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SIBO and Thyroid Q&A with Nathan Rose

I recently spoke at the International Congress on Natural Medicine in Hunter Valley, Australia.  There were lots of questions from the audience on gut and thyroid, which I did not have time to answer.  Today, I answer these questions with Nathan Rose, an organizer from the conference.  I think you will enjoy these questions, which get to the bottom line regarding what to do for improving gut and thyroid health.

Dr. R’s Fast Facts

When using natural antimicrobials, is it necessary to do breath testing when the breath testing data is mostly on the use of Rifaximin?

  • You could forego testing and perform a therapeutic trial w/ antimicrobials and see how they respond.
  • We don’t have to have breath testing in order to treat with Rifaximin antibiotic therapy or herbal antimicrobial therapy.
  • However, if someone does not respond optimally, it is helpful to have pre- and post-testing.
    • This helps answer the question: “Does the person have SIBO, but the SIBO is gone and they are still symptomatic, or is the SIBO still there after treatment and they are still symptomatic?”

Do different methods of herbal remedies work better for Methane-dominant SIBO vs. Hydrogen-dominant SIBO?

  • There is some speculation on this topic, but it has not been verified.

Does clinical testing for IBS have utility?

  • Quest Diagnostics offers a test known as IBSDetex.
    • Prominent utility – a screening test to help substantiate IBS or IBD
  • Could prevent a patient from having to go through more testing (especially if you rule out IBD).
  • Use caution with these tests, as they are good tools but they have their limitations.
    • Still a lot to learn on motility autoimmunity testing

Standard protocol for cases where SIBO is suspected?

  • Depends on who walks in the door.
    • For someone who has not tried a diet, we’ll hold off on testing and start simple and re-evaluate in a month.
      • Paleo or low FODMAP diet
      • Use a probiotic
      • Add Vitamin D and Fish oil
  • Consider testing if improvement from diet change is minimal.
  • If patient comes in with a more serious case, testing would start on day one.
    • SIBO breath test paired with a suite of GI markers – H. pylori, Candida, Yersinia, Toxoplasmosis, Amiba.
    • We use Biohealth, DiagnosTechs, Diagnostic Solutions, Doctor’s data, or use a profile through Labcorp or Quest.
    • We also do a standard health and wellness panel that looks at CBC w/ differential, thyroid, lipids, vitamin D, inflammatory markers, iron status.
  • If we suspect IBD, we’ll look at lactoferrin and calprotectin and potentially the IBD antibody.

Any tests you do not recommend?

  • GI mapping – these tests are not ready for clinical use.
  • Take pause with any other tests outside of the ones mentioned above until you have tried to improve your gut health.

SIBO Treatment – Pulsing Method

  • Unnecessarily complicated.
  • Try to move toward the simplest recommendations, be open to change and update as you learn.
    • Example: The co-administration of antibiotics with probiotics has a significant synergistic effect for H. pylori eradication.
  • The seeding philosophy has been updated to – most probiotics do not colonize you, but have a transient effect.

Are multiple rounds of Rifaximin necessary?

  • Sometimes people need multiple rounds to see a response.
  • There may be other factors at play.
    • Motility may be one the factors driving that
    • Immune system can also be a factor
    • There may be another symptom present

Prokinetics – do you use them?

  • We’ll have the moderate to severe SIBO cases go on a natural prokinetic after their SIBO.
  • Some patients with inflammatory and immune type symptoms are a good candidate for low dose Naltrexone.
  • Low dose Erythromycin, Resolor, and Prucalopride are also useful prokinetics.

Biofilm agents – do you use them?

  • When patients need a second or third round of treatment, we will consider co-administration of antibiofilm agents with antimicrobials.
  • pylori is another consideration.

Which ones do you recommend?

  • N-Acetyl-l-cysteine (NAC)
  • Biota-Dissolve
  • Samento
  • Many antimicrobial therapies and probiotics have antibiofilm action.

Other SIBO treatments to consider

  • Enzymes
  • Hydrochloric acid (be cautious with it, utility a bit overstated). If you see gnawing pain, burning, nausea or reflux, take them off of it.
  • Low histamine diet if someone is not responsive to treatment.
  • Elemental diet can be helpful.
  • Focusing less on the SIBO and gut and have fun and re-introduce new foods back into the diet.
  • If a patient is unresponsive to treatment, consider looking at the immune system.

Thyroid/SIBO connection

  • There is an association between treated or untreated hypothyroid and SIBO.
    • Doesn’t seem to be thyroid hormone level dependent.

Autoimmune Paleo Diet

  • Bit more strict – cuts out many foods that are inflammatory or can be irritating to the gut
  • Cutting out eggs, beans, nightshades, nuts, etc.

Reintroducing food after SIBO treatment

  • Best for patients to remain on the diet until they have reached peak level of improvement.
  • Once they have been stable in that, we will start to reintroduce.
  • Approach depends on the person and their treatment/response history.

In This Episode

Prelude … 00:00:39
Episode Intro
… 00:05:04
When using natural antimicrobials, is it necessary to do breath testing … 00:06:01
Measuring Methane and Hydrogen … 00:11:48
IBS testing … 00:13:50
Standard protocol for suspected SIBO … 00:18:10
Any testing you recommend against … 00:23:32
SIBO treatment pulsing method … 00:27:14
Prokinetics … 00:38:08
Biofilms … 00:40:18
Other SIBO Treatments … 00:44:33
Thyroid/SIBO Connection … 00:46:52
Autoimmune Paleo Diet … 00:52:20
Reintroducing food after SIBO treatment … 00:54:17
Episode Wrap-up … 00:58:42

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SIBO and Thyroid Q&A with Nathan Rose - 3d MC L

Hey, everyone, before we get into the body of today’s show, I wanted to talk about the best probiotics to use and how to find your ideal intake of fiber and prebiotics. Regarding the best probiotics to use, in Chapter 15 of my book, Healthy Gut, Healthy You,—yes, it’s finally here—we review what probiotics have been shown effective or ineffective for various conditions like IBS, IBD, celiac, diabetes, weight loss, mood, fatigue, according to the clinical studies, not speculation, not mechanism, what the actual clinical data says.

