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Can a Short-Term Elemental Diet Help Treat SIBO?

by Kelsey Kinney, RD

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elemental diet for sibo, elemental diet
SIBO symptoms can be debilitating. The elemental diet may provide relief. istock.com/Heiko119

For those with small intestinal bacterial overgrowth (SIBO), the symptoms can sometimes be unbearable. Bloating, gas, diarrhea, constipation…the list goes on. While simply getting diagnosed in the first place is half the battle, when it is diagnosed, how do we treat it? If you’ve tried some of the options out there like rifaximin or herbal antimicrobials with no luck, what’s left?

What Is SIBO?

Before we talk about treatment options, it’s important to know exactly what SIBO is. Small intestinal bacterial overgrowth is exactly what it sounds like – an overgrowth of bacteria in the small intestine.

Normally, the small intestine has very little bacteria compared to the large intestine, which houses most of our gut bacteria. However, bacteria from the large intestine can translocate to the small intestine under some circumstances, leading to the development of SIBO.

There are many underlying factors that relate to this translocation, including low stomach acid, pancreatic enzyme insufficiency, and intestinal motility disorders, among others. (1)

The usual treatment of SIBO can include diets like the Specific Carbohydrate Diet (SCD) or the GAPS diet (usually in combination with a low-FODMAP approach), antibiotics or herbal antimicrobials. (2) The SCD and GAPS diets help reduce the bacterial load of SIBO, but it can take a long time for dieters to feel significant improvement in their symptoms without the addition of other helpful treatments such as antibiotics or antimicrobials.

Rifaximin, the the antibiotic most commonly used to treat SIBO, is expensive, thus many patients cannot afford treatment. These patients may choose to forgo antibiotics completely and opt for natural antimicrobials such as oregano oil or berberine. These can be very useful in eradicating SIBO, especially in combination with a low-FODMAP SCD or GAPS diet.

However, I’ve had more than one client claim that they can’t tolerate the herbal antimicrobials. For these people, waiting months to over a year for relief with the SCD or GAPS diet can seem like eternity, yet they feel as though they don’t have any other options to try. Others have tried antibiotics or antimicrobials and failed. This is where the short-term elemental formula can be helpful.

What Is an Elemental Formula?

In the simplest terms, an elemental formula is one that contains pre-digested carbohydrates, proteins, and fats. This means that it is absorbed very quickly from the digestive system.

This is key for those with SIBO as we don’t want food sitting in the small intestine, where it would be used as fuel for the unwanted bacteria living there. Instead, an elemental formula provides a way to nourish the patient while starving the bacteria. When implementing the elemental diet, the patient will drink the formula instead of their regular meals for two to three weeks, depending on their case.

How Effective Is It?

In a study using the elemental formula Vivonex Plus, patients were instructed to consume only the formula for 14 days. On the 15th day, they were re-tested for the presence of SIBO. Remarkably, 80% tested negative. Those who were still SIBO-positive were instructed to continue the formula for another 7 days, after which the cure rate went up to 85%. (3)

So how does this compare to the other SIBO treatments I discussed above (rifaximin, herbal antimicrobials)? Though figures vary for the efficacy of rifaximin, the majority of studies I’ve seen estimate it to be around 50% effective, but some studies show even lower rates. (4) One study in particular showed the cure rate for rifaximin to be 34%, while herbal antimicrobials were more effective at 46%. (5)

An 85% cure rate for a three week elemental formula diet is impressive and should certainly be considered as a treatment option for those with SIBO. However, that doesn’t mean that it’s for everyone.

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What Are the Drawbacks?

There are definitely some downsides to the elemental formula. First, and probably most important in terms of compliance – it tastes pretty nasty. A patient has to be willing to stick it out for at least two weeks (where we get the 80% cure rate) and potentially up to 3 three weeks to see results. While this doesn’t sound that long, it can  be tough to stick to when the drink doesn’t taste so good! This means that anyone about to try this treatment has to be very committed.

