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Probiotics Work BETTER if You Have SIBO & An Elemental Diet – Case Study

Did you know that probiotics have been shown to work better if you have SIBO? A recent study provides insight on how to use probiotics when you have SIBO.  We will also detail a case study using the elemental diet to provide relief when all other treatments had failed.

Episode Intro

Dr. Michael Ruscio, DC: Hey, everyone, welcome to Dr. Ruscio Radio. This is Dr. Ruscio. Today, I’d like to talk with you about two opposing case studies which provide, I think, a very valuable juxtaposition of when it’s necessary to do more to help someone get healthy. And then conversely, when it’s needed to do less in order to get someone healthy.

And I’m going to provide kind of a middle ground between not going into complete detail, but also not giving you a 30-second summary. And I’m hoping that I can strike a good balance here. And bear with me in case I can’t. But I’m going to try to find the right balance of detail.

[Continue reading below]

Dr. R’s Fast Facts Summary

Case Study 1

  • SIBO returned quickly after Rifaximin, non-responsive to herbal antimicrobials but responded well to 2 weeks on Elemental Diet
  • Patient previously diagnosed with pancreatic insufficiency

Chief Complaints

  • Low abdominal pain, bloating, irregular bowels, food allergies, fatigue, insomnia, anxiety, depression, irregular cycles, pain, cramping and PMS

Previous Diet

  • Gluten free, Dairy free, Egg free
  • Fasting
  • Low FODMAP with SCD

Previous Treatments

  • 2 rounds of rifaximin – helped a little
  • Herbal antimicrobials – no response


  • Aerodiagnostics lactulose SIBO breath test
  • Optional comprehensive Doctors Data stool test
  • Labcorp full GI panel + general health and wellness Labcorp test

New Protocol

Improved Symptoms

  • Abdominal pain, bloating and bowels improved some

Symptoms Without Change

  • Food allergy and reactivity, fatigue, insomnia, anxiety, depression

Lab Results

  • SIBO – high hydrogen
  • Labcorp – evidence of dysbiosis
  • Further assessment for IBS performed – motility autoimmunity

New Protocol

  • 4-6 weeks on Rx Rifaximin
  • B12 injections due to parietal cell autoantibodies
  • Pregnenolone DHEA – adrenal support
  • Limited carb reintroduction (gluten free bread, pasta, potato) and caffeine

Lab Results

  • Negative for motility autoimmunity


  • Rifaximin – no change in symptoms
  • Addition of gluten free carbs was very helpful
  • All chief complaints were improved

Protocol 2 weeks


  • Feeling great after elemental diet
  • Returned to normal foods continued to feel great
  • All symptoms improved

Protocol 1 Month

  • Maintain diet plan and add back in vitamin D with K
  • After 1 month – add back in  probiotic and enzymes to see if they are helpful
  • After 2 months – follow up and perform dietary reintroduction

Case Study 2

  • Previously diagnosed normal thyroid with Hashimoto’s
  • Previously Prescribed Blood pressure rx , T3, and anti-anxiety rx

Chief Complaints

  • Bloating, fatigue, constipation, insomnia, fatigue, cravings
  • Intolerance for fasting
  • Vaginal dryness
  • Low libido
  • Hot flashes
  • Starting to resent food


  • SIBO breath test
  • 2 stool tests
  • Health and wellness blood profile

New Protocol

  • Diet
    • Loose paleo diet
    • Only avoid foods you have noticed do not agree with you
    • Experiment with nuts, beans, legumes, gluten free grains and High FODMAP foods
  • New Supplements
    • Pregnenolone DHEA – adrenal support
    • Probiotics – 1 from each category
    • Fiber
    • Magnesium Citrate
    • Continue with Miralax when needed


  • Probiotics helped bowels
  • Fiber caused patient constipation
  • More foods made her happier

Two Studies

Probiotics work better when someone has IBS with SIBO

  • In those with IBS plus SIBO – After being given probiotics
    • 71% decrease in IBS score
    • 10% decrease in IBS score in those without SIBO