When you look at the evidence for probiotics, from a big picture perspective you clearly see two conclusions emerge. One, you see what conditions probiotics can and cannot help with. And two, you see four general classes of probiotics. And this then allows you to be able to try a probiotic from each one of the four classes, instead of randomly experimenting with the hundreds of probiotic products that are available.

It’s also important to mention maybe as a side note that most probiotics do not colonize you. And they also act as antibacterial agents, meaning they can kill off other bacteria and fungus. So there’s definitely some information in the book I cover that turns some of what we think about probiotics on its head a little bit in terms of some think that probiotics colonize you.

And actually, what may end up happening is probiotics may actually act more like antibiotics or antimicrobial herbs, in a sense, because they don’t stay in your system. They don’t colonize you. And they also may kill off unwanted bacteria and fungus and protozoa, also.

So what about when to use probiotics and for how long? Well, this is what’s nice about the guidelines that are laid out in the personalized self-help plan at the end of the book. We walk you through when to use probiotics, for how long, in what dose, and then maybe equally as important, when to go through a wean off experiment and try to get yourself on little to no probiotics in the long term. So I’m very excited about that aspect of the book.

And then also regarding another area where I think people are often confused, how to find your ideal intake of fiber and prebiotics. In Chapters 11 and 21, we go into detail about dietary and supplemental fiber. And again, we review what the actual outcome studies show of higher or lower fiber diets and what the outcomes of fiber supplementation shows. And to put it simply, the utility of high-fiber intake has been grossly overstated. It’s important to keep this in mind, because some people may actually need to reduce their fiber intake, at least in the short term.

Now, supplemental prebiotics are often marketed as being massively important for gut and overall health. But again, this has been overstated. In Chapter 22, I will detail when supplemental prebiotics are a good idea and when you may want to save your money. And again, when reviewing the info from these chapters, we can see what a reasonable recommendation for fiber and prebiotic intake would be. And again, this is all detailed in the self-help plan at the end of the book. So the end of the book closes with a “putting it all together section.”

So again, all this probiotics, fiber, prebiotics is detailed in my new book, which I’m very, very excited about, Healthy Gut, Healthy You, which thankfully has received some very positive feedback from those who’ve read it. You can learn more or purchase a copy at

And you can also get the book before anyone else. For our audience only, we are opening up a pre-sale campaign, which ends February 2nd. So if you want to know how to apply everything that we discussed into an efficient and effective treatment plan, this is it. If you want to know how, when, and what sequence to use things like elimination diets, a low FODMAP diet, probiotics, enzymes, antimicrobial herbs, adrenal support, etcetera, this is it.

So again, you can purchase a copy or learn more about the book at I hope you’ll pick up a copy. I guarantee you it will be well worth it. And all right, on to the rest of the show.

Episode Intro

Dr. Michael Ruscio: Hey, everyone, welcome to Dr. Ruscio Radio. This is Dr. Ruscio. Today, I am here with Nathan Rose, who is a very smart naturopath down in Australia. And he was nice enough to invite me down to the International Congress on Natural Medicine, and I had a chance to speak there earlier in the year. We had some leftover questions from the audience that I didn’t have a chance to answer during that Congress, and Nathan asked if we could go over those on a podcast. So he’s here today to ask some questions. And it’s nice to have you here with us, Nathan. Welcome!

Nathan Rose: Thanks, Dr. Ruscio. Thanks for the opportunity to speak to you.

DrMR: Absolutely, always a pleasure. You had a bunch of questions leftover from the Congress. You just want to fire in and we can start going through those one by one?

NR: Yes. Certainly. We’ll go through in no real particular order. But a lot of them are around SIBO testing and treatment, particularly in Australia where naturopaths don’t get access to things like rifaximin and so forth, so rely heavily, obviously, on herbal remedies.

When using natural antimicrobials, is it necessary to do breath testing?

So I’ll start from the top. The first one, which has been asked a lot of that is, if using natural antimicrobials, is it necessary to do breath testing seeing that the breath testing data is mostly on the use of rifaximin?

DrMR: I certainly see both sides of the position on this being protesting or being anti-testing. And I think you can make a case for both. I certainly think that you could forego testing and just try a therapeutic trial or perform a therapeutic trial with herbal antimicrobials and see how someone responds.

This is essentially what’s being done in some circles with rifaximin now. Because rifaximin was FDA approved for IBS type D, diarrheal-type IBS, it doesn’t necessarily require a doctor. Let’s say you go to a conventional gastroenterologist, and you have IBS-D. They don’t have to do a breath test to substantiate the use of rifaximin. Now, I’m not necessarily following all of the FDA’s recommendations in my clinical practice, but I don’t think we have to have breath testing to perform rifaximin antibiotic therapy or herbal antimicrobial therapy.

However, if someone does not respond optimally to that treatment, it is helpful to have pre- and then post-testing, because this can help you answer the question, “Did the person have SIBO? We treated them. And their SIBO is now gone. But they’re still symptomatic. Or did the person have SIBO? We treated them. And their SIBO is still there. And they’re still symptomatic.” So it can help you get a better understanding of what’s happening underneath the surface.

So what I tell my patients when they ask me this question is essentially that, which is if you’re someone who responds well, then we’re not going to really need the testing. But if we treat you, and you don’t respond that well, it may be helpful if we had done that initial baseline testing. And so, as a clinician, or I guess as a patient trying to steer some of your self-care, you can look at your own case or the case that you’re working with to help answer that question.

If it’s someone who has had a fairly mild presentation in terms of severity of their symptoms, that can be very suggestive that they may not need testing. If this person hasn’t changed their diet or hasn’t done other therapies, I would go back to some simple therapies like diet and probiotics first, before even considering testing.

On the other side of the spectrum, if someone’s already changed their diet, they’ve done maybe one or two dietary trials. Let’s say they did Paleo. Didn’t respond that great. Did low FODMAP. Didn’t respond that great. If they’ve been dealing with this for a while, maybe if they’ve done a round of rifaximin and haven’t responded, if they’re looking like a more complicated or non-responsive-type case, then leaning towards the testing, I think makes a little bit more sense.

So, in short, you could make a case for it either way. Looking at the presentation and some of the history of the individual can be helpful in steering which way you go.