Second, typical elemental formulas are not what we’d call “real food”. Vivonex, produced by Nestle, contains the following ingredients:

Screen Shot 2014-07-14 at 5.34.12 PM

That said, you can make your own elemental formula if you choose. If you’re interested to see what goes into a homemade formula, check out this recipe from SIBO researcher, Dr. Allison Siebecker. Both homemade and commercial elemental formulas are expensive (though less expensive for most than a course of rifaximin), which is also a barrier.

Also, for those who are underweight already, embarking on a two to three week elemental diet can cause them to lose even more weight. This is potentially dangerous, thus an elemental diet should be very carefully implemented or not implemented at all in those who are underweight. Whether you’re underweight or not, an elemental diet should always be implemented under the supervision of a medical professional.

An elemental diet is also a short-term fix. SIBO is a condition that recurs frequently, thus during and after any type of treatment for SIBO, it’s imperative that the patient addresses these underlying factors to prevent future SIBO episodes. This means that those looking to an elemental diet to solve their problem forever still have a long road ahead of them after completing the diet.

Lastly, we’re not sure how it affects the rest of our gut bacteria. Does it starve the bacteria in the large intestine? If so, to what extent? We just don’t know, and only future research can tell us.

Chris’s Experience

I asked Chris to share his experience with elemental formulas with me for this article. He responded:

“I created my own elemental formula, back when I was still struggling with my own gut issues. While it did reduce bacterial overgrowth, it seemed to exacerbate the fungal overgrowth problem I was also dealing with. I developed a thick, white coating on my tongue and the symptoms I associated with fungal overgrowth worsened. I also experimented with it in my work with patients with SIBO early on, but I found that compliance was low (because even the homemade formulas are pretty gross) and the SIBO tended to return soon after the patient started eating real food again. Nevertheless, elemental diets may have a place for patients that don’t respond to anti-microbial treatments (whether botanical or pharmaceutical).”

When to Consider an Elemental Formula

There certainly are benefits to an elemental formula, namely its short duration (2-3 weeks). This is equal or one week longer than a course of rifaximin (14 days), and potentially up to four weeks shorter than a course of herbal antimicrobials, which are usually given for 4 to 6 weeks. Its effectiveness is also quite good (80-85%) compared to other treatment options. It might be worth considering for someone who doesn’t want to take antibiotics but wants a short treatment period, or for someone who has tried antibiotics and herbal antimicrobials and failed. It certainly wouldn’t be my first choice of treatment if I was going through it (mostly due to the taste and lack of real food), but if I had trouble with some of the other options, I’d certainly consider it. It’s a careful decision that one should make with their medical team and not something to take lightly, but its 80-85% cure rate deserves a look. Hopefully reading this article has made you think about the pros and cons of an elemental diet and allows you to make this decision more easily!

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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. Reading about the elemental diet treatment reminded me that I have met inflammatory bowel patients who were on a study where they consumed ‘ensure’ type formulas as their only source of nutrients. Surprisingly they were able to be compliant. I found that amazing in itself.

  2. Would a juice feast work to solve sibo and yeast overgrowth? (veggie juices, little or no fruit)? Perhaps supplements with Thorne Mediclear plus, aloe, and probiotics, systemic enzymes, and oregano and cats claw? That’s a plan I’m considering

    Another thing that keep in mind is hcl levels, and also a sluggish or faulty motor complex. So, addressing adrenals and thyroid can help too, as well as b12/d

  3. I once inadvertently did a VERY thorough gut microbe cleansing when I inadvisedly swallowed a whole garlic clove like a pill. Near as I could tell from the results afterward, I killed off all my gut flora. My bowel movements were just some nasty liquid, not even really diarrhea. I didn’t start getting normal/solid feces again until I started taking some probiotics. So I have been leery about eating garlic ever since! I still eat it, but try not to overdo it.

  4. I have that white coating on my tongue that Chris described. So maybe my problem is fungal, and I am hoping you will also do a write-up on symptoms, mechanisms, and treatments for fungal issues.

