SIBO: The Definitive Guide

This Is Educational Content

Before we get started with this definitive guide to SIBO, I need to clarify that science isn’t perfect. What is understood to be “definitive” today, may be turned on its head with advances in research tomorrow. At Autoimmune Wellness we are always striving for a grounding in science, but that also means a willingness to accept cutting-edge information that may contradict previous information. Scientific truth is a process of continual refinement, not a dogmatic position. From that standpoint, read this guide for educational purposes only. SIBO is one of the most quickly advancing areas of health science right now and much that we know is likely to change.

What Is SIBO?

SIBO is an acronym for Small Intestine Bacterial Overgrowth. Normally, the small intestine is almost sterile, only populated by select bacteria in very small numbers. SIBO occurs when there is an increase in the number of bacteria and/or changes in the types of bacteria. In the majority of SIBO cases this overgrowth is caused by bacteria that should be in the large intestine, not from the select bacteria normally present in the small intestine.

The overgrown bacteria “eat” sugars, via fermentation, found in certain foods we consume. The fermentation produces gases, like hydrogen and methane, and it is those gases that create the uncomfortable symptoms of the SIBO sufferer. More of the effect of these gases later.

With that said, it’s important to note here that what we currently understand to be SIBO is changing. What seems to be emerging is a more sophisticated interpretation that is about more than just numbers. It’s about strains of bacteria, how they function, and how they interact with each other and us as humans. And this definition leaves out SIFO, which refers to fungal overgrowths. In the future what we now define as SIBO may be broken down into many different conditions based on the kinds of bacteria, archaea, and/or fungi present. (For more depth on this check out Chris Kresser’s podcasts with Dr. Mark Pimentel, a leading SIBO research, or this article by Lucy Mailing.)

What Are the Symptoms?

Folks with SIBO may not know it’s SIBO, but all of them could easily tell you all the ways it’s making them feel awful. The symptoms of SIBO are hard to ignore and include:

  • Abdominal pain and cramping
  • Bloating (which can severely distend the abdomen)
  • Diarrhea, constipation, or both
  • Flatulence
  • Belching
  • Nausea
  • Weight loss and nutrient deficiencies (in severe cases)

What Causes SIBO?

The causes of SIBO are complex and can be different from one person to the next. A healthy digestive system requires a highly acidic environment in the stomach to break down food and act as a first-line defense against pathogenic bacteria, a complex signaling system to properly move food along and sweep the small intestine almost clean of bacteria, and a correctly functioning valve (the ileocecal valve) between the small and large intestines to keep the billions of bacteria that belong in the large intestine from entering the small intestine. SIBO occurs when something goes wrong with this healthy functioning.

For example, it’s now well known that a bout of food poisoning caused by a bacteria species like Campylobacter, can result in an autoimmune reaction which damages the nerves in the gut, especially those in the small intestine. This nerve damage changes the natural wave movement of the muscles in the digestive tract, called the migrating motor complex or MMC, responsible for the necessary cleansing action. The leftover food and bacteria in the small intestine are then ripe for SIBO to occur, because there is now a motility disorder (in other words, the MMC is broken).

Other examples of damaged nerves or muscles impacting the MMC and potentially leading to SIBO are autoimmune diseases, like Type 1 diabetes or celiac. A person could also have physical changes to the digestive tract, like scars and adhesions caused by surgery or autoimmune diseases like Crohn’s. These physical changes can allow bacteria to build-up inappropriately in the small intestine.

Back to pathogenic bacteria, like Campylobacter, that can tip off an autoimmune response… if stomach acid is adequate, it can help defend against such an “invader” in the first place. There are medications that can decrease acid levels, like acid-blockers or proton pump inhibitors (like Prevacid or Pepcid), and that lets bacteria in that shouldn’t be there, potentially leading to SIBO. It’s also true that without proper acid levels being reached, the signals for the next steps in the digestive process will be off, which could lead to improperly digested food that the bacteria can thrive on. This article on understanding the digestive process explains this is greater detail. (It should be noted that Dr. Pimentel’s research might be contradicting this, check out this podcast.) Other medications that disrupt the normal flora of the gut, like antibiotics or steroids, can also lead to bacterial overgrowth. There is even speculation that there may be a possible link between birth control pills and SIBO.

Finally, there is diet itself. A diet that is high in sugar, refined carbohydrates, and alcohol (even moderate consumption can feed specific bacterial strains causing overgrowth) not only leads to damage in the small intestine, but it can set the stage for SIBO to take hold.

What Are the Risk Factors For SIBO?