Antibiotics can be more effective in IBS with SIBO

  • Rifaximin and other antibiotics can help IBS

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In this episode…

Episode Intro … 00:39
Case Study 1 … 03:00
Case Study 2 … 18:40
Two Studies Reviewed … 25:26
Episode Wrap-up … 30:40

Case Study 1

In the December 2017 issue of the Future of Functional Medicine Review, we covered a case study entitled: SIBO that Relapsed Quickly After Rifaximin was Non-Responsive to Herbal Antimicrobials, but Responded Very Well in Two Weeks in the Elemental Diet (subscription required). Okay, so this is that case I mentioned a moment ago, where the key to success was really having to do more. In this case, escalate to the elemental diet.

Gut Health Diet

Now, this patient, her name was Kim. She’s a 36-year-old female, previously diagnosed with pancreatic insufficiency by her naturopath, on no RX – no prescriptions. And her chief complaints were lower abdominal pain, bloating, irregular bowels oscillating between constipation and diarrhea, and also food allergies.

Symptoms expressed in her paperwork but not listed as her chief complaints: fatigue, insomnia, anxiety, depression, irregular cycles, pain, cramping, and PMS.

Okay. So previous diet history: gluten-free, dairy-free, low-carb, and egg-free helps. Fasting, very helpful. Low FODMAP with SCD, very helpful. Previous treatments: Rifaximin, two times, helped slightly, but then she regressed. Herbal antibiotics or antimicrobials, no response.

Testing and Initial Recommendations

Okay. So, we follow-up a few days later and lay out our initial recommendations. We performed an Aerodiagnostics Lactulose SIBO breath test. I list an optional doctor’s data comprehensive stool with parasitology 3x stool test. Optional, because we will be performing a LabCorp full GI panel. So it can be helpful to have redundant stool testing, meaning two overlapping stool tests or parasitology investigation. Sometimes, you also test blood and urine. But with every passing few months, I’m actually doing this less and less. And I’ll illustrate this in a future podcast of one case study.

And there’s actually been a number that I’ve outlined in the Future of Functional Medicine Review clinical newsletter, wherein we didn’t need to treat the lab results. In fact, there’s been a number of cases now where after some simple dietary changes and a good probiotic protocol, by the time we get to the follow-up visit to interpret the patient’s labs, all of their symptoms are gone. Not to mention the fact that when you run two tests in tandem, they often times disagree rather than agreeing.

So for all these reasons, I am becoming more judicious with the use of testing. Because, again, the promise is that these tests will tell you exactly what’s wrong with you and exactly how to fix your gut. And I think, often times, if you understand how the gut works well enough, then you see that the promises that these tests purport are really not delivered on.

In any case, we ran a GI panel through LabCorp and also a general health and wellness lab panel through LabCorp. The initial recommendations were to follow a modified fast for two to four days. Then start on a low FODMAP plus SCD diet. And to continue to fast during the day; and she was kind of doing an intermittent fasting periodically. So I encourage her to continue with intermittent fasting and consolidating her meals to a shortened window of lunch and dinner.

I also asked her to discontinue coffee and started her on a supplement plan of vitamin D with K, a Lactobacillus-Bifidobacterium probiotic blend category one probiotic, S. boulardii, Saccharomyces boulardii category two probiotic, and also a digestive enzyme and acid formula.

Lab Interpretation and Treatment Evaluation

And I list the rationale in the full case study. I’m going to gloss over that right now. Essentially, when we follow up a number of weeks later, the modified fast—she actually could not tolerate either version. So the modified fast, you can use a bone broth or a cleansing lemonade. And this can help people from what can be kind of a stress-fatigue response, where they don’t do well on a strict fast. But in her case, she couldn’t tolerate either.

But she did do a water fast instead. And she noticed her digestion was a lot better. But she was tired and hungry, so that’s why the modified fast. But she couldn’t tolerate that. The low FODMAP with SCD diet, no surprise, was very helpful. But she also reports, it’s hard to follow. Her gut was great but she was tired. No caffeine, she commented that the withdrawal was very hard. She was fatigued. But now, she’s okay and she notices her gut feels better off coffee. And then from the initial supplement program, the probiotics, enzyme, and the vitamin D with K, she reported no change.

