic or intermittent re-treatment w/ antibiotics may be considered.

The small intestine microbiota is largely shaped by the capacity for conversion of small, rapidly fermentable carbs while the colonic microbiota is largely driven by efficient breakdown of complex indigestible carbs (i.e. fibers).

There is growing research in the area of SIBO regarding standardizing breath testing but, sadly there is very little research looking at the impact of diet change in managing SIBO or eradicating it or better yet, curing the condition. (And, yes, I talk to researchers all the time encouraging nutritional research!)  There have been some dietary trials with individuals w/ SIBO that have shown the low FODMAP diet helps with symptom management (de Roest 2013 )—but these are short term trials.

When testing for SIBO, a lactulose or glucose breath test is undertaken. The test should evaluate both hydrogen and methane gas. Let’s talk a bit about methane gas as I find this topic interesting. 🙂

Mark Pimentel, MD, gastroenterologist at Cedars-Sinai Medical Center, one of the key leaders in research and treatment of small intestinal bacterial overgrowth notes“Methane is an important gas to assess during breath testing because it is nearly universally associated with a  phenotype of constipation. More importantly, methane appears to be an agent that slows intestinal transit. As a result, recent efforts have focused on reducing methane. One such effort is the use of antibiotics, although the benefits appear short lived. Lovastatin, on the other hand appears to block methane production by these organisms and is being evaluated as a novel microbiome therapy in ongoing clinical trials.”  Methane and hydrogen + SIBO is associated with a higher body weight and body fat. ( Muther 2013

From my clinical experience, patients that are methane positive often require more than one antibiotic to eradicate their symptoms. A combo approach with neomycin + rifaximin may be used.  Some of the GI docs, I work with,  have been utilizing a combo of flagyl and rifaximin with good results as well.  Again, this area is somewhat uncharted from a research standpoint (yes, again more research is needed!!). Here is one paper suggesting a dual antibiotic approach is more therapeutic for methane + SIBO. (More on dual therapy in Q & A section).

There is a great interview with Dr. Mark Pimentel here to learn more about current treatments for SIBO and what’s on the horizon in research.

Role of Meal Timing and Prokinectics

If you have read anything on my blog or other areas of the Internet on SIBO, you might hear that meal timing is important, as well, that prokinectics are a must after antibiotics. Dr. Ali Rezaie, a leading SIBO researcher and clinician at Cedars Sinai, weighs in on these topics, “Phase III migrating motor complexes (MMCs) are the housekeeper waves of our gut! They occur every 90-120 minutes when we are not eating (i.e. fasting). They last less than 10 minutes, but hey, are strong enough to push the residual food and secretions along with the excess gut microorganisms from small bowel to the large bowel. These waves are weaker and less frequent in a proportion of IBS and SIBO patients. This makes bowel rest in between the meals very important, so these waves are not suppressed further. There are multiple medications that can accentuate these waves. Low dose erythromycin and prucalopride are among these medications. While erythromycin is cheaper, prucalopide is more potent and its effect lasts longer which makes it (at least theoretically) an ideal option to help the MMCs. It should be noted that large comparative trials are lacking in this field.” Prucalopride (Resolor is available via Canada) More on prokinetic dosing here. 

Update December 18, 2018: Prucalopride has been recently by approved for use in the USA for chronic idiopathic constipation.  Prucalopride enhances colonic peristalsis, increasing the motility of the colon.

In short, SIBO is growing area of research but there is very little on diet for therapeutic benefit in the medical literature. It is quite common for patients to develop food related fears and guilt, along with malnutrition trying to eradicate SIBO. Although I understand the fear and frustration SIBO can bring, I urge patients to work with a health care team to provide guidance. Becoming malnourished will worsen GI function and overall health and well-being.

Here are a few common Q & As I receive in my practice:

Q1.  My doctor prescribed rifaximin is there anything I should change about my diet while on meds? What is the typical dosage?  Answer: Pimentel’s group suggests that some fermentable carbs remain in the diet while treating with antibiotics. This is based on microbiology concepts that microbes are more easy to eradicate when active. There has been no formal research to reveal whether this approach is best or not.  Most practitioners that I work with prescribe 550 milligrams rifaximin three times per day for hydrogen positive SIBO.  For more on SIBO medications and other topics, check out my previous SIBO post here.

Q2. Is the treatment for a positive methane small intestinal bacterial overgrowth different from the treatment for a positive hydrogen test? Answer: Pimentel’s group, one of the leading authorities and researchers in SIBO treatment, utilizes a dual therapy approach of neomycin and rifaximin together. This approach has been shown to have greater efficacy than rifaximin alone. Neomycin does has some harsh side effects (potential for hearing loss).  In some case, flagyl may be used as adjunctive therapy with rifaximin, instead. Ref: Low 2010

Q3.  My symptoms seem to be worsening on the antibiotics. Am I missing something? Answer: ALWAYS discuss your symptoms with your health professional as you would not want to miss anything serious. In my personal experience (yes, I have experience SIBO, likely due to the surgical resection of my ileo-cecal valve), my symptoms worsened with enhanced bloating while on the antibiotics, but this resolved completely, within one week of completing the antibiotics.  I have found that some patients note immediate improvement on the antibiotics while may others feel worsening of symptoms while on the antibiotic treatment.

