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Why Diet Alone Is Not Enough to Treat SIBO

by Kelsey Kinney, RD

Last updated on

SIBO diet

If you’re using a low-FODMAP diet to keep your small intestinal bacterial overgrowth (SIBO) under control, you’re not alone.

However, diet on its own does not cure SIBO. In fact, eating a higher-FODMAP diet in combination with your antibiotic protocol leads to more successful eradication of the bacteria.

Can you get relief for your symptoms by following a SIBO diet? While diet is an important part of healing your gut, it’s not enough to really treat the condition. Check out this article to find out what works for SIBO.

What Is a SIBO Diet?

Are you dealing with SIBO? If so, you may be looking for a way to treat the condition without antibiotics. In most cases, that means adopting a SIBO diet that limits your carbohydrate intake and removes carbs that are difficult for your body to digest or absorb. Some common SIBO dietary protocols are:

  • Low-FODMAP diet
  • Specific carbohydrate diet (SCD)
  • Gut and Psychology Syndrome (GAPS) diet
  • Elemental diet
  • Low fermentation potential (FP) diet
  • Low-starch or even no-starch diet

While these specific diets differ from each other, their general goal is similar: limiting the types of carbs you consume to avoid feeding the bacterial overgrowth in your small intestine that’s driving your SIBO. The low-FODMAP diet, for example, limits FODMAPs, or short-chain carbohydrates that aren’t completely absorbed in the gastrointestinal tracts. FODMAPs can linger in the gut and feed bacteria, resulting in a variety of digestive symptoms.

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What Is Considered the Best Diet for SIBO—And What’s the Problem with It?

The low-FODMAP diet is a common choice for SIBO (and other digestive disorders like irritable bowel syndrome). This diet has been shown to provide at least short-term relief by reducing bacterial overgrowth in the small intestine. (1)

If you’ve tried a low-FODMAP diet for SIBO and noticed significant improvements in your symptoms, it’s easy to think that this must be the answer—a low-FODMAP (or low-carb) diet has cured you!

Unfortunately, this is not the case. A low-FODMAP (or low-carbohydrate) diet will keep symptoms under control simply by starving the bacteria in your small intestine. When these bacteria don’t have food to eat, they aren’t able to metabolize that food, and produce gas as a result. This gas is what causes the common symptoms of SIBO—bloating, abdominal pain, diarrhea (in the case of hydrogen gas), and constipation (in the case of methane gas). (2)

But starving the bacteria over the short term does not eradicate the bacteria, which is what we’re trying to accomplish, as the small intestine is not supposed to contain much bacteria. If you continue this restriction for a long period of time in an effort to kill the bacteria, you’re also starving the bacteria in your large intestine that should be there and that play a vital role in your health.

Simply put, a low-FODMAP or low-carb diet does not eradicate an overgrowth in the small intestine in a short period of time, and continuing on a long-term low-FODMAP/low-carbohydrate diet in an effort to starve the bacteria to death has potential detrimental effects on the bacteria in the large intestine. I have had clients who have been on long-term low-FODMAP diets before working with me who still have positive breath tests for SIBO despite their restricted diet. There is a difference between controlling symptoms and actually clearing the bacteria. We want to do the latter, which has the added benefit of improving symptoms, as well.

What Is SIBO?

The large intestine contains the majority of the digestive system’s bacteria. The small intestine is typically relatively sterile (compared to the large intestine), so when bacteria translocates and overgrows in the small intestine, it causes problems. If there are changes in the number or type of bacteria present in the small intestine, SIBO occurs. For many people, this is caused by an overgrowth of a variety of bacteria that should be in the colon. (3)

SIBO impacts the structure of the small intestine and its ability to function. The condition often causes damage to the mucosa lining the small intestine, which can impair nutrient absorption and lead to leaky gut—a condition where protein molecules can pass through the intestinal barrier into the bloodstream, causing an inflammatory response.

Symptoms of SIBO

SIBO doesn’t always cause symptoms (some studies suggest that up to 15 percent of healthy people are experiencing SIBO without any symptoms). (4) However, some of the most common signs of SIBO include:

  • Diarrhea
  • Constipation
  • Abdominal pain and discomfort
  • Bloating
  • Gas and belching
  • Weight loss and vitamin deficiencies (in severe cases)

SIBO is, unfortunately, an under-diagnosed condition. Many people aren’t aware that SIBO could be causing their symptoms, and many doctors don’t realize how common this condition really is. Some of the most commonly used testing methods (breath tests) have some issues with accuracy. All those factors play a role in making SIBO difficult to diagnose and treat.