NR: Great. So yeah, it’s certainly the patient that presents their symptoms, and their history, and so forth will help determine which way to go. And you probably negotiate or have the conversation with the patient, as well, about the pros and cons of doing the test.

DrMR: Exactly. And the approach that I’m using more so now is we do baseline testing on most of our patients. And so if someone responds beautifully to that initial round of treatment, we oftentimes won’t even bother retesting, because now if we’ve established our clinical goal, then in my opinion, there’s not a need to do testing to quantify what I’m anticipating is already going to be present.

And what I typically am doing now is if we do one round of treatment and we don’t see an optimum response, we may continue treating, modify treatment, try a different treatment approach entirely and try to come at the case a few different ways and try to get to a point where we’ve achieved a notable clinical response, and then retest in those cases just to verify that we are where we should be. And the reason I do that is I try to avoid retesting a patient who I know is likely still going to have SIBO, because that just wastes time and it wastes money. And it’s tempting to try to be “scientific.” But you have to balance that out with being able to get a patient’s results quickly, and not getting too distracted with testing.

NR: Yeah. And just on that topic, I suppose now that you’ve been an expert in SIBO and gut for a while now, would you think you’re getting a different cohort of patients coming to you now that is more trickier cases than perhaps the more general practitioner?

DrMR: Yes, I see a spectrum. And I try to keep my practice balanced. And I think one of the things that has been helpful in keeping the practice balanced is mentioning and being an advocate of simple, practical, and cost-effective functional medicine. So I think that message is very appealing to patients that are more treatment naïve, if you will, and they haven’t undergone much treatment. And they tend to be more simpler cases. So we have that on the one hand.

Then on the other hand, my deep focus in SIBO does bring in some of the more challenging cases. So I have a mix of both. And so I’m not sure if that answers your question, but—

NR: Yeah, yeah.

DrMR: Yeah, there’s definitely a mix.

NR: Yeah. Yeah, I just wasn’t sure if the patients you see are different as the general practitioner in the sense and whether you’d be doing more testing than you would have done, say, three or four years ago because you saw a different group of symptoms in patients.

DrMR: Sure. Sure.

Measuring Methane and Hydrogen

NR: But, obviously, the SIBO testing, we can measure methane and hydrogen. And a lot of clinicians are looking now at employing specific herbal remedies for each gas, in this sense. What’s your views on employing that strategy? Do you follow that?

DrMR: Well, there is speculation as to certain herbs being better for hydrogen or methane. And I’m certainly open to it. But I think, at this point, it’s much more speculative and anecdotal than it is something that’s been highly verified. So I guess maybe to answer this with what I typically do is I typically start patients of with a standard, broad-spectrum protocol. And my thinking here is with a broad-spectrum protocol, we can address bacterial dysbiosis, fungal dysbiosis, and potentially protozoa overgrowths, also.

So I like that broader approach of giving the microbiota a nudge. Nudge down the population of any overgrowth of bacteria, fungus, and protozoa so as to allow a healthier equilibrium to be established in the gut. Now, you can make the argument that if someone has higher methane, you should give them…Alcyclin’s been claimed to be better for methane. There’s also another formula known as Atrantil that has been claimed to be better.

You could do that. I don’t think it’s necessary. And I think that may be over complicating things slightly. And I would caution clinicians slightly about this, because if you let this speculation cloud your clinical observations, then that’s going to hinder your ability to successfully steer the case, so to speak.

So I’m certainly open. And if the right information is presented, then I will update accordingly. But right now, it seems to be very speculative. So I would be cautious. And I would just make sure not to let this speculative information, again, cloud your clinical observations. You don’t want to have this bias ingrained in your head where you’re expecting to see X and you have this almost created confirmation bias that you see.

IBS testing

NR: Yeah, definitely. Moving away from SIBO testing to breath testing, I wanted to ask about anti-vinculin autoantibodies. Dr. Mark Pimentel has really mapped out the pathology of certainly post-infectious IBS causing SIBO and how the antibodies attack the gut wall and so forth. And there is a commercially available test now for this. Have you looked into this? What’s your thoughts in a clinical setting?

DrMR: That test was first released in the U.S. through a lab known as Commonwealth Labs and a test known as IBSchek. That test is no longer available. I’m not sure if they are revamping, or reorganizing, or rebranding, or if they were acquired. But that test is no longer available. However, Quest Diagnostics now offers that test as a test known as IBSDetex.

And I wasn’t huge into using the Commonwealth, because it was not or was very difficult to have covered by insurance. And you had to have the patient go through the rigors of a separate standalone test. So it was hard to fit conveniently into a clinical model unless you were doing phlebotomy in office, which we don’t. And so it was logistically difficult. Now that Quest is offering it, we’ve been ordering it more. I think it’s terrific that we have mapped out some of this pathophysiology.

However, it’s important, again, not to confuse academic research with clinical research. The clinical utility of that testing, right now, is prominently consolidated to the use of trying to differential diagnose inflammatory bowel disease from IBS. That’s where it has been recommended for its prominent utility. If you have a patient with the symptoms of IBS mixed or IBS diarrheal, that can also look very much like IBD.

And so this can be a screening test to help substantiate this is IBS, and not IBD. And if this can prevent a patient from going through more in-depth testing, especially for some of the IBD testing being a colonoscopy, then that can certainly save a patient from the rigor, and the expense, and the inconvenience of more invasive testing.

Now, one of the reasons why I recommend caution between looking at academics versus clinical is, at least in my thinking anyway, knowing that the autoimmunity against motility apparatus is present, you would be inclined to think would correlate with patients with constipation, because the motility is damaged. And even though this is motility in the small intestine, my mind stands to reason that we would see an association between everything slowing in the small intestine and things also slowing in the colon, and, therefore, a constipative-type presentation.

However, recent research has shown that the anti-vinculin and CdtB antibodies do not correlate with constipative-type IBS. And those positive antibodies only correlate with mixed-type or diarrheal-type IBS. And so it throws a little bit of a monkey wrench in terms of the inferences that we would draw from academic observations.

And so again, this is why, I don’t try to be like a party pooper, but we need to have a treatment mapped out when we see these antibodies elevated, what do we do? And outside of the screening tool utility that I mentioned a moment ago, it may suggest—and this is speculation—but it may suggest that someone would be a better candidate for a prokinetic drug if they have these antibodies positive.