Q4.  I just finished my course of medicine.  What next?  Do I assume I can eat everything again?  Are their foods I should avoid?  Answer:  Again, we do not have research to support diet therapy for SIBO. I do find, however, in my practice, that following a low FODMAP diet for a few weeks followed by the low FODMAP reintroduction phase, that many of my patients, can start to liberalize their diet a bit post antibiotics with good symptom control.  I also suggest food choices be selected carefully to avoid risk of food borne illness. Being on antibiotics increases your risk of food borne illness and food borne illness increases your rate of SIBO.  {This food safety guide detailing ways to avoid food borne illness is geared for the older adult, but is applicable to all of us.}

Q5.  If this is something I’m going to be battling with again in the future, I want to get educated on the most up to date research and information coming out in the area of SIBO. Where can I get accurate information? Answer: I try to post topics about SIBO on my blog. Dr. Pimentel’s group at Cedars-Sinai Medical Center hosts a yearly SIBO symposium. Also, the  Gut Microbes conference offers a yearly event on all topics regarding the gut microbiota. The National University of Natural Medicine in Portland, Oregon also features a yearly symposium.

Q6. What diet should I follow post antibiotics? Answer: There is no evidenced based diet for SIBO and a variety of different diets are used in various centers around the globe.  In my practice, I find that the Low FODMAP diet is enough for symptom management for the majority of my patients and my goal is to liberalize the diet as much as possible while maintaining good symptom control. Some patients do need modification of other carbohydrates, but in my practice, this is not common.

Q7. I want to go out to a restaurant for a celebratory dinner with my friends. What are some safe choices that might work for me in terms of food/drinks?  Answer: While dealing with SIBO symptoms, my clients do well with salads with low FODMAP ingredients, or grilled chicken, fish, beef with a baked potato, and steamed low FODMAP veggies or a side salad, lean burger with a baked potato works too –or a few fries, if fat intolerance isn’t an issue.  Sometimes, diet is a bit of a trial and error at restaurants. Most patients learn which items settle best and will frequent those restaurants that have tolerable food options more often. For celebratory drinks, a glass of white and red wine, champagne, vodka with a splash of cranberry and lime, tend to work well. Overdoing alcohol is not a good idea, obviously! Again, I suggest you work with your dietitian to ensure you are eating a well balanced diet while managing your symptoms. I do sell a cocktail guide for the low FODMAP diet, if you want to learn more about low FODMAP cocktail recipes for special occasions.

Q8.  What can I carry in my purse/car for emergency snacks when I can’t find anything to eat?  With the onslaught of new low FODMAP food options, I recommend FODY food bars (super tasty and filling) as well, the 88 Acres Dark Chocolate & sea salt bars work for my clients. Another option, try a banana or rice cake with an individual peanut butter or almond butter package for an easy snack on the go.  Disclaimer: I consult with FODY foods but I really do like their bars!

And for the last part of my post today, I thought I would have one of my clients Kari,  provide her tips and vantage point, after being diagnosed with SIBO.

Favorite websites:  “My favorite website is Kate’s blog and website and the SIBO Discussion/Support Group on Facebook.

Selecting a doctor: ” I work with a doctor who focuses on functional medicine and lifestyle changes along with medicine to promote healing: exercise, eating, meditation, &  supplements to support gut healing.”

Focus on the positive: “I like to focus on the positive so tend to carry Kate’s low FODMAP checklist  in my purse. If I must, and this is rarely, I pull up the high FODMAP list,  just to check an ingredient. Focusing on all the foods I CAN eat is encouraging!

Reduce stress and control what is control-able: “In addition to diet, reducing stress, focusing on what works, keeping a food/diet/lifestyle journal to notice trends and keeping track of SIBO symptoms,  goes along with good meal planning.”

Non-food outings are fun too: “I try to plan social events with friends and family that don’t involve food…hikes, pedicures, book talks, crafting, coffee….”

Make meal planning easy but balanced: “I focus on simple foods that work for me and combine in different ways when eating at home. I am always prepared and try to bring something I can eat or drink when going to someone else’s house. I bring along an 88 acres dark chocolate and sea salt bar in my purse and often an extra in my car! I keep almond butter packets in both places as well for a quick addition to a banana or an 88 acre bar to get me through the next 3-4 hours till I can eat again…I think meal spacing is key. I truthfully usually don’t snack. During the day, I do 3 meals spaced out and occasionally have popcorn with coconut oil and sea salt if I’m hungry again after dinner. I stick to a simple routine that includes protein at every meal: lactose free yogurt or oatmeal or eggs for breakfast, lunch: a salad with whatever greens I have plus cheese, nuts and any leftover protein (steak, turkey meat, etc) and use basil, olive oil and salt for a dressing. Dinner might be low FODMAP veggies and  protein (beef, poultry, fish)  with a baked potato, jasmine rice or quinoa.  

