Why Diet Alone Is Not Enough to Treat SIBO and What More Can Be Done

Why Diet Alone Is Not Enough to Treat SIBO


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If you’re using a low-FODMAP diet to keep your 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.

sibo diet
Eating a nutrient-dense SIBO diet is a good start. istock.com/Brzozowska

Are you dealing with SIBO? If so, you’ve probably tried a low-FODMAP diet and noticed significant improvements in your symptoms. Once you’ve noticed such an improvement, 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) (1).  

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.

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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/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 prior to 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.

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 we have showing 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.

Is your SIBO diet controlling your symptoms or actually clearing the bacteria? #sibo

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% in this study), along with a decline in bacteria that produce butyrate (a beneficial substance made when probiotics feed on fermentable fibers) (2). While this particular study did not show a decrease in the probiotic strain bifidobacteria, another study has (3). 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.

Treating SIBO

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

Rifaximin is the most commonly used antibiotic for treatment of SIBO and has been shown to be safe and well-tolerated (4). Figures vary on its efficacy (with rates as high as 87% in one study), but on average it is about 50% effective (5). 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% effective (6). 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 have been shown to be at least as effective as rifaximin, and about 57% of those who fail on rifaximin will succeed on herbal antimicrobials (7). 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!

Healing from digestive disorders can be a long and difficult process. Many people with these disorders get frustrated with doctors who don’t understand the problem, solutions that don’t work, and chronic discomfort. Where can people with this experience turn for answers? Functional Medicine practitioners are a great option, and they can help diagnose and prescribe treatment. Health coaches are another great source of support, and they can actually be the key to unlocking improved digestive health.

ADAPT-trained health coaches have a background in Functional and ancestral health, and they understand the root causes and range of treatments for digestive disorders. Although they can’t diagnose or treat these disorders directly, health coaches can often refer clients to a trusted Functional Medicine practitioner, help clients understand a diagnosis or follow a treatment plan, and support clients in dealing with the frustration that comes with digestive disorders.

Want to know more about digestive disorders and what you can do to help people overcome them? Learn about the ADAPT Health Coach Training Program.

Diet during SIBO Treatment

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

If you listened to Chris’ recent 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 be starving them, as they will “hide” and become more difficult to eradicate. Eating FODMAPs and carbohydrates is exactly what you want to be doing!

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% (rifaximin alone) to 87% (rifaximin plus guar gum) (8).

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 is not interrupting their life or causing pain, the more FODMAPs or carbohydrates they can eat, the better.

Diet After SIBO Treatment

As many SIBO sufferers know, SIBO has a high rate of recurrence, which begs the question: what should you be eating 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, and so on. 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 be doing to heal from SIBO with the knowledge we have now.

Now I want to hear from you: What has been your experience with SIBO?

Kelsey MarksteinerThis is a guest post written by Kelsey Marksteiner, RD. Kelsey is a Registered Dietitian with a Bachelors degree in Nutrition from NYU and a Master’s in Human Nutrition and Functional Medicine. She works in private practice and recommends individualized dietary therapy focusing on biologically appropriate diet principles to aid her clients in losing weight, gaining energy, and pursuing continued health. She is a firm believer that everyone is different, and she tailors her plan for each and every individual. Through her work, she aims to meld the dietary wisdom of traditional cultures with the latest science in integrative and functional medicine to create plans for her clients that work in the modern world. You can learn more about Kelsey on her staff bio page, or by visiting her private practice website. Join her newsletter here!


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?

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