I’m not totally sold on that. I’m certainly open if the right evidence is produced. But for right now, I think we still have a lot to learn on the motility autoimmunity testing. If you do use the testing, just be cautious and don’t try to over utilize the testing. Realize that it may be helpful, it may not be helpful. And I wouldn’t put all of your eggs in that basket, so to speak.

Standard protocol for suspected SIBO

NR: Okay, great. So it sounds like it’s a tool in our toolbox. It has its limitations like pretty much every test we have. And I might use it as a bit of a segue to look at your broader toolbox you’re currently using, say for an IBS suspect, SIBO patient, what sort of—and perhaps, maybe more of a more difficult test—what would be your standard work up of functional tests or conventional tests you would consider performing?

DrMR: Great question. And part of this depends on the patient that walks in your door. Now, I mentioned a moment ago that we have a mix of patients. And I should probably clarify that we don’t often see patients who have done nothing, right. We usually see patients who have at least improved their diet, trying to pull out processed foods and maybe trying a Mediterranean diet or maybe trying a Paleo-like diet, maybe tried a probiotic or two.

But that’s still fairly treatment naïve relative to the spectrum of some people come in. And they know all about the anti-vinculin antibodies, right. So that’s still, I think, more towards the beginner end of the spectrum. However, if someone comes in, and they’re on no diet plan, they’ve never taken a probiotic, they don’t even know what fermented foods are, then we’re going to start really simple and not even do any testing. We’ll probably have them go on either a Paleo diet or a Paleo low FODMAP diet. Have them use a probiotic, some vitamin D, maybe a fish oil, some basic fundamentals and then reevaluate in about a month.

And then, if they see 70%, 80% improvement, we’ll probably ride that wave for a while. If they’ve only minimally improved, then we’ll go into some testing. Of course, if they’re a more complex case right out of the gate, we’ll go right into that testing on day one. A SIBO breath test is definitely something, of course, that many patients get. And then, we usually pair that with a suite of GI markers, your traditional testing where you look for H. pylori, candida, yersinia, toxoplasmosis, amoebas. You’re generally looking for dysbiosis and Oberlin parasites.

Sometimes we do this through certain functional medicine labs. BioHealth, DiagnosTEX, Diagnostic Solutions, Doctor’s Data, all pretty good companies in my mind. Or we’ll use a profile through LabCorp or Quest. And there’s some advantages actually through LapCorp or Quest because you can get blood antibody testing for things like candida. And you can also get an H. pylori breath test, and actually H. pylori antibodies via blood.

So that’s typically what we will look at. There’s some specific markers in there that are a little bit beyond the scope of this conversation. But if people did want to see exactly what all of those markers look like, we do have our monthly clinical newsletter, the Future of Functional Medicine Review Clinical Newsletter, wherein you’ll see exactly what labs they ordered and the results. So if clinicians really want to get a deep dive there for all of the 20 markers that we may order from LabCorp or Quest, then that’s included in the case studies.

And then, we also will do a standard health and wellness panel that looks at liver and kidney, a CBC with differential, a comprehensive metabolic panel, thyroid, lipids, vitamin D, some inflammatory markers, iron status. That’s pretty much what our initial testing looks like. You can make an argument for adrenal testing. But that is, yeah, a very poor argument in my opinion.

You can make an argument for female hormone testing. Again, in the initial phase, that’s a very poor argument. Food allergy testing, also, would not recommend that. Organic acids, I wouldn’t recommend that out of the gate. And we had a podcast recently where Jeff Moss was on and went into detail about that.

So our initial panel, it’s gut focused with a few other relevant markers included. And that’s really as complicated as it needs to be for most patients to give you a good handle on what’s going on and give you some keys in terms of where to go next.

Now, the one exception to that, sorry, is if we’re suspecting inflammatory bowel disease, and then we’ll include some specific inflammatory markers like lactoferrin and calprotectin, and then also potentially the IBD antibody assay.

NR: Okay. Also there, I recall at our Congress this year when Professor Rob Knight was speaking, he mentioned there was an emerging microbiome marker that he felt correlated better than fecal calprotectin. And I remember looking at you. And it piqued your interest. Have you looked into that?

DrMR: Yes, because that would be something that would be clinically applicable. So that definitely, always things like that peak my interest. And we actually had Rob Knight on the podcast. Him and I spoke, I think, it was last week actually. And that podcast will be going out in maybe another month or so.

Essentially, they’ve done one study where they’ve shown that a certain signature can be more accurate in predicting IBD relapse than, it was either lactoferrin or calprotectin. I don’t recall which one exactly. But they need to replicate that outside of that setting. And then, so it’s getting close to being clinically applicable. But it’s not there just yet.

Any testing you recommend against?

NR: And just one more on testing. I know you’ve got views on like DNA testing and microbiome, which I completely get from a clinical perspective. Are there any other tests, perhaps, that you don’t recommend that maybe you’ve either emphasized in functional medicine, say like intestinal permeability, because it’s pretty common, etcetera? Any of those other tests?

DrMR: One that I think is probably important to mention—and I think the audience has probably heard me say this before, but it’s just I think important to mention again—is mapping of the microbiota, right. And there’s different DNA tests. And there are DNA technology tests that do this that are direct-to-consumer. There are many different companies that offer the ability to map your microbiota. Give you a full readout of all the bacteria. Sometimes all the bacteria in the fungus.

And I just can’t emphasize enough that these tests are not ready for clinical practice. They don’t have any clinical meaning. And Professor Knight collaborated that when he was on the podcast a few days ago. He made that statement at the Congress on the Q&A Panel. So if you don’t take it from mine, I’ll take it from one of the leading researchers specifically in that niche. These things cannot be used clinically yet.

And why this is frustrating is I had a patient who spent $400 on one of these direct-to-consumer map your microbiota test. Only to find out later from me that that is clinically useless. So I don’t make this criticism just because I have anything against the companies that are doing that. The only issue I take is if these companies are marketing the test as something clinically relevant, which unfortunately many of them are.

I just saw a Facebook post the other day. And unfortunately, it was endorsed by a pretty big name in functional medicine. But if you click through to this company’s website, the homepage makes all these claims, “What if disease was an option? What if you could have the body that you wanted? What if you no longer needed to have food allergies?”