Based on the information shared so far, many readers are probably starting to draw some conclusions on what puts a person at risk for developing SIBO. If you’ve had or experienced any of the following, plus have any of the above-mentioned symptoms, it might be appropriate for you to pursue testing and treatment:

  • Structural issues of the digestive tract (diverticulosis, inflammatory bowel disease, gastric bypass surgery, or other GI surgeries, especially any that resulted in removal of the ileocecal valve or gall bladder, scarring or adhesions)
  • Medication use that impacts the digestive tract (narcotics or any others that slow motility, PPIs, H2 blockers, antibiotics, birth control pills)
  • Autoimmune diseases that impact motility or cause digestive tract damage (diabetes, long-standing celiac disease, lupus, scleroderma, Crohn’s, ulcerative colitis, Hashimoto’s, endometriosis of the bowel, etc.)
  • Lowered immune system function (HIV, immunoglobulin A deficiency, etc.)
  • A history of eating disorders
  • An IBS diagnosis (up to 60% of IBS cases are actually SIBO)
  • Hypochlorhydria (low stomach acid, caused by H. pylori infection or other reasons)
  • Food poisoning (there is an especially clear link with food poisoning in a developing country setting, but it can also happen in more developed countries)
  • Organ system dysfunction/disease (like liver cirrhosis, pancreatitis, or kidney failure)

How Is SIBO Diagnosed?

Like SIBO itself, the testing methods for determining if SIBO is present are definitely being debated, researched, and refined at this time. Diagnosis is tricky and can be frustrating, but hopefully knowing about these approaches will help you in advocating with your healthcare provider.

Sampling and Culturing

The gold standard is taking a sample from the small intestine via endoscopy and culturing it in a lab. However, this is an invasive, expensive process, and there is some doubt that culturing is effective, because many bacteria species that live in our guts are difficult to culture.

Breath Testing

Even though sampling and culturing is the gold standard, a more favored method is breath testing, especially because it is relatively easy on a patient and cheap. Breath testing measures the gases produced by the overgrown bacteria, gases humans do not produce, that have circulated into the blood and are being exhaled via the lungs. The test can be done at home with a kit or at a clinic with a breath testing machine. A patient follows a specific diet for about 24-hours, then fastest for about 12-hours prior to the test, and then drinks a sugary solution, either of lactulose or glucose. The bacteria ferment the sugar (as described above) and the person exhales the gases into a baggy or machine over three hours. The kind of gas produced, how much of it, and at what points is graphed and this is interpreted to determine SIBO diagnosis. However, like sampling and culturing, there is increasing doubt, for a number of reasons, as to the accuracy of this testing method.

Stool Testing

Another option for diagnosis is PCR-based stool testing. PCR is an acronym for polymerase chain reaction and very simplistically is a process of magnifying DNA found in the stool to understand what bacteria, in what numbers, may be present there. In the past I often heard at conferences that stool testing was not reliable, since it is more a reflection of the large intestine’s microbiome, than the small intestine, but there are practitioners who use it to reach SIBO diagnosis.

Blood Testing

As you know now from the “Causes” section, not all SIBO is the result of food poisoning, but in cases where that is suspected, the IBS blood test may be helpful. It measures antibodies that are created in the resulting autoimmune process from the food poisoning. The development of this test is amazing and happened during the time since I first started following and learning about SIBO, but the limits are that it doesn’t apply to every situation.

Intraluminal Gas Testing

Lucy Mailing, a PhD/MD candidate and researcher at the University of Illinois, recently wrote about what may be the future of SIBO diagnosis, intraluminal gas sampling. Intraluminal means inside the intestine. Up until now researchers and physicians likely new that the most accurate way to measure gases was to get samples from inside the intestine, but there was no way to realistically achieve that. However, a company in Australia has developed and is currently testing a capsule that can be swallowed and provides gas measurements as it makes its way through the GI tract.

Observe and Experiment

Mailing points out in the same article that because all of the diagnosis options currently available have the potential for inaccuracy, treating a patient based on their signs and symptoms and waiting to see if the issue responds to the treatments might be the best option. She is not alone in this idea. Over the years working with many, many clients who seemed to have SIBO, I learned to guide them in discussions with their doctors requesting treatment on symptoms alone. A majority of doctors were open to this with my clients, including very well-known practitioners, and it often led to resolution of the problem or enough improvement to clarify that SIBO was likely, helping the doctors further experiment in helping my clients.

Gases Explained

Before getting into treatment of SIBO, it’s important to dive a little deeper into the “gas” aspect of SIBO. Understanding it thoroughly is crucial to understanding potential treatments.