  5. I’m wondering if you’ve ever used calcium bentonite clay to treat SIBO. I’ve had gut issues ever since I had Cushing’s syndrome and afterward took steroids and statins for about 6 years. I have been drinking hydrated clay four times a day on an empty stomach for about a month now and have experienced a great improvement. In particular, most of my bowel movements are normal, and my intolerances to most all foods have disappeared. Would be interested in your reaction to this therapy.

    • Nutrients have to be predigested so I would say no. Having things predigested insures that your body will absorb them quickly and leave nothing for the bacteria to feed on.

  6. How do u know u have it? As I suffer from intestional bloating on left side of intestines! Just started higher doses og probiatics.

  7. I’ve done the elemental diet multiple times.

    I actually have an article from pubmed where they tested gut flora levels each day someone was on an elemental diet.

    In summary, it appears to affect Lactobacillus spp. after one week, but other levels in the colon were not statistically significant.

    Maybe if it was longer, one would see a big change, but 2-3 weeks may not be long enough to have this effect.

    Thanks for the article

    • Andy,

      Could you please post the link to this article… just curious about how they obtained samples of the flora from the small GI each day? That is not easy to do. I would love to present this to my GI doc.


      • The name of the article is ” Effects on an Elemental Diet on the Faecal Flora in Patients with Crohn’s Disease”

        it should be easy to find

  8. Monolaurin works well, I think the issue with tolerance to herbal antimicrobials is the “die-off” or Herxheimer reactions. I have seen practitioners manage this with things like activated charcoal, proteolytic enzymes, reduced glutathione, testing for MTHFR mutations, general liver/biliary support

    • Hi Alex,

      Could you elaborate more on the MTHFR mutations please and how it relates to SIBO treatment? I have Factor 5 leiden, and SIBO, and not once have doctors said those relate. Curious about your thoughts?


  9. My 10 year old daughter has SIBO (my diagnosis). It has been extraordinarily difficult to get any information about SIBO in children and testing is virtually impossible. Per Chris’s advice, we started her Prescript Assist in addition to a FODMAP/Paleo diet. In less than a month she had significantly improved. Now, about 5 months later, she has the bowel function of a normal child. However, it can still be a challenge to maintain a FODMAP/Paleo diet with a 10 year old. I can’t even imagine trying to get her to follow an elemental diet. I wish more discussion would focus on kids with SIBO. My guess is there are many parents with SIBO kids who have no idea what to do with them. My daughter is from China, so we tried a lactose free diet, an auto-immune protocol, and strict Paleo. Nothing helped her at all until we combined FODMAP and Paleo.

    • Risa,

      Did your daughter work directly with Chris? I have a 9 year old with SIBO and feel the same frustration with lack of guidance for children. Perhaps we should start a Facebook support group?

    • Hi Risa,

      I have been diagnosed with SIBO and my 5 year old son. We both took Xifaxan b/c we have been doing Paleo for 5 years and not getting better. He did allergy testing recently and is allergic to many of things. Although allergy tests can yield funky results, we knew they were accurate b/c his mouth and throat swell and GI starts getting super upset after eating certain foods. He has eosinophilia and allergies to nuts, dairy, gluten, oats, peanuts, corn, soy shellfish, citrus EGGS (that one is super hard to give up since Paleo’s reliance on it for most foods) That said, have some allergy testing done. If your daughter’s gut is super inflamed by things such as nightshades, or eggs, Paleo diet can be a nightmare. So we are on GAPS diets and see more success with strict diet over anything else.

      My son did fine on Xifaxan and we were very happy to see improvement but his allergies will persist until gut is healed. (For me it is a longer road.) His pediatric GI doc also has him drink oregano tea (literally oregano steeped in water) This is a new territory for GI docs and I have been working very hard with them to get things right. (we see docs at Stanford who actually seem very open to alternative healing)

      I did the elemental diet for two days… that was enough and I was super super committed to do it… however i just vomited it up and really sick. Not the best solution in my experience. Probably not a good idea for little ones.

      I still struggle with SIBO daily and it is just a chronic dysfunction until the root of the issue is better understood. I don’t think doctors or other healers have a handle on this issue so until then, you are your best doctor when you listen to your body.


