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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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Join the conversation

  1. Oh God! Please! No! Not coffee enemas. My God, that’s right out of the 1950s, with ALL current research showing they likely do more harm than good. Same with colonics! Barbaric, AND a reason NOT to have a colonoscopy. All of this can just remove the last feeble remnants of GOOD bacteria along with the bad. SIBO is an “upstream” illness, and that’s where you should treat it. Liver support–NOT detox–is imperative, but not this absurdity from old, outdated pre-genetic-discovery research and Victorian superstition!

  2. My doctor wants me to eat a low FODMAPS diet while taking Rifaximin? I thought you shouldn’t do that because then the bacteria go into hiding and it’s harder for the antibiotic to kill them. I would appreciate any advice.

    • Elizabeth, Do Not eat a Low FODMAP diet on Rifaximin (Xifaxan). You are right; the bacteria go into hiding, are harder to kill. Do start Low FODMAP diet After you finish Rifaximin. This info comes from The primary M.D. involved w/ SIBO treatment, Mark Pimentel (Gastroenterologist). Read Here: kresserinstitute.com/RHR: SIBO Update – An Interview With Dr. Mark Pimentel. *They also discuss that you should take partially hydrolyzed guar gum while on Rifaximin to help kill the bad bacteria. I’m not sure of the dose/ frequency, so if it isn’t stated in the link I gave you, you can look up the study they talk about.

  3. Here is How to get off of antacids & proton pump inhibitors (like Prilosec & Nexium): Buy Jarrow D-Limonene (Orange oil) capsules from Amazon or a health food store. (Not expensive). Take 1 capsule every a.m. for 20 days. *During this 20 days, do Not eliminate your antacid “routine”. After 20 days on the D-Limonene, you Then stop the antacids. I know, the thought of stopping antacids can be scary. Be assured, this works. There are 60 capsules of D- Limonene in the bottle, so take one if/ when you get breakthrough heartburn. This regimen works for ~ 5-6 months. If heartburn starts to come back, start the 20 day regimen again. *If you take acid reducers, You can’t properly digest your food or absorb the nutrients from food or supplements. Another helpful item for constipation And problems sleeping is “Natural Calm”, which is ionic magnesium citrate: 2 Tsp. w/ water before bed, tastes great, no carbs. When having SIBO symptoms, these help me: Oregano oil capsule (510 mg.), Black Cohosh root capsule for abdominal cramping (540 mg.), & 2 Peppermint oil gels (stated as total of .4 mL/ 362 mg.). You can do this 3 X day.
    The foremost expert on SIBO is Dr. Allison Siebecker (same 1st name, not me). Definitely google/ visit her website! Much of what I have learned is from her & C. Kresser’s sites & Lots of research. Also, remember to Drink plenty of liquid (When bloated, regular sipping helps “fit” the water. Move your body, even walking around the house @ a good pace if you can’t be far from a bathroom. We all know these last 2, but forget/ don’t feel like it when in SIBO mode. Make yourself do it anyway, to help gut peristalsis… I hope this helps any of you. <3

  4. Hi – how do you treat impaired intestinal motility? I’m guessing you treat lie stomach acid with HCL….

  5. My husband was out on a SIBo diet with no mushrooms or probiotic foods such as sauerkraut or yoghurt. I do not understand the relationship here. Is this not counter productive or am I missing something? Very grateful for insight. Michelle (Ba HSc (Nut. Med)).

    • Hi Michele,
      I’m no expert, and I ended up not having SIBO, though I have been interested in gut health for a few years so it’s on my radar…I think with SIBO bacteria that is in the large intestine, like beneficial bacterias, as well as bad ones, have entered the small intestine, where there isn’t meant to be any at all, which ais the issue, and the idea is to starve or eradicate (such as with antibiotics and hebal remedies). It’s meant to be very difficult.

  6. Hi, all with SIBO symptoms should check out Atrantil developed recently by Dr Ken Brown, a Gastro. I have read 100’s of reviews on that website plus Amazon and listened to podcasts he has done with several functional Dr’s (including Chris Kresser) Many, many have found quick relief. i have learned so much through his podcasts and am now following several Dr’s podcasts that are so enlightening. Good luck to all!

    • I checked out this product, “Atrantil ” and found it to be not only pricey, but you have to take 2-3 tablets before each meal daily. It would cost approx. $180.00-200.00 per month once you start. I wish the cost was not so high, but thanks for sharing.

        • It’s not a cure. It relieves symptoms. I’ve met this Gastro by chance at a restaurant recently here in Dallas. He was very interesting to talk to.

  7. Hi guys, I know this forum is a little bit old but I’ve just got a few things to ask! Im 16 years old and about 7 months ago I started to get really badly constipated, bloated and I just felt rotten. I had some food allergies, my glands are constantly swollen and I am depressed and have anxiety. I eat a really poor diet and I think this is why it could be SIBO. I also have symptoms of b12 deficiency which I know canned caused by sibo. My doctor isn’t much help and he just says stop worrying it’s just ibs and anxiety. But I’m not happy with that. I think it could be sibo. It started after I ate a lot of junk food for birthdays in September, and I still feel pretty much the same now. My question is, is there an underlying cause do you think? Or just to do with my diet that I eat? I eat so much sugar and carbs and hardly any healthy foods….. I don’t think it’s crohns or something because I haven’t had any blood. I’m just worried because I’m 16 and this shouldn’t be happening to me. I know it’s my fault for eating poorly, but I just want it to go……. ?☹️

    • Hi bud!
      Sorry to hear that you feel so unwell. If you can, please try another doctor- and get a thorough assessment, just in case. Also, maybe a dietician, esp. one who deals with allergies and intolerances. Coeliacs has a relationship to b12, I think. Have a look at the Monash Uni FODMAPS APP, which is like $10, heaps of info, and gives a guide to a 2 week diet trial to see if your intolerant to FODMAPS, after which you can see a dietitian, or if you can’t afford it, there is heaps of good info online. Magnesium will help you to go, lots of water, soft foods like fruit and veggies, fibre, pscyillium husks. Terrible it got this far but you will feel better with time. It’s not your fault this modern society encourages us to eat so much junk.
      Good luck!

      • Hi there, so do you not think that it’s methane sibo then? I’m not sure wether it’s SIBO or candida or what. So do my symptoms sound more like candida?

        • Hi Dylan. It’s hard to tell which type of SIBO it is. I do know however that a large percentage of IBS patients have SIBO. I’m not saying that you do, but you might have it as well. Anxiety has also been linked to iBS. Can you get a doctor to run a SIBO test?