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The Negative Impact of a Long-Term Low-FODMAP Diet

There have been limited studies on the long-term impact of low-FODMAP diets on microbial balance in the large intestine. The studies that show the impact of short-term FODMAP restriction on the microbiome, however, do not bode well for the long-term implications.

FODMAPs are fermentable carbohydrates that help to feed the beneficial bacteria in the large intestine. When you begin to think about them this way, it becomes a lot easier to understand why adhering to a diet low in the substrates that our healthy gut bacteria thrive on may not be a great idea.

Indeed, the studies to date on the effects of FODMAP restriction show exactly what we would imagine would happen when restricting these beneficial substrates: the overall amount of bacteria was decreased (by 47 percent in this study), along with a decline in bacteria that produce butyrate (a beneficial substance made when probiotics feed on fermentable fibers). (5) While this particular study did not show a decrease in the probiotic strain Bifidobacteria, another study has. (6) In my clinical experience, it is very common to see low levels of both the Bifidobacteria and Lactobacillus strains in my client’s stool tests if they’ve been on long-term low-FODMAP diets.

While these bacteria would likely thrive once again with the addition of prebiotic substances, staying in a chronically diet-induced altered microbiological state is likely not a healthy choice when you start to think about the importance of our microbiome and its effect on our health.

Clearly, more research needs to be done in this area if patients are going to be on long-term low-FODMAP diets. However, after reading this article, it is my hope that you won’t need to be on a long-term low-FODMAP diet to keep your symptoms under control.

What to Use as an Effective SIBO Treatment

So, if you’re not treating your SIBO with diet, what is used to treat it?


Rifaximin is the most commonly used antibiotic for the treatment of SIBO, and has been shown to be safe and well-tolerated. (7) Figures vary on its efficacy (with rates as high as 87 percent in one study), but on average, it is about 50 percent effective. (8) However, this may not take into account the necessary difference in treatment for those with methane-positive SIBO. A study on those with methane-positive SIBO shows that when rifaximin is combined with another antibiotic, neomycin, it is about 85 percent effective. (9) If you’re getting tested for SIBO, make sure you’re getting tested for both methane and hydrogen. These tests will guide your practitioner in treating you more effectively.

Herbal Antimicrobials

Herbal antimicrobials have been shown to be at least as effective as rifaximin, and about 57 percent of those who fail on rifaximin will succeed on herbal antimicrobials. (10) I have personally seen this the other way around, as well; those who fail on herbal antimicrobials usually do well with rifaximin. Others may need to do multiple rounds of either herbal or pharmaceutical antibiotics to clear the overgrowth.

Whether you choose herbal or pharmaceutical antibiotics, the important thing is that you are using something that will eradicate the bacteria instead of covering up the symptoms with diet change. You’re getting to the root cause of your symptoms!

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Diet during and after SIBO Treatment

Now that you’re being treated with herbal or pharmaceutical antibiotics, what should you eat?

If you listened to Chris’s podcast with Dr. Pimentel, you’ll know that having happy and fed bacteria is a good thing when treating SIBO—this is not the time to starve them, as they will “hide” and become more difficult to eradicate. Eating FODMAPs and carbohydrates is exactly what you want to do!

Your Diet during SIBO Treatment

In my own practice, I recommend that clients undergoing treatment eat as many FODMAP foods as they can tolerate and that they do not go on a low-carb diet. (I like to see a minimum of 100 grams of carbohydrates daily, and more, if tolerated.)

I also will typically add some kind of prebiotic if the client can tolerate it. A study that compared rifaximin alone versus rifaximin treatment plus partially hydrolyzed guar gum supplementation showed that providing fermentable carbohydrate along with the antibiotic improved success rates from about 62 percent (rifaximin alone) to 87 percent (rifaximin plus guar gum). (11)

Of course, I don’t want my clients to be miserable with digestive symptoms during this time, so treatment is always personalized to each client. Some may have no problems whatsoever eating FODMAPs or high-carbohydrate foods, while others may be very sensitive. I encourage clients to eat the maximum amount that they are comfortable with and remind them that, in the end, feeding these bacteria is a good thing. They may experience some uncomfortable symptoms like bloating or gas during this time, but as long as it does not interrupt their life or cause pain, the more FODMAPs or carbohydrates they can eat, the better.

Your Diet after SIBO Treatment

As many sufferers of SIBO know, SIBO has a high rate of recurrence, which begs the question: what should you eat after treatment to prevent another overgrowth? In my eyes, that’s the million-dollar question right now, and it’s a question we don’t have the answer to quite yet.