As stated previously, in SIBO the overgrown bacteria in the small intestine “eat” sugars, via fermentation, found in certain foods we consume. The fermentation produces gases, like hydrogen and methane, and it is those gases that create the uncomfortable symptoms of the SIBO sufferer.


Sometimes the bacteria that have overgrown produce hydrogen gas. Large amounts of hydrogen shouldn’t exist in our digestive systems, especially in the small intestine. The hydrogen leads to diarrhea by increasing motility. Some of these same bacteria producing hydrogen can also produce serotonin, a neurotransmitter, that further speeds up motility. A patient with Hydrogen-Dominant SIBO may even be acutely aware of this when they do a breath test, as the sugary solution they drink may cause them to immediately have severe diarrhea.


You may have noticed that in the describing SIBO earlier, I used the word archaea. Archaea are different from bacteria, but can also become overgrown in the small intestine, where they produce methane by eating hydrogen! The major pre-dominant methane producing organism in humans is called Methanobrevibacter smithii or M. smithii. The methane it produces leads to constipation by decreasing motility. A patient with Methane-Dominant SIBO, might also experience more bloating.

Hydrogen Sulfide

There is a third gas, hydrogen sulfide, but I won’t go far into it here. In attending three conferences, reading extensively, and listening to tons of podcasts on SIBO, I’ve never felt that there is any clear or actionable information about the role it plays, if any, in SIBO.

How Is SIBO Treated?

Finally, we can move into the piece I’m sure most of you are curious about, the treatment of SIBO. Like everything else related to SIBO there are lots of thoughts about what may be best here, and the guidance is changing all the time. Use this information as a way to have an informed discussion with your healthcare provider, not as “gospel” about how to eradicate SIBO.


The organisms producing hydrogen and methane are different, so the medications used to treat them are also different. In the case of Hydrogen-Dominant SIBO, an antibiotic called Rifaximin (also called Xifaxan), which seems to be mostly non-absorbable, meaning it stays in intestines and doesn’t cause system wide damage, is used. Methane-Dominant SIBO is harder to treat, because there are not specific drugs developed to deal with M. smithii. In this case it’s usually best to combine Rifaximin with another antibiotic, either Neomycin or Metronidazole.

Herbal Antibiotics

There are many herbs that have antibiotic properties and have been proven effective. Dr. Alison Siebecker, a leading naturopathic doctor in the SIBO field, lists some of the following as useful in her practice:

  • peppermint oil
  • allicin (derived from garlic)
  • oregano
  • berberine
  • neem
  • cinnamon

This is not an exhaustive list of potential herbal antibiotics or herbal blends that can be used.


One of the big issues with SIBO is that the automatic cleansing wave motion, the MMC, is often damaged in some way. Every 90 minutes while we are not eating, especially overnight, the muscles should be contracting and releasing in a way that sweeps the small intestine clean. When this doesn’t occur properly, SIBO can take hold. Restoring that movement through prokinetic (pro-movement) medications can help treat SIBO. The following are some pharmaceutical and natural options commonly used:

  • Low-dose Naltrexone (LDN)
  • Low-dose Erythromycin (this is an antibiotic, but it is given at such a low dose when used as a prokinetic it does not have an antibiotic effect)
  • Prucalopride (Resolor/Resotran)
  • Iberogast
  • Ginger Root


There are many different kinds of diets used by conventional and natural doctors in treating SIBO, but the very big and important thing to know is that DIET ALONE WILL NOT TREAT SIBO. In fact, you can actually worsen dysbiosis (more explained below) by using dietary treatment methods for too long, as it can starve the microbiome. I have had at least two clients who accidentally did this to themselves and ended up with a very narrow range of foods they could tolerate and increased health issues.

Why is diet useful in SIBO if it is not effective in eradicating it? Diet is useful, because it addresses two main problems that occur in SIBO. The first is that bacteria feed on and then ferment the sugars found in carbohydrates. These sugars are monosaccharides (one sugar), disaccharides (two sugars), oligosaccharides (3-10 sugars), and polysaccharides (10+ sugars). The second, like we’ve explored in this guide, is that this fermentation process leads to the gas production that causes uncomfortable symptoms in the patient. Bloating, distention, pain from muscles contracting against the gas (the intestines are sensitive to pressure), burping and farting from the gas exiting, and GERD and nausea which is caused by gas back pressure or reverse motility in some methane-dominant cases, are the result.