And then, the solution is this three, four, or five-hundred-dollar microbiota mapping test, which, it’s appalling. I hate to say that. But when you have something that has not been shown to be actionable, or helpful, or to produce a result, and you market it as such, and it cost a lot of money, that’s not great. I’m filtering. What I want to use is a profanity right now. But I try to keep this podcast clean. But it’s frustrating.

So I would definitely recommend against microbiota mapping. And I would take great pause with any other tests that are recommended outside of the simple ones that I laid out. Gut permeability testing, probably not needed. Food allergies, probably not needed. I would even make the argument that Lyme testing, or metal, or mold testing may not be best positioned until you’ve tried to improve your gut health.

It’s not to say that those tests should never be done. But I think it’s a fairly safe perspective to say, “Get your gut healthier first, and then move on to those other treatments.”

And to give you two examples. Some of the herbs that are used for Lyme can be a little irritating to the gut. Some of the detox or pseudo-chelating compounds that are used for chronic inflammatory response syndrome can be constipating. So it can be helpful to get your gut in the best shape possible so you can tolerate some of these further treatments, amongst other reasons why starting with the gut is a good idea.

So and to answer your question, there’s a lot of tests we could potentially run through. But I would say start with the gut-focused tests—and most specific are the ones I mentioned a moment ago—and try not to get pulled into anything outside of that.

SIBO treatment pulsing method

NR: Certainly great is to stick with the basics. And you also did the ones outside the gut, which was quite thorough and so forth, which I think are really important, as well.

All right, I want to move on to SIBO treatment. Now, something that’s popular, at least in Australia, is this like post-dosing of antimicrobials. Say it comes from a bit of the old view of weed, seed, and feed. And basically, the practitioners prescribe antimicrobials say two days a week, typically on the weekend because they felt there’d be these Herxheimer on the reactions. And it was debilitating for the patients and so forth, and then, during the week, the “the setting and healing phase.”

And this would be repeated after 6 to 10 weeks, as opposed to say a two week of refaximin or four weeks of antimicrobials. What’s your views on this pulsing method?

DrMR: My take on this is it is probably unnecessarily complicated. And I think something that is very important for the entire field to do is to try to move towards the simplest and most effective recommendations, rather than trying to move to the most exotic recommendations. And oftentimes, these more exotic recommendations aren’t any better. And all they do is increase cost and decrease compliance. So those are things that are definitely not going to help anybody—doctor or patient.

And also as we’re learning more, we should expect these recommendations to change, right. As we’re getting better, as a profession, we should expect change. So hopefully, people are on the same page with me in that regard that changing does not mean that you made a mistake or you were doing the wrong thing, it’s just part of learning and growing. So I’m doing things differently than I was a few years ago. And it’s just because we learn more. And we have to update.

So hopefully, everyone’s embracing that kind of philosophy, where if you update, it doesn’t mean you’re necessarily admitting that you’ve done something “wrong,” but rather now, we know a better way. So let’s update to that better way.

One of the things that we used to think was that if you take an antibiotic or an antimicrobial along with a probiotic, then you’re going to kill the probiotic. And it’s not going to be effective. And I think that’s been pretty disproven, very well disproven. Specifically, in the model of H. pylori, there has been a lot of data showing that the co-administration of antibiotics, along with probiotics, the addition of the probiotics has a significant synergistic effect for H. pylori eradication.

And so when we look at that, in the context also that probiotics can be antibacterial like anti-SIBO, anti-fungal, anti-protozoa, help with the gut immune system, help with gut permeability, in my mind, it’s a really good idea to be using antimicrobial therapy at the same time as using probiotics.

The seeding philosophy has been somewhat updated to now understanding that most probiotics do not colonize you, but rather they have a transient effect. So I don’t think that that’s necessary. I think that’s making things much more difficult than they have to be. And you can consolidate this to a very simple approach, where you can do antimicrobials and probiotics at the same time.

I like to start people with probiotics and diet change. And, typically, what we do is we have them start on a diet. So if they’re changing their diet, they’re usually on the diet for two or three weeks before, then adding in probiotics. This way when we follow up, I can get a sense of how effective the diet was in isolation.

And then, after usually two to three weeks, they’ve seen a leveling off from the impact of the diet. Now, they add in the probiotics. And we can get a somewhat isolated indication of how effective the probiotics have been. And then, if there’s still need for a response, then we can add in antimicrobial therapy while we keep them on a probiotic.

NR: Right, I like that stepwise approach. And yeah, I couldn’t agree more with that simplicity. I think, yeah, sometimes, as you’ve said many, many times, that the mechanistic speculations tend to override our clinical judgement.

So I want to move on to the use of rifaximin. Looking at the data there. So the data, sometimes people boast that rifaximin seems to be quite a panacea. But when you dive into the detail, it’s typically maybe 30% to 50% of people respond after the first round, and many does follow up rounds. So what’s your interpretation? Not to say that rifaximin’s not effective. But to me, there’s something else going on. What’s your take on the need to do multiple rounds? And if that’s the case with you, do you start diving deeper into what’s going on?

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SIBO treatment pulsing method (cont.)

This is probably a multi-factorial answer. And I think we also still have some more here to learn. But I do have some thoughts. Sometimes someone is going to need more than two weeks of rifaximin or the equivalent one month on antimicrobials to see optimum response. And so we don’t necessarily have to make this any more complicated than that where the reason people may be “relapsing” after a course of rifaximin for two weeks is because the course wasn’t long enough to reestablish equilibrium in the gut or to get SIBO to the appropriate levels.

So that’s one consideration. And that’s where I would start, is someone may just simply need a longer term on the antibiotic. Or if you’re using herbal antimicrobials on the herbals to see the response. And some people may need to repeat treatment. Quite simply, they may see a good response and then they may regress a few months later and need a shorter, more milder course of treatment.

Now, oftentimes, what is cited there as the reason for that regression is problems with motility. And that certainly, I think, is one thing to consider. And there was one study showing that the administration of prokinetics, namely tegaserod and low-dose erythromycin, helped prolong time in SIBO remission. However, people still tended to have a relapse. So the prokinetics extended time, but people still had these relapses.