So overall, symptoms that were improved: Abdominal pain and bloating, she remarked were way better. And her irregular bowels were gone. So the probiotics may have actually helped with this to some extent also. But anyway, symptoms that were the same: Food allergies and reactivity, fatigue and insomnia, anxiety, and some of her female hormone-related symptoms. And her depression was actually a little bit worse. Now, part of this might be because she’s going to a more restrictive diet. And for some people, this does not go well. It may go well for their gut. But then metabolically, they may be fatigued. Or in this case, have problems with mood.

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Now looking at her labs, the SIBO breath test showed a peak hydrogen value of 179. That’s very high. LabCorp showed elevated benzoate—which is essentially a dysbiosis marker—and parietal cell antibodies. And there was a couple other abnormalities found in her blood work. But nothing I would consider overly important. But that’s all listed out in the full write up.

So my impression: Today’s finding of severe hydrogen SIBO perfectly fits her presentation. She has been diagnosed and treated for SIBO in the past. She has responded, but then relapsed, historically. So we will likely need a more comprehensive plan.

Based on this, the fact that she’s responded but then relapsed will—is, today, leading me to request an IBSDetex, which is Quest’s version of IBS check. It’s essentially an assessment for antibodies against Vinculin and CdtB antibodies to see if they’re—essentially, antibodies against motility apparatus in the gut. And this may—we haven’t really definitively documented this yet—but if someone has positivity with this test, it may predict they would be a responder to prokinetics.

So additionally, my impression: Today, she’s responded very well to low FODMAP with SCD. Coffee removal and the initial supplement plan appear to not have led to much improvement. We will start her today on four to six weeks of rifaximin. I believe her GI had already written her a script for this. B12 injections for the parietal cell autoimmunity. Pregnenolone and DHEA as an adrenal support.  And a limited carbohydrate reintroduction and a limited caffeine reintroduction. Because it seems that she needs a little bit of stimulation, whether from carbs or caffeine. And at her follow-up, we’ll determine when the appropriate time to transition her on to prokinetics, maybe.

Okay. So, that’s essentially what we did with her next. We had her continue with her previous plan. But we started her on the pregnenolone and DHEA, a little bit more carbs. My recommendation is gluten-free bread, yogurt, and other dense carbs like potatoes as you tolerate them; and also the rifaximin. And then we followed-up three weeks later.

Follow Up Assessments & Recommendations

Now, interestingly, at her follow-up three weeks later, the IBSDetex, the request was negative for motility autoimmunity. And this is one of the reasons why. And if you guys have, maybe per chance, though I might a bit critical at times, I’m not critical without due reason. And I’ve seen cases like this where she has consistently relapsed after antibiotic therapy. Yet, the mechanism that is purported to be the reason why people relapse is missing. She does not have autoimmunity against her motility apparatus.

So this is why I don’t just blindly follow some of the crazes in any niche of functional medicine because you need to have some kind of documentation. I am open. I am watching that literature regarding motility autoimmunity testing. And hoping that we can pull something out from it that’s useful, outside of just being a screening for IBD or to distinguish IBD from IBS.

But really, right now, I think we’re not quite there yet. And again, I’m happy to hear any arguments to the contrary.  I think we still have much to figure out there. But it’s for reasons like this that I’m a bit skeptical.

Okay. So her subjective assessment, now that she’s gone through some of those recommendations, will be outlined at her last visit. Well, she recently had setbacks from drinking. She had a couple of weddings, I think. And so she was drinking, maybe eating some bad food. And that had led her to regress. From the rifaximin, she felt about the same. It’s hard because you have to adjust from the fact that she was drinking and partying a little bit and eating off plan. But the rifaximin did not lead to any noticeable improvement. The addition of gluten-free bread, pasta, and carbs was very helpful. And the pregnenolone and DHEA seemed to be slightly helpful.

So improved her fatigue. And regressed her GI. Progressed back to baseline—her anxiety and depression were at baseline; and so was her sleep.