Fiber, a non-starch oligiosaccharide or polysaccharide, is indigestible by humans. However, bacteria have enzymes that can break the bonds. Fiber is a prebiotic that can feed bacteria (both our good and bad bacteria). Fiber is in all plant food, therefore ANY SIBO diet has to allow for some compromise in order to allow for proper nutrition and also our psychological well-being.

The current approach suggests the best thing to do is not restrict the diet during antibiotic treatment. Basically, well-fed, happy bacteria come out to play where they can easily be targeted by the antibiotic. A SIBO patient should eat as many carbohydrate-rich foods as they can comfortably tolerate.

Following treatment, utilizing a Low-FODMAP diet with a lot of experimentation for a limited time can be helpful. FODMAP is an acronym that describes the sugars I mentioned above, “fermentable oligo-, di-, mono-saccharides and polyols.” Each individual will have to use guidance on FODMAP levels in different foods to discover what works best for them. The most accurate and extensive guidance on FODMAPs is available through the Monash University app built by researchers in Australia. If you are combining dietary approaches in your SIBO treatment (for instance, AIP + Low-FODMAP), I strongly suggest hiring a health coach, nutritionist, etc. to help guide you in order to best avoid over-restriction.

One last important point about diet, is that a patient should be working toward at least four hours between meals, not snacking all day. This is to address the cleansing wave issue that is so important to proper SIBO treatment. Every time we eat, the migrating motor complex stops (remember it happens every 90 minutes while not eating), so that we don’t push food along our GI tract too quickly, leaving no opportunity for proper digestion and nutrient absorption.

Recurrence Rate

Over my years learning about SIBO one of the most important things I learned was from a presentation given by Dr. Mark Pimentl. SIBO is notoriously recalcitrant, often requiring multiple rounds of treatments. He noted that in his clinic if he saw rapid recurrence rates, patients relapsing with SIBO symptoms within three weeks or less of finishing treatment, that was a strong indicator that there are deeper causes to be addressed, most often anatomical changes in the GI tract. If you have experienced this, it’s worth deep exploration.

Experts to Follow for Further Help

This guide is intended to be thorough, while acknowledging that the science on what we currently recognize as SIBO is shifting fast. It provides a great starting point but is by no means completely comprehensive. If you are interested in further detail, you can check out my older SIBO 8-part series here based on information from the 2014 and 2015 SIBO Symposiums (be aware that some of what is shared in those articles may be outdated). Additionally, following these leaders in the SIBO research field can be helpful in staying up-to-date on the quickly changing landscape:

Was this guide helpful? Share with us in the comments about your SIBO journey.



RHR: A New Understanding of SIBO and IBS, with Mark Pimentel [Audio blog interview]. (2019, July 3). Retrieved July 13, 2019, from

RHR: SIBO Update—an Interview with Dr. Mark Pimentel [Audio blog interview]. (2019, May 21). Retrieved July 13, 2019, from

Mailing, L. (2019, March 26). What the latest research reveals about SIBO [Web log post]. Retrieved July 13, 2019, from

Marksteiner, RD, K. (2019, June 28). Why Diet Alone Is Not Enough to Treat SIBO [Web log post]. Retrieved July 13, 2019, from

Nett, MD, A. (2016, July 5). SIBO—What Causes It and Why It’s So Hard to Treat [Web log post]. Retrieved July 13, 2019, from

Siebecker, ND, A. (n.d.). Small Intestine Bacterial Overgrowth. Retrieved July 13, 2019, from

Small Intestinal Bacterial Overgrowth (SIBO) [Web log post]. (n.d.). Retrieved July 13, 2019, from

About Angie Alt

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


  • Diana A says

    Thank you for such an informative article. My “old school” GI Dr does not acknowledge causes for GI distress that may possible, including being tested for SIBO. (I have Systemic Sclerosis with GI involvement). Taking an acid blocker was his only solution to the problem. I decided that just wasn’t enough– I needed answers to get to the root of the problem. Therein was my introduction to the AIP lifestyle.
    I have several symptoms as described above, and have been on a self educated journey to relieve my symptoms through experimentation with AIP diet and most recently low FODMAP diet. It has brought some relief and am so grateful for all the research and studies that you and Mickey have embarked on. I have most, if not all, of both of your cookbooks. I am a believer in food as medicine and how important it is to pay close attention to the subtle reactions when a food product is not tolerated, eliminating specific food products has helped my healing journey, thanks to your guides and research.
    Thank you for helping me take charge of my life again! Follower for life!

  • Amy Kaser says

    Will peppermint oil kill the good bacteria I have as well as the bad? I don’t want to do that. I’m probably pretty short in that department. Please advise.