So there may be this situation where people may need a couple nudges to the microbiota, over the course of many months, to fully allow everything to heal and to recalibrate. Motility may be one of the factors driving that. But my suspicion is that the impact of motility may be slightly overstated. I think it’s definitely important.

But sometimes, I think, we forget that the immune system is also very important. It’s an important part of IBS, of inflammation in the gut, of reactivity. And I think sometimes that is discounted. And so sometimes people may need to make sure that they’re using other factors to help create a favorable environment in the gut, because sometimes people relapse.

And it hasn’t been truly quantified that the SIBO, by repeat breath testing, an assessment of the gas levels, is what’s driving the relapse. And this happens in a lot of circles where people are just saying, “Oh, my SIBO.” And they’re using it as a catch-all term for everything. And that’s not good, because what that ends up doing is you’re blaming something that you’re not sure is actually the cause of your problem. And why that can be problematic is if you think it’s just SIBO, then you’re limiting yourself potentially to only the “SIBO treatments.”

Now, it may be that the immune system in the gut needs some time to unwind and no longer be as zealous with attacking or reacting. So low-carb diets, FODMAP restriction, periodic fasting, those things can be very helpful in trying to increase the likelihood that you won’t have a regression of symptoms. So that’s just something important to mention, also.

And another thing is there might be a different condition present. Sometimes people have SIBO plus something else. Every once in a while, you’ll see a case of SIBO plus, lately we’ve been discussing gastritis as something that is sometimes overlooked and being attributed as a cause of their symptoms.

And then, sometimes, people get too fixated on their SIBO, on their diagnosis. And they’re actually being too restrictive with their diet. And the thing they need to do in order to get to that next level of healing is think about SIBO and their gut less and actually make sure they move into a food reintroduction. So those are some thoughts.

Now, there’s also some patients who are dealt a very difficult hand. And then, we need to look into other therapies for patients that have a very difficult time responding. And so the things here, maybe low-dose naltrexone can be helpful. There’s some interesting protocols from Dr. Lawrence Afrin, who was recently on the podcast who talks about mast cell activation syndrome.

I think helminth therapy potentially may have some benefits for these people. And then, at the end of the line, something to consider, if all else has failed and someone is still fairly symptomatic, could be fecal microbiota transplant therapy. So I know I just gave you a lot there. But those are some things to think about.


NR: There’s plenty of gems in there from the whole spectrum all the way to FMT. Just on the prokinetics, yeah, you feel there’s many modest benefits to those. Do you ever employ them at any stage? And what do you use, if you do?

DrMR: We typically have our patients after SIBO go on a…Or I shouldn’t say typically. But oftentimes, it depends on the severity of the case. If it looks like a case that’s not as severe, then I’m not having everyone go on prokinetics. I used to. But oftentimes, we’ll have a moderate to severe cases go on a natural prokinetic after their SIBO.

There are, in some cases, the medication. Sometimes we’ll use low-dose naltrexone if they have symptoms that may make us think that they would be a good candidate for low-dose naltrexone inflammatory and immune-type symptoms. Also, low-dose erythromycin is a consideration. Resolor or prucalopride is probably the most effective. But it’s also a little bit harder to get. So there’s definitely some options there.

We’ve been trying to start a study where we would be looking at natural agents’ abilities to prolong time in remission of SIBO. We’ve just had a very difficult time with one formula we were going to study was taken off the market. And with another compound, we were having a very difficult time with placebo procurement.

So we’re trying to replicate the tegaserod and low-dose erythromycin medication studies that showed that those medications had prolonged time being SIBO-free. We’re trying to replicate that with a natural agent to see if they actually do because there’s really, to date, there’s no data, no published, verifiable data showing that they actually do work. It’ likely that they will. But it’s important to mention that we have no data that truly shows that.

So we use prokinetics on a lot of patients. I’m using them a little bit less than I used to because I try to reserve them for the cases where I think they’re going to be most likely beneficial.


NR: Okay. Great, that’s very helpful. And then, one last here on the SIBO is biofilms or the association with biofilms. Now, biofilms are something that’s thrown around or mentioned a lot in functional medicine. I’m still not sure if they’re that relevant or not. I know you had some in-house trials of this. So I’ve got a couple of questions like can you know if biofilms are necessary? Can you test it? And how do you really know if you’re actually treating biofilms, per se?

DrMR: Mmm hmm. Yes, so we did perform a retrospective chart review in my office. And we’ve had that drawn up. And I’ve been slow to actually get that published due to being busy with the book. But that’s something that we’re going to publish soon. So at the top of my list for as soon as the book publishes in February.

The co-administration of antibiofilm agents with antimicrobial herbs has a significant effect on hydrogen and combination SIBO. But even after that, I’m not using it as a frontline therapy, because it’s one thing to show a significant impact, it’s the other thing for it to be clinically meaningful.

NR: Clinically, yeah.

DrMR: And so it’s important to keep that in mind, because if you keep spackling on every therapy that has shown any kind of benefit, you end up with what some patients, unfortunately, experience, which they leave a doctor’s office taking 15 to 20 supplements, and I’m open to that. But that really limits how many people that we can help, because not everyone is motivated to spend that much money on supplements and to swallow that many pills, nor do I think it’s actually needed.

So I’m open to using this. And we do use the antibiofilm agents in some cases. But we typically reserve those for cases that have responded, both symptomatically and from a lab perspective, but the treatment hasn’t fully eradicated symptoms and/or their lab tests. And so if we’re going to do a second or third round of treatment, now this is when we consider using an antibiofilm agent synergistically.

For H. pylori, it’s another consideration. But we have studies showing that the co-administration of probiotics enhances the cure rate or the clearance rate of H. pylori. So when we do probiotics with antibiotics for H. pylori, that works better than antibiotics alone. Well, we don’t have any data that shows this specifically.

I’m assuming that the same thing will hold true, or evidence will show the same thing to hold true for SIBO that when we use antimicrobial therapy along with probiotics, we have a better clearance rate for SIBO than using one of those alone.

So when you start looking at this, the question starts to become, “How much would the—if you’re doing both antimicrobial therapy and the probiotic—how much additional would the biofilms help?” And so this is why I reserve some of these therapies, and I don’t give people seven therapies right out of the gate.