For now, I have my clients eat whatever they can tolerate on a healthy, real-food, ancestral diet. If they need to restrict FODMAPs slightly or eat rapidly digested carbohydrates to keep symptoms under control, that’s okay. (However, if you can’t tolerate FODMAPs or complex carbohydrates after your treatment, you’ll definitely want to retest to make sure that you’ve completely eradicated the overgrowth in the first place.)

We’ll also investigate any potential underlying causes of their SIBO, such as:

  • Low stomach acid
  • Pancreatic enzyme insufficiency
  • Intestinal motility disorders
  • Poor diet
  • Stress

I know from speaking with Chris that he has come to believe that SIBO—and especially recurring SIBO—is often a symptom of a deeper problem. The solution in that case isn’t just to keep treating the SIBO, but to address that root cause.

There’s a lot we still don’t know about SIBO. As we learn more, some of these protocols may change, but I hope this article has given you a better idea of what you should do to heal from SIBO with the knowledge we have now.

Additional Resources on SIBO:

Kelsey Marksteiner
Kelsey Kinney, RD

Kelsey Kinney, RD, is devoted to helping the world achieve great digestive health through her blog, private practice, and prebiotic & probiotic drink mix company Gut Power Drinks. Check out her blog, Gut Power Drinks website, or visit her on Facebook for more.

Kelsey is a registered dietitian specializing in digestive and hormonal health. She graduated from New York University with a Bachelor of Science degree in Nutrition and Dietetics and went on to complete her dietetic internship at Milford Regional Medical Center in Milford, Massachusetts. She also has a Master of Science degree in Human Nutrition and Functional Medicine from the University of Western States.

Kelsey loves helping people find their unique, personalized diet that will help them heal, not anyone else. She has always been interested in nutrition and health, and is honored to now help people find a diet that brings them happiness and longevity.

Professional website: https://kelseykinney.com

Gut Power Drinks website: https://gutpowerdrinks.com

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    • Personally, I don’t like to see someone on a strict low FODMAP (meaning they’re cutting out all classes of FODMAPs) for more than a few months (if they even need to do that). I always try to keep it as un-restricted as possible; even if they need to cut out one or two classes of FODMAPs, they’re still eating others.

  1. Wow, what an incredible and timely article! I was diagnosed with SIBO 6 months ago and have found a combination of low FODMAP and SCD diet helpful in managing symptoms. But, I was extremely miserable on such a restrictive diet and the moment I deviated from it my symptoms would return so I agree that it isn’t a cure – but rather just a way to manage symptoms.

    I didn’t know walking 60 minutes a day helps SIBO symptoms. Does jogging/running havd the same effect? Apologies if it sounds silly but just want to clarify if it’s just walking or other exercise which can help too?

    I’m based in the UK and under the care of a functional medicine practitioner but she cannot prescribe antibiotics. Are there any practitioners you can recommend in the UK who understand the points you have made in this article? E.g. carbs are actually required along with antibiotics

    Many thanks!


    • I have been dealing with these issues for years and no matter what other situations may be in play at any given time, my daily 25 minute walk makes a profound difference.

      A couple years ago I had the privilege of attending the first SIBO conference at the Naturopathic College of Natural Medicine which featured Dr. Mark Pimentel and Dr. Allison Siebecker (along with Dr.Leonard Weinstock and Dr Steven Sandberg-Lewis). They repeatedly emphasized that the fundamental component of SIBO is poor gastrointestinal motility which both results from the bacterial presence and in turn enables those bugs to keep hanging around. (which comes first, the cause or the effect and which is which?!)

      Where the healthy human digestive tract has about eleven complete peristaltic cleansing waves per day, the SIBO experiencer—with methanogens present—has only three!

      Digestive systems have made use of locomotion to aid in its motility since before there was life on dry land and we are not exceptions to that. But extended running and jogging are too hard on internal organs (shaking and jostling) to be recommended by me; they also seem to require too many costume changes. With walking though, I can just head out and am half done before I even start thinking about it. I am lucky enough to have a hill that I include in my route. Also.. six or seven days a week!

      • Hey Peter,

        Seems like you learned a lot about SIBO, I see to have some issues with a liver detox and a sluggish gall bladder/ low bile acid. Do you think that this may be a cause for my recurrence of SIBO? (I tried Candibactin AR/BR & Rifaximin and it came back)

        I have both methane & hydrogen, I don’t have too much bloating, and no mild constipation i.e. I have 1 bowel movement a day (not sure if that qualifies as constipation) ? .. would love to hear your thoughts!?