  • Nancy says

    Thank you for all that you and Mickey do for this large and ever growing community. Your work is invaluable and very much appreciated. Thank you for writing a clear and easily understood article on something that has so much confusion around it. It is definitely helpful. God bless you.

    • Angie Alt says

      Nancy, I’m so glad this helped! It’s our pleasure & privilege to do this work & serve the community.

  • Jana says

    Hi Angie!

    Timely and great info! Love the new info you’ve shared! It’s been 2+ years since I took your SAD to AIP in Six Group class and that’s when you first suggested I had SIBO symptoms. I’m finally getting tested next month after looking for a local Functional Medicine doctor! Thanks for the continuous update. I appreciate you and Mickey so much and will gladly organize an AIP National Convention for you all one day.😊

    • Angie Alt says

      LOL! Thanks for the support, Jana. It would be awesome if we have that convention some day. And I’m so glad to hear you are doing some further investigating to help feel your best. Good luck!

  • Britta says

    Dear Angie, Thank you so much for all your work for autoimmune community. Your website (of course including Mickey) was my first „go to place“ when confronted with my autoimmune diseases. The website and cookbooks helped tremendously! I did the AIP for about a year, but some symptoms won’t go away. Your article about SIBO is great! Easy to understand and with quite some aha moments for me. I followed your advice and I‘m on the mailing list from Dr. Siebecker. She announced today a upcoming docuseries: Digestion SOS™: Rescue & Relief From IBS, SIBO, & Leaky Gut: August 13-21st 2019. „Shivan Sarna of SIBO SOS has worked for over a year on this extensive documentary series. It features yours truly and more than 60 of my colleagues.“ Maybe this could be of interest for the community.

    • Angie Alt says

      Hi Britta! So glad our resources helped you. And yes, we know all about the SIBO SOS series. In the past I’ve been part of Shivan & Dr. Siebecker’s work. We’re excited to see more come out.

  • Cyndi says

    Thanks so much for the thorough information! I have to eat AIP + Low Fodmap and I get so frustrated that I don’t seem to be able to reintroduce any foods, especially ones that are always listed as good for the microbiome. I didn’t see it in this article, but is there a connection between not being able to tolerate any fermented foods and SIBO?

    • Angie Alt says

      Hi Cyndi-
      There is a possible connection there. I’d talk to your healthcare team about proper SIBO treatment so that you do not need to remain on Low FODMAP indefinitely, as it will starve your microbiome & further add to an inability to tolerate foods.

  • Cirelo says

    Is doing the AIP diet recommended if you have untreated SIBO?
    Also, how do you recommend bringing up a topic like SIBO with your doctor when it isn’t his or her idea? I’m always reluctant to sound like I’m telling them how to do their job.

    • Angie Alt says

      You can do AIP w/ untreated SIBO, but you may find that some aspects of the AIP template worsen symptoms like bloating, since AIP has many high-FODMAP vegetables. AIP will not correct SIBO on its own. As far as bringing up SIBO w/ your doctor, explain your symptoms, tell them that you’ve done some research & are wondering if you may be dealing w/ SIBO & would like to know their thoughts about possible testing. You aren’t telling them how to do their job, you are advocating for your healthcare needs!

  • Lauren says

    Hi Angie!
    Thank you for this great article, and everything you do for the autoimmune community!
    I wanted to ask for clarification regarding Iberogast: is it AIP compliant? I know it’s in an ethanol base and that adding boiling water to a dose of tincture can burn some of that off, but are the herbs compliant? They seem unusual!

    • Angie Alt says

      Lauren, the herbs are AIP compliant, although sometimes we have to be careful about licorice as it can be immune stimulating. I think if you need Iberogast as part of SIBO treatment, the benefits outweigh any possible negative.

  • Robyn Kardos says

    hi there. do you have a menu plan that incorporates lowfodmap for SIBO treatment with your AIP?

    • Mickey Trescott says

      • Ragnhild says

        Hi! I’m considering using this link you posted here to treat my SIBO as I also feel the need to do AIP. Would you use antibiotic treatment/herbal treatment to kill the SIBO simoultaneously, or would you do that after this diet? Also, is it just these 28 days?
        Regards, Ragnhild

        • Mickey Trescott says

          Hi Ragnhild! Unfortunately I am not a medical practitioner and I can’t advise you on SIBO. My recommendation is to find someone qualified to help you with treatment. Diet alone has not been shown to be an effective treatment for SIBO. You can find a list of practitioners knowledgeable about AIP here:

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