      • Hi Andrea. Can u email me please ASAP about sibo and symptoms. I’m looking for someone to talk to and share my experience with

  10. Can the elemental diet be helpful if you dedicate a few days a week to it and then eat “clean” foods other days.. grass fed protein, organic greens etc. Maybe even doing this in combo with herbal anti-parasitic supplements or to try to prepare the gut before or after an anti-parasitic regimen?

    Or even do a few days a week when trying to heal a leaky gut?

  11. As you mention, http://www.siboinfo.com is a great resource, full of detailed information and references.

    Listening to many functional medical practitioners, they talk a lot about stool testing, and the prevalence of false negatives. It doesn’t seem like many of them use the lactulose breath test, which might be more reliable in detecting the bugs in the small intestine that often don’t get into the stool samples.

    At this point, I am using betaine HCl and digestive enzymes to try to overfeed myself, and get my weight up before trying some combination of elemental diet, SCD, and possibly even fasting. Getting tested should probably be part of the plan.

  12. Good summary of a complicated subject matter!

    Wondering if you have experience with using both Rifaximin and elemental diet at the same time? Or would that be too much? Or do one first and then follow up with the other treatment: ie. Rifax first for 2 weeks then elemental protocol for 2-3 weeks.

    Thanks Kelsey!

    • I don’t have experience with that (not a doc, so don’t deal with prescriptions!) but my guess it it would be a bit overkill. I’d go for rifaximin first if that’s what you wanted to try.

    • If I remember correctly, according to Dr. Pimentel antibiotics work best, while the bacteria is still feeding, meaning that you have to eat real food, and that also means no SCD diets while on treatment.

    • In his book, Pimental says that the Rifax only works on bacteria that are replicating (ie eating/thiving) so doing the elemental diet at the same time is contraindicated.

  13. Surprised to see such low figures for the effectiveness of the antibiotic approach – Siebecker (whom you mention in your post) touts a success rate of 80-94% for different antibiotic regimens.

    I noticed this since I’m currently taking rifaximin for exactly this reason, having already tried the elemental diet. The diet was effective but made me too sick to continue for the full 2 weeks.

    • Perhaps she’s referring to her own success rates in her practice (which includes dietary changes as well), while studies that study just rifaximin treatments (no dietary changes) may have lower rates. Not sure, but that’d be my guess.

    • Shouldn’t we all be extermely careful about becoming resisitant to antibiotics except where they are essential for lifesaving conditions?

    • Dr Siebecker is probably refering to the studies by Dr Pimentel, which I’m pretty sure he gets such rates, because they always adjust for methane producers, meaning that they give rifaximin+neomycin. Which significantly increases succes rates, in people who produce methane gas. Rifaximin does not work for methane.

  14. I know some people get constipated after this kind of treatment. Also, I believe it is possible for SIBO to be so high up in the intestine that it could still feed it. And you did not mention those with insulin problems. One would consume huge ammounts of starch, and that doesn’t sound too good. I’m also struggling because I can’t tolerate herbals… That’s a huge problem….

  15. Just reading the first line of the ingredients of Vivonex is enough to turn me off, and make me angry. I was considering purchasing lysine in supplement form, and yesterday discovered that most chemically made supplements at the health store that I was at were derived from corn. Not GMO-free, or pesticide free.
    And from Nestle, a company we can all trust!? RIGHT.
    First they create the problem, then they get rich off their garbage solution, and create a whole new raft of problems.
    I am exploring Functional medicine solutions, but now wonder about vested interests.

    • Wow, thanks for this reminder! Are capsules also likely to contain corn? is it the filler or the actual active ingredient. Did you find some clean lysine? I have been using NOW (brand).

      • Penelope, There were 4 or five different brands at my local store, and all were derived from corn. Lysine is in lots of different foods, so that’s probably where I’ll get mine.
        This whole temporary fix, instead of determining cause and eliminating all possible triggers is just another rabbit hole ( to get lost in).
        Are we 100% sure that it’s bacteria? What about viruses?