So my impression at this point is the IBSDetex was negative. I mean there’s no autoimmunity against the motility apparatus. And therefore, post-antimicrobial prokinetic therapy is likely less important. And today, we may want to consider the elemental diet. And so, essentially, we’re going to start her today on the elemental diet and follow-up at the end of her second week on the elemental diet. And decide either to extend to a third or to transition off.

So that’s essentially our recommendation, continue with the previous aspects of her program. I kept her on the probiotics. Even though she didn’t report a notable response, I know that probiotics have anti-SIBO effects. And so as long as she’s not seeing a negative reaction on the probiotics, I want to keep her on those, because probiotics are and should be combatting the SIBO that she’s currently positive for.

And let’s see here. So we had her start on the elemental diet, exclusively, for two weeks. And I believe she used the elemental heal formula.  And then, we followed-up a few weeks later.  And her subjective assessment at her follow-up, the elemental diet, 14 days of it, she reported she was feeling great.

So my impression at this point of time is Kim has responded very well to two weeks on the exclusive elemental diet. Then, when returning to normal foods, she continued to feel great. And this has persisted for over two weeks at the point of our follow-up. I’m assuming here what had happened was, we were supposed to follow-up right at the end of that two weeks. She potentially couldn’t get in quickly enough. And so she just elected to end at two weeks and then go back to normal food. And she felt that when returning to her normal diet, she felt great. All of her chief complaints were now improved. None were at baseline.

support probiotic

Okay. And today, we will have Kim first maintain the current plan of just diet. But we’ll also add back in the vitamin D with K. Then after one month, we’ll have her experiment to see if any of the previous items in the program were helpful. So she’ll add back in the probiotic, add back in the enzymes. And then finally, in two months, we’ll follow-up and have her perform a dietary reintroduction.

So essentially there, what we found was, Kim, even though she had returned to her normal diet after the elemental diet and been on that for two weeks, she had seen improvements she had never seen previously and maintained that improvement for two weeks. And I didn’t write this up in this case study, but I saw Kim a number of months later and she was still doing fantastic.

Overall Impressions

So in this case, we really needed to escalate therapy. This is the case where knowing when to do a little bit more was very helpful. And also knowing when not to, I guess, use prokinetic therapy, because it didn’t seem like prokinetics were what was needed for her, and I had the sneaking suspicion, they’re not as helpful for as many people with SIBO as you would potentially be led to believe. I do think there’s a subset of probably the most severe cases where the prokinetics are helpful. But I think for many people with, I guess, mild to moderate SIBO, then it’s not needed. And when I say ‘mild to moderate’, I don’t mean just their gas level. I just mean their presentation, their tendency toward relapsing, the underlying pathophysiology. So for the majority of cases of SIBO, I am starting to think that post-treatment prokinetic therapy is not necessarily needed.

Now, Kim was a good example of that. She didn’t have the autoimmunity. And even though she had relapsed, even though she had a history of relapsing after rifaximin, it just seemed that the missing link in her case was finding the right treatment. And you’ve probably heard me say this, which is this navigation isn’t always incredibly guided by labs. It’s sometimes just getting the right person matched up with the right treatments.

So in her case, elemental diet, that was a game changer. And she’s done fantastic and hasn’t looked back. Also, elemental dieting in conjunction with loosening up her diet, so this is kind of a hybrid, I guess, of doing more and doing less. Doing more with the elemental diet but doing less by loosening up some of her dietary restrictions.

Case Study 2

Okay. So, let’s contrast that extreme of having to go all the way to the elemental diet with another case (subscription required) where we actually did quite a bit less. So, Kim, a 57-year old female. Her previous diagnosis was euthyroid Hashimoto’s, meaning she has Hashimoto’s but her thyroid hormone levels are normal. So she is not hypothyroid. She is normal thyroid but with Hashimoto’s.

Her prescriptions included lisinopril for high blood pressure; Tirosint, which is the liquid gel tab T3; and Buspar, which is an anti-anxiety medication. Her chief complaints were constipation, bloating, fatigue, and insomnia. Other symptoms detected: Fatigue and intolerance for fasting, insomnia, cravings, vaginal dryness, low libido, and hot flashes.