    • Ash, Any body movement helps because it increases intestinal mobility + gets blood/ oxygen moving well to all parts of body. So, jogging would help too. What matters is what kind of activity motivates You to get moving daily. It doesn’t have to be the same thing each day. I like to swim, but paying for a gym membership + the time to & from the gym is a negative for me, but maybe not for someone else. I like walking (or jogging on dirt, not hard pavement) because I put on my shoes & I’m good to go. You can also ride a bike, & don’t forget to lift weights now & then (I think any aerobic exercise is more effective for SIBO, but everyone should fit in some strength training). : )

  2. Thank you for the very helpful article, Kelsey. Could you tell me which herbal antibiotics you recommend to your patients for SIBO (hydrogen gas type)? After having problems for almost two years I’ve now developed a histamine intolerance. All symptoms go away when I supplement with bio available quercetin. But I’d like to deal with the original problem which I suspect is SIBO.

  3. Thank you so much for sharing updated information on the subject. I have one question: has there been done any research on how long one can safely be on herbal antimicrobials? What could be possible side-effects of being on herbal antimicrobials (f.ex. oregano) for a long time? Thanks a lot in advance, Best Regards.

  4. 100 carbs a day, eaten at least 5x a day (20g each time) would even out your BG levels. Just dont inhale all 100g at once and eat protein with the carbs. And take some time to get back up to 100g daily. A few weeks.
    If youve just started the very lowcarb WOE tho, I d still do it for 6-12 mos to heal lots of disorders caused by the out of control BG so your body can handle the additional carbs eventually.

  5. hello
    very good article . after experience with different diets a have found that gaps diet is the best for me .

  6. Great article, lots of good information. Thanks. For the post treatment diet, Dr Siebecker recommends low fodmap/SCD for a year after treatment. Do you think that seems overly restrictive? Also can you recommend an herbal over-the-counter prokinetic agent? All of the one Siebecker recommends are by prescription. Does exercise improve the condition of the migrating motor complex?

  7. Kelsey, have you checked into Turmeric? I have been having a lot of improvement taking this 2x per day. I have tried the probiotics, diet, antibiotics, low fodmap, etc. This has given me the most improvement.

  8. Thank you Kelsey!
    I have tested positive multiple times for SIBO (high methane and hydrogen), and at first we tried CandiBactin AR/BR then Rifaximin with no luck. After organic acids testing it appears I am having a really sluggish liver/gall bladder, and serious need for Glutathione. I am curious would this be a reason why my SIBO would have come back? …

    Now that I am addressing the liver/gall bladder issues, I am keen to try kicking the SIBO again, this time with Uva-Ursi, Plant Tannins, Berberine , and maybe Oregano oil.


    • I got rid of my SIBO with a month on Oregano oil, Berberine, Allacine and Neem leaf oil twice a day. I then started using Iberogoast and Betaine HFC and Pepsin while following the Fast Tract Diet.

  9. You folks gather and translate great research.

    Please, more research on what fixes or upregulates both peristalsis and the migrating motor complex, as well as how to diagnose a vagal nerve problem.

    Give us hardcore SIBO sufferers who’ve tried it all some daily exercises, some things that address the mechanical aspect of this disorder, besides what to eat, what not to eat, how much and more supplements. It’s a merry-go-round.

    • Listen to Chris’ interview with Dr. Pimentel. They talk about the new test for antibodies to the bacterial toxin thought to be responsible for the damage to the migrating motor complex. I think it’s commercially available as IBSChek but I could be wrong about that.

    • The best test to diagnose a vagus nerve problem would likely be the R-R interval study. I have yet to find a doctor to perform one, but Dr. Richard K. Bernstein also recommends searching for tests for cardiac autonomic neuropathy.

      His recommendation is in regards to diagnosing gastroparesis, an almost guaranteed complication of longstanding, uncontrolled diabetes. I suspect this is what caused my case of SIBO.

  10. I have had Sibo on and off for years. When I get a bad gut infection. It goes and kills my nerves and I have no phase 3 movement. Dr. Pimentel says it will come back in 10 years, but the chance you will get a bug in 10 years is high!? for me the only way I could remain healthy enough to think of solutions (brain fog and abdominal pain) was to be on a SCD/lower FODMap diet (Dr. Seibecker has a good handout) In most cases a whole foods diet isn’t completely FODMAP free. That was my case. I found some that I tolerated. What brought me out of the pit of propetual Sibo demise? Taking care of negative emotions in my life. And they rack up even faster when you are sick. Finding the genetic nutrient deficiency problems and supplementing. And getting a handle on a prokenetic. I used ginger EO and 5-HTP. Lately I have been using this special water to flush out the years of toxic build up from a total body system breakdown and 7 years to figure out what it is. Praise the Lord I am coming out of this Health Pit. Thanks for this article. The fast people can get this information the faster they will feel better. I had to become a Nutrial Theropist to solve my problems, because no one wanted to be better more then me. ? and it is such a new field that it is hard to find information. Blessings all and don’t give up!