And I tell my patients when they ask me about using an antibiofilm agent, I say, “We don’t know right now that you’re going to be a very hard case. So let’s not treat you as such. Let’s see how you respond initially, and then we can consider these other therapies like antibiofilm agents should you not be responding optimally. So we do use them. But I try to reserve them for when they seem to be most indicated, namely for when patients are a little bit more minimally responsive.

NR: Okay. And what else on the biofilm agents that you’ve used or use now?

DrMR: N-acetyl cysteine is one.

NR: Okay.

DrMR: Interfase Plus is another. And Semento is a third. Now, I should mention that most antimicrobials, and I believe antibiotics, have inherent antibiofilm action. So when you use something like oregano or garlic, you’re getting some antibiofilm activity. And when you use probiotics, they have also been shown to have antibiofilm activity.

So please don’t think that the only way you’re going to have any impact on biofilms is by using something specifically for biofilms. Many of the antimicrobial therapies and probiotics have antimicrobial action.

Other SIBO Treatments

NR: Great. Playing the percentages with probiotics, and antimicrobials, and things like that is great. All right, so that’s prokinetics. That’s biofilms. Otherwise, any other general recommendations or things you want to talk about for the treatment of SIBO?

DrMR: Well, of course, diet, we’ve talked about a few of those. You may want to consider some enzymes and some hydrochloric acid.

NR: Of course.

DrMR: I’d be a little bit cautious with hydrochloric acid. I think the utility of that has been a bit overstated. You can still use it. And I just don’t believe in the, “Keep taking it until you feel burning. And then, take one or two less capsules per meal.” I think that’s a mistake. Also, keep in mind that some people will react negatively to, especially, hydrochloric acid. And so if you see gnawing pain, burning, nausea, reflux, then take them off of that.

And some people will actually have their diarrhea provocated by bile, because bile is actually a laxative. And we’ve had a couple of cases where everything improved except for their diarrhea. And the solution was not an OAT test, was not a Lyme test, was not anti-vinculin antibodies, it was taking them off bile, right. So it’s just important not to overlook some of those simple things, especially with bile.

Although, a histamine diet can be something to consider if someone’s not initially responsive, as can an Elemental diet, that can definitely be helpful, and also fun and thinking less about their SIBO or their gut. And also reintroducing their diet like we talked about a little while ago, that can be helpful. We talked about the Mast Activation Syndrome to consider and helminths to consider.

The Mast Activation Syndrome and the helminths are something that I’ve been experimenting with in the clinic. And I’m curious to see if they seem to be effective for people. But those both may be more so immune system treatments, and I think for many patients, the miss—we know a lot about the dysbiosis, the SIBO, the candida, or whatever, but I don’t think as much attention is paid to the immune system. And that’s important. So my speculation is we may start seeing more of these therapies go in that direction, because that may be one of the less addressed components of non-responsive care.

Thyroid/SIBO Connection

NR: Right. That’s very useful. All right a couple more. I want to go to cause and effect. That’s been bothering me for a while, is the connection between SIBO and thyroid. Many argue that the hypothyroidism is caused by the SIBO. But on the other side, you could argue that the hypothyroidism slows motility and allows the bacteria to flourish. How do you tease that apart? Or can you?

DrMR: Yeah, good question. As you know, I have a lot to say on thyroid. Unfortunately, I think it’s one of those very attractive-to-market topics. And so there’s a plethora of information out there on this, and it’s not all very accurate. We do know that there’s an association between hypothyroid. Irrespective of if you’re on medication and your levels are now normal, there is an association between treated or untreated hypothyroid and SIBO.

Now, is that cause or effect? We don’t really know. But it does appear that it’s not thyroid hormone level dependent because we see the same association occur whether or not someone is on thyroid hormone and now has normal thyroid hormone levels in the blood. So there’s definitely association. But whether or not it’s causal, it’s hard to say.

My speculation—and this is admittedly extremely speculative and only based just upon my thinking about this and trying to imagine what the solution or the association may be—is perhaps small intestinal bacterial overgrowth decreases selenium status. Bacteria in the gut can sequester selenium. And that may create a subtle deficiency in selenium, which could then exacerbate the underlying genetics for thyroid autoimmunity.

We know that selenium deficiency is one of the environmental factors, that when accompanied with the right genetics, can initiate thyroid autoimmunity. So, perhaps, the SIBO is there eating selenium and therefore potentially exacerbating the genetics of a thyroid autoimmunity.

Yeah, that’s my speculation. That may or may not be true. But we definitely know that there is an association. And it’s important to address both, thyroid function and the SIBO. Just be careful because sometimes patients are told that they have hypothyroid when they really don’t. And some patients end up on medications when they don’t really have to be.

I’m open to using thyroid hormone as a support. It’s just important that we clarify if you’re a provider, we’re going to do a therapeutic trial of thyroid hormone and see if you respond, compared to, “You have diagnosed hypothyroidism and you require medication.” But certainly, checking for hypothyroidism and treating it if it is present is definitely very important.

With the antibodies, if you’re below four to five hundred for your TPO antibodies, you’re probably okay. Looking at a TSH and a free T4 is adequate to diagnose for any type of hypothyroidism. I would make sure to use the dialysis method for testing the thyroid hormone, the T4s and the T3s, because the dialysis method seems to be more accurate.

And someone may actually be, they actually look subclinical hypothyroid on their lab testing. What is that? That means that your TSH has been flagged high, but your T4 is actually normal. So this is called subclinical hypothyroid. And this does not generally require treatment. However, if that T4 has been evaluated with the immunoassay methodology, you may actually be seeing a false normal. And if you repeat that test with the dialysis method, you actually may now see the T4 low. And if the T4 is low, paired with a high TSH, now you are hypothyroid.

And why this is relevant, to put it very simply, the binding proteins in the blood may skew the read on the T4s and the T3s. The dialysis method filters out those binding proteins. That bit of academic minutae is only relevant because there have been studies done showing that TSH and the T4s and T3s are more representative of patient symptoms using the dialysis method compared to the immunoassay.

NR: Okay. Great. And just for the record, if you can do it briefly, I’m sure…But you could probably do another whole podcast in your head. When you say elevated TSH, I think I was guilty in the past of being a bit thyroid-centric. This is not mild elevated TSH. This is frank elevated TSH.