So, essentially, and I’m just going to really give you a gloss over this one. But essentially, when—and this is all written up in the case study – you pick out a few key points where you see notes that she’s starting to resent food. So there’s a few times where she said, “It felt a little better on this diet, but then also felt like I was starting to resent food.” And so that language is very important to key in on. Because this can tell you when you may need to pay attention to some of these dietary and lifestyle factors.

Testing and Initial Recommendations

Now, essentially, the way this played out, we performed a SIBO breath test, two stool tests, and essentially a health and wellness blood profile at her first treatment visit. And I also recommended to her to follow a loose Paleo diet and only avoid foods you have noticed do not agree with you. Experiment with nuts, beans, legumes, gluten-free grains, and high FODMAP foods.

And here’s maybe a key point, please do not follow the results of your Cyrex food allergy test, because we’re going to work to broaden your diet. And we put her on pregnenolone/DHEA for adrenal support; three probiotics, one from each category; fiber; magnesium citrate. And had her continue with MiraLAX, which she found to be helpful when used as needed.

Follow Up Assessments & Recommendations

And essentially, what I’m thinking here is, Kim has been too restrictive with her diet and we need to start giving her some leeway. So at our follow-up, she noted that the probiotics markedly helped her bowels. The fiber might constipate her. And eating more food makes her feel happy. She was also able to decrease her Tirosint dose and felt fine. And I told her, “I don’t think you need Tirosint.” And rightfully so, or in her other provider’s defense, he was using it to try to bring down her antibodies which were historically a little bit elevated or actually quite elevated. And her remark was, overall, she feels really good. And she said, “really good”, with a huge smile on her face.

Now, looking at her labs, she was essentially SIBO negative. Her BioHealth stool test was negative. Her LabCorp profile was negative. Her reverse T3 was a little bit high. This potentially could be due to the fact that she’s taking T3 and doesn’t need T3, or could have been due to the fact that she was overly restrictive with her diet and stressed out about food at the time of this test. In any case, I don’t think the reverse T3 is something that requires any remedy further than what we’re already doing.

Overall Impressions

And essentially, what we found in this case was someone who had had somewhat chronic health complaints was—and I didn’t include all these details in the write-up, but some of them are. But she essentially had seen a number of other providers. And they kept giving her more restrictive diets and suggesting these diagnoses. And Kim was internalizing all these things.

And so, she kept dieting harder, not feeling any better. Maybe even feeling worse. Resenting food and kind of withdrawing into this lifestyle that was very restrictive. And essentially, we had her expand her diet. And told her to think about her health less and try to enjoy her life. And what do you know? When we look at her labs, really nothing came back abnormal. And when she reported in on how she was feeling after making the changes, she felt fantastic. And really, she said, “I don’t need any other improvement. I feel as good as I’ve wanted to feel.”

So the only maneuver needing to be made on her case was just getting her off of the health worry merry-go-round or black hole. Black hole might be a better description. She had clearly gone over the event horizon and was just getting sucked deeper and deeper in. And this was the case where she did not need to do anything more to feel better. She really needed to do less.

Okay. So, two differing case studies. And these things are important. And I’m really hoping for the clinicians who are listening to or reading this, you will start delving in to these case studies. Because it’s easy for me to say, “Well, this person needed to do more. That person needed to do less. This person, we didn’t have to treat their lab results.” But I think to really help clinicians be able to make the adjudication on their own, you need to see these case studies evolve in these write-ups from visit to visit to visit. So I do hope, as a clinician, you will go have a look.

Two Studies Reviewed

Now, let’s talk about what we discussed in the May 2018 edition of the Future of Functional Medicine Review. So there’s actually two studies I reviewed in this issue. One, showing that probiotics worked better when someone had IBS with SIBO. And another showing that rifaximin actually works better when someone has IBS with SIBO.