    • What is the special water? I am doing a major detox and would appreciate! Also, what are the best herbal microbials

  11. Hi and thank you for the article. Trying to figure out what to do for SIBO and Crohn’s has been extremely difficult. Currently in a flare. Was on the scd diet for way too long. These articles helped me switch to a low fodmap diet just recently. Great to have carbs again. My system is very fragile. This flare has me reacting to everything. My functional doctor has recommended me taking monolaurin, cytistatin and cat’s claw drops. These are to kill off H. Pylori and SIBO. Also taking prescript assist. What are pro kinetics? Will these supplements help that I am to take? My breath tests results say I have a mild overgrowth. I have low stomach acid. And am more constipated than having diarrhea. Was hoping to start protocol not in a flare, but can’t seem to get out of it. Been in it about 4 months. Any suggestions would help. Thank you so much.

  12. After 4 months of rotating herbal antibiotics and a very restricted diet with little improvement, I am now feeling like I’ve wasted so much time and money.

    Yes, my extremely low-FODMAP diet controlled my symptoms quite well, but I also had no energy at all. When I started trying to add a few FODMAPS back my symptoms came back with a vengeance.

    I feel like I am starting over again, and am feeling pretty defeated. I am miserable when I eat those fermentable starches, but I also know I cannot sustain the restricted diet for the rest of my life.

    I’m so grateful to my doctor, and to everyone who is doing research that relates to SIBO. I realize that information is still limited at this point and treatments are still somewhat experimental. Thank you for this article!

  13. Just purchased the book by Dr. Mullin- have not read it but just from the gist of it- he does eliminate FODMAPS but it appears t be in phases that he integrates foods back in. How does this differ from your point of view and experience?

  14. I’ve tested positive for SIBO, including increased methane production. I’ve been on lo carb diet and lo FODMAP to control symptoms.
    Can you say more about the natural antimicrobial protocols…especially timing…when and what to take (I’ve been taking Oregano Oil (2 caps) and Nattokinase (200mcg) to break-up biofilms once per day, a few hours after my evening meal, and Interphase soil bacteria (2 caps) in the morning with my am meal. I’ve been eating a small amount of carbs to feed the bacteria, (carrots, sweet potato, winter squash) at every meal. My symptoms are under control, but I don’t know if I’m timing my protocols correctly. Do you think my present protocol is sufficient to eliminate the SIBO? Can you direct me to more information on how/when to use the antimicrobials and soil probiotics? –thanks!

  15. Kelsey, I know this is a problem for me and I am wondering, in a small, rather isolated town, how I find medical assistance or make progress without it? The naturopaths I’ve seen here haven’t had exposure to SIBO and current treatments. Any suggestions?

    • There are lots of great practitioners that help people online! If you need an antibiotic though, that’s where it can get tricky because of course someone needs to prescribe that to you and that is only done in person. Check out primaldocs.com

  16. How do you feel about the use of Atrantil for SIBO? (atrantil .com) Was recommend by my GI Dr. Thx.

  17. I’d suggest a 30 day dose (3 capsules/2 x per day / x30 days) of a probiotic that contains Saccharomyces boulardii and Lactobacillus reuteri……..anything that has acidolphilus would be best to avoid (I know…..they “all” have that….acidolphilus is only needed in children up to 2 years old and can be detrimental to the descending colon in adults)….also PREbiotics are needed (eg inulin/ guar gum/ glucomannan)
    FLORASTOR from CVS has the S.boulardii, but only that. The best ( and only) source I know of with all the above ingredients is called IMMUNO-SYNBIOTIC. References for the above statements can be found at NUTRI-SPEC.NET.
    I’ll be glad to share what I know if contavted
    Dr Z [email protected]

      • How is that working Ashley? what diet are you doing?

        I am thinking of adding those, as well as plant tannins, and oregano oil. 4 day rotations of each, so that the bacteria do not become resistant.

    • I would also like to know this! What type of herbal / natural treatment protocol do you recommend?

    • Yes! Please answer this! I am soooooo reticent to use antibiotics because the are what got me into the problem in the first place! I am trying to cure my SIBO using no pharmaceuticals.