DrMR: Frank elevated TSH. And here is something…And I’m really glad you asked that question, Nathan. Now, there may be something to the narrower ranges that functional medicine uses for the T4s and the T3s. But if we use the dialysis method, because it filters out for this confounding binding protein, we can more so rest assured that if it’s high or low, according to the conventional ranges, then it’s truly high or low.

So what I’m saying is that when you use the more accurate methodology of the dialysis method, you can use the conventional ranges, and not have to worry about the narrower functional medicine interpretation ranges.

Autoimmune Paleo Diet

NR: Okay. Great. All right, a couple more. Just turning off topic somewhat, well autoimmune. A question we had from Congress was your autoimmune Paleo diet. We wanted to know how that differed from a conventional—if that’s a term—conventional Paleo diet?

DrMR: There is a couple different derivations on the Paleo diet. Essentially, the autoimmune Paleo diet will cut out eggs, nuts, seeds, beans, legumes, and nightshade vegetables. So it’s a more restrictive iteration of the Paleo diet. So Paleo has the most food you can eat.

Autoimmune Paleo is a bit more strict. It’s not to say the autoimmune Paleo diet is the best diet for every autoimmune condition, but it does cut out many foods that are inflammatory or can be irritating to the gut, and so it’s certainly a consideration. If someone’s, for example, responded only partially to Paleo, then considering having them go to the autoimmune Paleo, could definitely be helpful.

And interestingly, there was recently a published study that showed that the autoimmune Paleo diet was quite effective and quite helpful for inflammatory bowel disease. And so we are starting to see some evidence showing the benefits from this diet. But, essentially, it’s a few foods that are restricted on top of the Paleo diet that make the autoimmune Paleo diet different.

NR: And the rationale for those ones briefly.

DrMR: You’re just cutting out more foods that could potentially be inflammatory or irritating. So the nightshades, the nuts, seeds, eggs, beans, legumes, they may contain capsaicin, or lectins, or other compounds, other immunogenic compounds in the eggs, for example, that people may react to. So you’re cutting out more foods that have been shown, to some extent, to be irritating or to cause reactions in people.

Reintroducing food after SIBO treatment

NR: Right. All right, one final question. Back to the SIBO. How long after you’ve achieved remission do you allow or encourage the reintroduction of more fermentable things such as fiber and particularly prebiotics?

DrMR: So I like to have someone stay on the diet until they’ve reached their peak level of improvement. And typically, you see that within a few weeks to a month or two. And then once they’ve hit their peak level of improvement and they’ve been stable in that for two, four, maybe six weeks, we can start to reintroduce.

Now, the healthier someone is, the more strongly they’ve responded, the more quickly we will go into that. If someone’s more of a complex case and it’s taken us months to get improvement, we may not want to go too quickly. We may not want to rock the boat too much. And that fits in the clinic. Patients who have had a hard road to improve are usually gun shy about blasting right into a reintroduction. They’re okay with the slow, steady approach. So you partially have to play that based upon, or make that call based upon the person who’s sitting in front of you.

Also, sometimes what you can do is not go into a full reintroduction of everything, but ask someone, “What are the two or three foods that you want to eat the most?” “Okay, let’s have you try those foods. If you’re okay with them, you can keep eating them. If not, just try to only eat them sparingly.” And what this can do is it doesn’t launch you into reintroducing everything. But if there is two foods that someone is dying to eat, there’s a good chance they may be okay eating those foods. And if they can get back on those and their motivation becomes a lot higher because of that, then that’s a great maneuver clinically.

NR: Excellent. Well, thanks for all those answers. There’s certainly some clinical gems in there for, not only patients, but also practitioners. I’m curious to see if your selenium-SIBO-thyroid hypothesis eventuates. And so one last question. Tell me about the book. How’s that coming along?

DrMR: The book is great. It’ll be out, presale should start on January 15th. And then, the book will be available on February 15th. And you’ll see some updates on the website and an updated store to go along with some of the protocols that are available in the book. But I’m very excited about it.

Essentially, all these things that you’ve heard me talk about with a simple approach, stepwise approach to improving someone’s gut health had been laid out into the action plan at the end of the book. And I’m either going to retire after this book, if it sucks, I’m just going to hang up my doctor hat or I’m very hopeful that it’s going to help a lot of people and be a very impactful read that will right some of the wrongs where we’ve maybe been a little bit off the mark in natural medicine and also really showcase where we’ve been really right and we have a lot to offer and help people navigate that in a simple, efficient manner. And get well. So yeah, as you can tell, I’m very excited about it.

NR: I’m sure it will be the latter of those two options where you’ll really help a lot of patients and practitioners. And hopefully you’ll have a bit of time off to yourself after all this hard work, as well.

DrMR: Yeah, that would be nice. I’m definitely looking to work a little bit less on the other end of this.

NR: Fantastic.

Episode Wrap-up

DrMR: Awesome. Well, if that’s it, Nathan, I guess we’ll put it there. Is there anything that you want to make the audience aware of? I know you have a Congress coming up soon. So please, anything there that you want to…?

NR: Thank you. Yeah, so the Australia Metagenics 2018 in Congress will be down in Melbourne this year, June 9 to 11. The theme is hormones. And we’ll be covering things from the thyroid, having a look at this adrenal fatigue story, maybe debunking that. We might look at the MCAS, the master activation syndrome. You’ve heard Lawrence Afrin on sex hormones, and stress hormones, and everything like that. And if I can quickly plug our podcast, the Metagenics Clinical podcast, where we have similar guests to yourself, including yourself obviously, looking at all these topics.

DrMR: Yeah, Nathan, I have to give you a hat tip, because you seem to have a keen eye for finding people that are practical, evidence-based. And you’ve actually sent me a few names of people that I said, “Wow, like this person is great.” So I would definitely check out the podcast because Nathan has a pretty good nose for B.S. and getting the people who seem to be pretty practical. So yeah, good job with that. You’re doing terrific there.

NR: Thanks, I appreciate it.

DrMR: All right, my man, well until the next time, keep fighting the good fight. And thanks for all of your questions.

NR: Thank you.

DrMR: All right, take care, Nathan.

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