Lyme Disease Causing Chronic SIBO with Dr. Rahbar – Episode 33

In this episode, Dr. Ruscio interviews Dr. Farshid Sam Rahbar, a leading integrative gastroenterologist, practicing at LA Integrative Gastroenterology & Nutrition. They discuss how chronic Lyme disease might cause chronic SIBO.

If you need help diagnosing and treating your SIBO, click here

Dr. R’s Fast Facts

  • Chronic SIBO, especially methane SIBO may be caused by Lyme disease or Lyme co-infections.
  • This may occur due to the impact on the immune system or through affecting the nervous system in the gut.
  • IBS check testing for gut antibodies has not been positive in Dr. Rahbar’s sampling, which often suggests another mechanism is at play. Dr. Rahbar still finds this test valuable.
  • Common symptoms of tick born illness induced SIBO are
    o Bloating, fatigue, anxiety, abdominal pain, insomnia, constipation, food intolerances, irregular bowel movements, weight gain/loss, and joint pain
  • Testing for Lyme includes:
    o Igenix, Advanced Lab, Infecto Labs, Armin Labs
    o Babesia duncani may be an important marker to add to testing
  • Start with treating the gut and then see a Lyme specialist.


podcast-artwork newSubscribe:
stitcher button

Fast facts…..0:42
Dr. Rahbar intro…..3:28
Lyme and common co-infection testing…..8:37
Symptoms of tick borne illnesses…..13:42
Connection between Lyme disease and SIBO…..15:37
IBS check test…..23:02
Diagnostic sequencing…..27:49
Episode wrap-up…..30:09


  1. (14:24)
(Click link to enlarge)
(Click link to enlarge)

Download Episode
Right click on link and ‘Save As’


Lyme Disease Causing Chronic SIBO with Dr. Rahbar

Welcome to Dr. Ruscio Radio, discussing the cutting edge of health, nutrition, and functional medicine. To make sure you’re up today on this and other important topics, visit and sign up to receive weekly updates. That’s

The following discussion is for educational purposes only, and is not intended to diagnose or treat any disease. Please do not apply any of this information without first speaking to your doctor.

Now, let’s head to the show!



Fast facts

Dr. Michael Ruscio: Hey, guys. This is Dr. Ruscio. I just wanted to give you some Fast Facts on today’s episode regarding the connection — or the potential connection — between chronic SIBO being caused by chronic Lyme disease.

Chronic SIBO, especially methane-positive SIBO, may be caused by Lyme disease or Lyme disease co-infections. This may occur due to the impact on Lyme affecting the immune system or potentially through Lyme affecting the nervous system in your gut. IBSchek, the test that’s available for quantifying if you have autoimmunity against intestinal cells that can lead to SIBO, does not seem to correlate well with this type of presentation, meaning people that have Lyme and have SIBO, according to Dr. Rahbar. Although he still finds this test valuable, he just hasn’t found it correlates in this population.

Some common symptoms that may tip you off that you have a tick-borne infection, like Lyme or a Lyme co-infection as the underlying cause of SIBO: The most common 10 symptoms, according to Dr. Rahbar are bloating, fatigue, anxiety, abdominal pain, insomnia, constipation, food intolerances, irregular bowel movements, weight gain or weight loss, and joint pain.

Testing for Lyme includes IGeneX, Advanced Labs, Infectolab, and ArminLabs, in addition to your more traditional LabCorp or Quest testing, and Babesia duncani may be an important marker to add to panels, according to Dr. Rahbar again.

Start treatment with the gut, and once things in the gut are moving in a direction or clear or at least close to clear, then seeing or working with a Lyme specialist would be the next best step.

Those are your Fast Facts, and remember, if you want to have links and transcripts, you can go to the website and access all that good stuff there, and feel free to ask a question on the comments section associated with the transcript. And the clinic is still accepting patients if you’re in need of help, so feel free to reach out if you need it. OK, enjoy.

Dr. Michael Ruscio: Hey, folks, welcome to Dr. Ruscio Radio. This is Dr. Ruscio, and I am here with Dr. Rahbar, who is a medical doctor in Southern California, and he recently spoke at the 2015 SIBO Symposium, and he presented some really interesting information regarding Lyme disease potentially being a cause of chronic SIBO. He was gracious enough to take some time out of his schedule and speak with us today, so, Doc, welcome to the show.

Dr. Farshid Sam Rahbar: Great. Thank you so much.



Dr. Rahbar intro

DrMR: Now, tell us a little bit about what you’re seeing in practice, a little bit about your training, and kind of how you started to notice this association between Lyme and SIBO.