 For more on SIBO, I do offer an educational guide for sale on my site, here. 

13 replies on “Just diagnosed with SIBO, what next…

  • Madeline

    Last August I was (finally) diagnosed with SIBO – methane predominant and took the antibiotics Rifaxamin and Neomycin which was not successful in eliminating the SIBO but, left me feeling terrible. I had already previously eliminated gluten with some relief, which was then backed by tests, put myself on a low Fodmap/Paleo diet and, while managing, had researched enough to know there was a puzzle piece missing. Just to interject here that I am on specialist #3 and, have already seen two nutritionists. Specialist #3 had no further treatments to offer than a second round of antibiotics and, although I mentioned the possibility of herbal treatments, she said that type of treatment was not in her brief. I had listened to a Chris Kresser podcast about SIBO and a new herbal treatment, Atrantil and decided to order it while researching a new, Functionally trained nutritionist. Started the Atrantil and found nutritionist who said she had been using Atrantil in her practise for a year with success. Have completed a 30 day course and am now on maintenance dose and quite certain that this has made the progress that will lead to recovery.

  • Denise

    I have a question on the cleansing wave actions between meals and snacks. What is generally recognized as a good spacing to have between meals/snacks? Does drinking water or other beverages prevent the cleansing wave actions from occurring between meals? I have to take medication several times per day – does taking a pill prevent the cleansing wave actions from occurring?

  • Megan

    Hi Kate,
    Thanks for another informative post! I have a couple questions for you… Do you think eating disorders could be a cause of SIBO? I had SIBO and disordered eating. I am eating much more now, but I am still afraid that the SIBO will come back. I am not following low FODMAP because I don’t want to restrict any foods right now. However, I am still adamant about meal spacing because I feel like I am still at risk for developing SIBO again. I just wasn’t sure if this was really necessary if I am able to remove the main cause of the SIBO (reduced motility from the eating disorder). Also, many eating disorder recovery plans recommend eating often, which is the opposite of this. I’m just a little confused as to what would be best to do right now.
    Sorry for the long question!

    • Ashley


      I am in the same boat as you. Just wanted to let you know that you are not alone. And to be honest, it’s refreshing to know I’m not the only one either. I was diagnosed with SIBO around 5 years ago and because of the SIBO and IBS, I eventually developed an eating disorder. Some of it was because of fear of eating foods that would “harm” me, but then it turned into something much worse. I lost 40 pounds and I’ve been working on my recovery ever since (for the last 5 to 6 years now). It’s been hard journey, especially with gaining weight. Anyways, just wanted to say I feel for you.

    • katescarlata

      Hi Megan, there is a definitely an overlap btw eating disorders and GI distress, I wrote an article geared toward dietitians on this topic: http://www.todaysdietitian.com/newarchives/100614p14.shtml
      Eating disorders can be life threatening–so gear your therapies toward recovery first. Work with your health professional to provide a meal plan that works for both disorders, as possible. It is possible that you could eat multiple times/day–but with spacing (3 hour spacing) rather than grazing.

  • Beth

    Hi Kate, I enjoyed this post, so informative and practical. I was wondering if you have used unflavored elemental formulas, and if so, have a favorite low FODMAP flavoring for this. Thanks again.

  • Christine

    Hi Kate,
    Thank you for all of your information on SIBO- so very helpful and a great resource! I’ve had some trouble finding GI docs in my area that are well-versed in SIBO. I’ve been struggling for 4+ years now and have had a difficult time figuring out WHY it keeps returning. Do you have a list of GI doctors in your area/on the East coast that you recommend? Would be very much appreciated!

    • katescarlata

      I don’t have a list of GI specialists well versed in SIBO–though this seems like a great idea! Unfortunately, I would say most GI docs are not well versed in SIBO–and it is frustrating to me!

  • Gia Jelinek

    Hi Kate,
    I am wondering if you know the answer to this. If SIBO is a buildup of bacteria, then how will I know if a fodmap type is a problem without waiting for the buildup again. How long will the buildup take? And then I would have to start all over again with the antibiotics. I know you are not a doctor, and I will be speaking to mine after finishing the antibiotics. But the wondering about how it works is driving me crazy. I haven’t been able to find anything on it. I agree with your last comment though about the doctors. They just put you on Prilosec which can stop working and causes other problems. I am also waiting to get approval from healthcare to be covered for an RD.

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