  16. In attempt to save money would it be possible to do some sort of protein restricted fast with protein shakes? That way maybe you can save yourself some dollars by only buying maybe one or even two supplements to mix into your concoction. Just wondering if this would be feasible as long as the protein had a minimal amount of crap in it and assuming you don’t have an allergy to it i.e. whey protein.

    • I’m doing the elemental and could NOT hang with the vomit flavor of the amino acids, and I’m a body builder so I wanted to preserve muscle mass and I have higher protein requirements than the average person. So what I’ve decided to do is reduce the amount of aminos to half what I was using (reduces cost too) and added plain pea protein powder (tastes like cardboard). Makes the aminos a tad less disgusting to and the protein is fast digesting and doesn’t cause me any problems or irritation. I don’t know what others would have to say about this but it’s working for me.

      • Hi Shasta,
        Checking to see how you are doing. Did you finish the elemental diet? Any details you could share is appreciated!

        • YES! With great success! I’m still on a supplement for motility, addressing a hormone imbalance and taking some iodine and selenium for the thyroid. My belly fat is melting off as a result of this!!! I found the book Fast Track Digestion IBS with an eating plan for SIBO that has been hugely successful, most of the other diets (FODMAP, etc) aren’t quite right for SIBO but this one goes by the fermentation potential of various foods and rates them. So far it’s working for me very, very well and allows for more variety in the diet. My belly is flat for the first time in over two years, and inflammation and water retention are down to a human level. I’m back to bodybuilding and feeling better than I have in a very, very, very long time. Plan to do everything in my power to prevent this from relapsing but so far I can eat gluten free white bread, certain types of rice, certain fruits, and red potatoes (among other assumed “forbidden” carbohydrates) with no issues….amounts have to be watched but it made no sense to me that traditional SIBO diets eliminated carbs to the degree they did. The depression of thinking I wouldn’t be able to bodybuild was overwhelming….you HAVE to take in carbs to bodybuild!! So I’m overjoyed that I can make this work since this is my passion. I’m also still taking a small amount of herbals once a day that I’m rotating just in case I still have some bad bacteria in there. I refuse to let this become a problem again!!! And I really do recommend that book, if anyone is interested the website is
          There are links to the book, but I got a used copy off amazon.com for $8…..if you have amazon prime you can “borrow” an e-copy at no charge to see how you like it first. This diet approach makes WAY more sense than the other popular SIBO diet approaches for sure. There are two different books, the IBS version of the book is the one you want for SIBO problems, it sort of encompasses IBS as a whole and the various conditions that cause IBS. There is also a small section that addresses athletes and their need for carbs so I have to say, this book literally brought tears to my eyes when I found it! Happy, happy, happy girl here!

          I stayed on the elemental diet for a full four weeks and also addressed my leaky gut syndrome at the same time. So far I can eat eggs with no problems at all. I’m not really willing to test the water with other foods that were causing problems but I have a hunch that I healed up a ton of damage in there on the elemental diet! I rotated my herbals every four days so that the bad bacteria wouldn’t be able to adapt. I also religiously took a biofilm disruptor about 15-30 min prior to taking any herbals, and I also used medical grade manuka honey to help kill off bacteria (this stuff kills the MRSA virus, people! Use it to your advantage! I took it 15-30 min after the biofilm disruptor and would just take 1-2 teaspoons. But order off amazon and get a higher medical grade and read up on the stuff! It’s astounding in it’s capacity to heal and also kill infection!)

          Will my SIBO come back? I don’t know. But I am hopeful that I have this beat and that my current approach will prevent relapse.

          • So what was your recipe for elemental diet, I also do bodybuilding and had exact same idea to take protein isolate instead of amino acids. Did you used simple sugars? I am so curious how are you now. Thanks!!

          • Hi,

            Also curious how you are doing? I’m on day 6 of the elemental diet and looking for inspiration.

            • Zack2 – HANG IN THERE!! It is TOTALLY WORTH YOUR EFFORT!! You can do it!