And what does that tell you? If you take those two observations and kind of tie them together, it reinforces the concept that antimicrobial therapy works better in those with IBS who also have SIBO. This also means—and this is key point to connect here—is that probiotics are a fairly potent form of antimicrobials. As I’ve been harping on – as I wrote about Healthy Gut, Healthy You- as I’ve done videos on covering the meta-analyses, summarized in the clinical trials, finding that probiotics can clean SIBO out of the small intestine. And so, this was a very eloquent study that essentially found that in those with IBS plus SIBO, there was a 71% decrease in the IBS score. And in those with IBS without SIBO, there was only a 10% decrease in their total IBS score after being given probiotics. So what a difference there.

Now, this is only one study. And it is a small study. But it really reinforces that the line of thinking that’s been reinforced by a very high level science, like the meta-analyses, which is, probiotics can be very helpful for those with SIBO.

Okay. And I’ve put in there the summary of all the findings (subscription required). There’s a very interesting chart, essentially, where you can visually see the difference in these two subgroups, those with SIBO and IBS and those without SIBO and IBS. So that’s all in the write-up that you can access through clicking through.

Case Study

And the other study I wanted to cover is entitled: A Proof-of-Concept Study Showing Antibiotics To Be More Effective in Irritable Bowel Syndrome With Than Without Small-Intestinal Bacterial Overgrowth: A Randomized, Double-Blind, Placebo-Controlled Trial. And essentially, what they found was antibiotic is superior to placebo in relieving symptoms of SIBO associated with IBS. Or said another way, we know that antibiotics, most namely rifaximin, but not only rifaximin, can help IBS. This is why rifaximin is FDA approved for IBS. But we know that in those who have IBS with SIBO, the antibiotics may be more effective. That’s probably not as counterintuitive as a probiotic finding. But again, these things are important for clinicians to see. Because what I really never want to be a party to is just propagating a false belief.

And with all due respect to the SIBO community, which, I guess, I’m really a part of. I hope I can consider myself a part of the SIBO community because I think there are some fantastic people in the SIBO community. I think they’re doing some great work. But this is one—and I don’t think everyone in the SIBO community falls on a pro or a con side of this argument – but there’s definitely a cluster of people in the SIBO community who are vehemently opposed to probiotics. And I think that’s a real travesty. And, I mean, this is the evidence that supports that.

And you’ve probably heard me say that our recommendations should be evidence-driven, not expert-driven because sometimes experts are fallible. And experts don’t actually follow the evidence. The reason why the expert opinion should be valuable, and often times is valuable, is because experts are well abreast of what the science, the evidence shows. But there are some experts who have their niche, have their philosophy. And despite the fact that they’re experts, they’re actually not making evidence-driven decisions. And in the case where some notable gastroenterologists are recommending against probiotics in SIBO, this is really where the expert opinion is at odds with what the evidence clearly says.

Now, does that mean that everyone with SIBO is going to respond positively to probiotics? No. But what it does mean is that it would really be a travesty not to even consider a cautious trial of a probiotic in patients with SIBO. And I can tell you, there are a number of cases. Many of their case studies are written up in the Future of Functional Medicine Review clinical newsletter, documenting patients who had positive SIBO breath tests. And they never required anything other than diet and probiotics. So no antibiotics, no herbal antimicrobials, no prokinetics, no elemental diets. All they needed were probiotics. So when you combine my serial observations with the overwhelming totality of what the data is suggesting, I think it’s very hard to defend a non-supportive probiotic position for those with small intestinal bacterial overgrowth.

All right, so that really takes us through everything that I wanted to go through. Remember, guys, if you have not looked at the Future of Functional Medicine Review clinical newsletter, during the month of September, if you sign-up, you can obtain your first month of access, all access for just $1. And you can access everything I’ve discussed today plus all the back issues, nearly two years of content. You can access that through The links are on your podcast player for this. And I really hope you check it out. Especially if you are a clinician, because this is really my attempt to give you the gift of just a litany of clinical pearls, summarized in an easy-to-digest fashion. And I hope you will dive in, read, learn, apply.

And, yeah. I will talk to you guys next time. I hope you learned some interesting stuff today. Okay. Bye.

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