DrFSR: OK, just quickly to bring the audience into the context of what I do, I should say something quickly about my background. I am a gastroenterologist, an integrative and a holistic-type gastroenterologist. I have been in practice for almost 30 years now, and the last eight years we have incorporated an integrative model into the practice. Now, SIBO testing for bacterial overgrowth has been something that we have been doing in the office since 2005, and in the last two years we noticed a rash of patients who had somewhat-difficult-to-control SIBO or they had a lot of methane-producing results. These patients appeared to be harder to treat, and they also had other associated symptoms, such as mental issues, cognitive issues, energy, muscle, food sensitivities, and so a variety of things seemed to be going on at the same time, and even if we treated the SIBO, it appeared that the patient’s illness did not completely improve.

Now, I am going to say something because it’s purely our own observation and I hope that at one point this can be published with further research. I don’t want to give you a reference because it is simply an observation, but I do feel very strongly about it because what we noticed was the fact that the patients that have methane-producing bacteria in excess amount, they have positive markers for Lyme or other tick-borne illnesses.

Now, this area is extremely controversial, and I’m an outside comer into this in the last few years, and the controversy comes from two different schools of thought, one believing that maybe a latent or chronic Lyme condition doesn’t exist or it’s quite rare, and another school of thought that comes from the group of physicians that work with the International Society for Lyme Disease, and they do believe a lot of patients are out there and they have chronic symptoms and that they actually may have these infections in the background as a cause of chronic inflammation. So we look for manifestations of inflammation, and then when we look for a cause, we find that some of these tick-borne illnesses are out there. The question is then, what criteria do we use to make that diagnosis besides the patient’s story? Obviously their story is very, very important, and that’s why we are good listeners to see how is the presentation. If the patient feels good, I care less about the test results.

DrMR: Same here.

DrFSR: But if the patient does not feel well, if they have been lost in the system for years and they have seen many physicians, then I would value any small abnormality that may give me a clue about a hidden or stealth infection.

So when this scenario was revealed, we started to not only look at the traditional labs such as Quest or LabCorp that follow a standard algorithm in making a diagnosis of a Borrelia infection, we use other labs, and if it’s appropriate, I’ll share the name of the labs, but we’re not here to —

DrMR: Yes, I think people would really, really appreciate hearing the specifics on the labs, and before we transition into that, I just want to echo a couple of things for people listening because I think they’re really key points, what you said, which are that, of course, Lyme disease is a controversial issue, and I think most people listening of aware of that, that there are two ends of the spectrum and it can be a very controversial issue. Diagnosis can be a very ambiguous challenge, so I’m definitely looking forward to hearing your testing recommendations. But the other piece is the chronic methane-positive SIBO, which I think is a real problem for people with SIBO. Compared to the hydrogen, it really appears that the methane can be a much more resistant bug or a resistant gas to be able to treat. That really caught me when I heard you first mention that association because I think, at large, the SIBO community is much more frustrated with methane resistance than they are hydrogen resistance, so I’m really hoping that you’re on to something.



Lyme and common co-infection testing

DrMR: With that, please tell us more about the testing array that you’re using to try to firm up the diagnosis of Lyme.

DrFSR: Going back and responding to your question, there’s a clinical pattern or a pattern of recognition which comes from the patient’s story, and once we have that, most patients would like to have some additional information for which we provide testing. The methodology that we have used from different labs includes one from IGeneX Lab in Northern California, we have used Advanced Lab in Philadelphia, and we have also used two labs in Germany. One is ArminLabs, and the other one is Infectolab.

ArminLabs and Infectolab, they have similar technology, and recently Infectolab added another piece of technology to their panel, which may be of some additional value. One of the things with the German test is they look at the cellular function. It’s more or less like the test they use for tuberculosis, something called QuantiFERON, where the lymphocytes are actually placed next to the bacteria and they look at the release of cytokines such as interferon gamma. Now, the Germany test with Infectolab measures interferon gamma for a variety of antigens that they use. They’ve also now recently added IL-2, which is another one. We noticed that some patients may be simply IL-2 positive and the interferon gamma may not show any activity. Now, if there’s a story behind this, then that becomes valuable.

The Advanced Lab, we use the culture. It’s a slower process. They report it in 10 days, in eight weeks, and in 16 weeks, and the chances of a false positive would be very, very small. I cannot say it is none, but I’ve talked to them and I think overall the sensitivity and the specificity of the test is in a reasonable range for clinical use.