              I just finished 10 days of the Elemental Diet. I did the homemade version (21 free form aminos, honey, MCT coconut oil, mineral salt).

              I had intended to go the full 21 days, but ended up having a huge detox reaction (rash, fever) on day 10 and had to stop. I reintroduced food by starting with bone broth (chicken, no vegetable or spices in the broth). I was really glad to have something savory instead of sweet. The excessive sugar was a lot for my system to handle. Had I not gotten the herx, I would have stayed on for the full 21 days. I felt good on the diet. No bloat, no pain, no brain fog. It was quite a blessing!

              My tactics for the diet varied. I would mix the 2 tablespoons of aminos with a small amount of water, stir it well and shoot it down, then chase it with water. Separately, I would mix the honey, oil, salt. Sometimes I would add food grade orange or mint essential oils, or vanilla extract to the sweet oily mixture. Other times I would put dextrose, oil, and vanilla in the blender and make a liquid drink out of it. I also used different kinds of honey – whipped vs. liquid, and liquid MCT oil vs. dense coconut oil. I tried to keep it interesting and enjoyable.

              Honestly, I never thought I’d want to go back to the diet after being off it or eat honey again… though I don’t feel that way now at all. It’s been a week since I stopped the Elemental Diet and since then I’ve had a few meals of just the amino acid powder. My body really likes it, and the break from food feels good to my system.

              In the past week I’ve been sensible about what food to eat. I use the SIBO app to track which foods are supportive to my system or otherwise. I also bought an autoimmune paleo cookbook (which has been difficult to [literally] stomach, after being vegan for over a decade).

              I now eat smaller meals and don’t snack. I also feel WAY better if I go to bed on a relatively empty stomach.

              Supplements: 3 colostrum when I wake up and 3 some other time during the day on an empty stomach; 2 Nutrient 950 with NAC three times a day with meals; 3 cal-mag-zinc a bedtime. I also have both MTHFR mutations, so I take supplements for those.

              I am still free from boating and I have multiple BMs throughout the day. These were two major problems for me (massive bloating and severe constipation) before the Elemental Diet.

              If I were to do the diet again – and it is very likely I will because my system seems to like intermittent fasting, I might use bone broth instead of the honey.

              • I’m also still on Xifaxan and Flagyl. My methane numbers were off the chart for the last three breath tests I did.

                I think the key to ridding myself of SIBO is multifactorial and will take effort. I don’t mind these things, but they will require lifestyle changes on multiple levels.

                Including but not limited to:
                1) Daily exercise to raise heart rate and body temperature, as well as build muscle for increased metabolism
                2) Reduction in stress of all types – whatever that means to you. For me, I have to reduce the number of hours I work, which folds into changing the way I live and spend money. These are difficult changes, but it’s my choice. I’m O-V-E-R feeling sick. I’ve had enough.
                3) Choosing the better feeling thoughts regarding what I’m focusing on in life/day/work/relationships. Again, this is a mindset shift.
                4) More meditation for reducing cortisol.
                5) More time in the sun. I know I need more sun on my skin. I have to make this a priority.
                6) Mindful eating. Box breathing or 5 slow breaths before I eat food. This gives the brain a chance to start making digestive enzymes and for digestion to come online.

                _For ME_, SIBO isn’t only a bacteria that’s camped out where it’s not supposed to be. It is a physical indicator that I need to make changes in my life. This may or may not be the case for you. _For ME_, my physical symptoms are not isolated from my mental, spiritual, and emotional state.

                I am an investigative methods scientist by formal training and higher education. I do best when there’s logical reasoning behind what I’m doing – this includes matters of my own health.

  17. The “it’s temporary” part is nestled in there like an afterthought. How long does it last before symptoms come back?

  18. I’ve used the AbsorbPlus Elemental Diet shakes to address my IBD before I found the Autoimmune Paleo Protocol. These shakes have a very clean ingredient list and are also pretty tasty. You can add in MCT oil for extra nutrients/calories, too. The book “The IBD Remission Diet” by Jini Patel Thompson has helpful info about a healthier elemental diet.