The other test that we do is through IGeneX, and they have a variety of panels. I think physicians should review the different technology that they have and see which one would fit best to the patient’s clinical picture and the financial budget that they may have. Generally, when I order, I try to order the PCR test with it as well. Occasionally the antibodies for Western blot, they come back negative or borderline, and the PCR may actually come positive so it will help to resolve the dilemma.

DrMR: Sure.

DrFSR: And you know, if the patient has all the resources, you can order all the tests at the same time or you can put them in a sequence, depending upon how sick or how motivated they feel about the testing process.

DrMR: Now, do you have a panel that you screen for Lyme and the common co-infections, or are you doing that more based upon the symptoms that are in line with the particular sequelae of a co-infection?

DrFSR: IGeneX has a comprehensive panel for co-infections, which I think is pretty good. I think it may be a little bit more cost effective to order it as a panel, and if you look through it, you’ll see it’s called, like, a new comprehensive panel for co-infections.

As much as possible, I also order Babesia duncani, particularly for patients who have headaches, sweating issues, chest pains, and coagulation disorders or hypercoagulable states, and also body aches and body pains and synovitis-type symptoms. I think Babesia should be ordered in this scenario. Many times it’s not Babesia microti. It’s Babesia duncani, and that’s one that is not in the co-infection panel. You have to check it off extra.

So I’ve found that combination in conjunction with the Lyme testing is a kind of cost-effective way to quickly look and see what’s going on. There’s more testing to do, but obviously it will add to the expense.



Symptoms of tick-borne illnesses

DrMR: Now, you also said there’s a certain story, and I’m assuming some of this story is chronic symptoms that aren’t responding to other therapies, including SIBO symptoms, and I know some of the symptoms you mentioned are bloating, fatigue, anxiety, abdominal pain, insomnia, constipation, food intolerances, bowel irregularity, weight gain or weight loss, and joint pain. Is that a fair encapsulation of some of the main symptoms that someone might be suffering with if it might be warranted to investigate further?

DrFSR: Yes.


(Click link to enlarge)
(Click link to enlarge)

DrFSR: Absolutely. That summary that you presented, I think, comes from the slide that I presented with what I call the 10 top symptoms.

DrMR: Exactly.

DrFSR: I’m presenting this data again in Florida to the ILADS Society in October, and we have now looked at our patient population from the middle of 2013 to the end of May, and the numbers are about the same. Almost two-thirds of the patients came with a bloating problem, and my whole scenario about this was that patients with tick-borne illnesses may present primarily with digestive symptoms as opposed to cardiac or brain or muscle types of symptoms.

DrMR: Gotcha. Now, do you mind if I share that slide in the transcript along with these notes?

DrFSR: I don’t mind.

DrMR: OK, because I think that will be helpful for people just to kind of see what the top symptoms look like. And congratulations about presenting at ILADS. I’m sure that will be a great way to circulate some of this information.

DrFSR: Absolutely.



Connection between Lyme disease and SIBO

DrMR: So why do you think the association — or the potential association, the one that you’re trying to firm up — between chronic Lyme and SIBO exists? Do you think it might be some sort of neurological enteric Lyme that may be affecting motility? What do you think is going on?

DrFSR: Well, if I say something, obviously I’m speculating.

DrMR: Sure, of course!

DrFSR: This information is not really well written anywhere, but I had to do some research just to be able to have some understanding of what is the reason that you get more SIBO, a higher level of hydrogen or methane, and it’s even more difficult to treat it. There’s obviously something wrong with the immune system. Now, this could be a direct effect, maybe, from the T cell function or maybe it’s the effect of these tick-borne illnesses on the enteric nervous system that controls the neuroendocrine and immunology of the gut.

DrMR: Sure.

DrFSR: I am almost clinically convinced that the enteric nervous system is affected. There’s autonomic neuropathy involved here, and somehow, I think, that may be interfering with this process. I’ve looked around to see if there’s research on this. I heard that Johns Hopkins was counting the number of the neurons in some intestinal tissue samples. I’ve tried to make contact with them and see if they can take some samples from us and do the same thing, but it hasn’t really panned out to reality as yet.

So my thought would be that this probably has something to do with autonomic dysfunction, involvement of the enteric nervous system and also the immune system that may be suppressed in some specific areas.

If you look at the methane-producing concept, we notice that patients who have high methane on Genova stool analysis, they also have a high level of Methanobrevibacter smithii. Methanobrevibacter smithii, if you look at their new technology on the — I think it’s called the 2200 panel that they do PCR technology and they look at the bacterial distribution, practically always the Methanobrevibacter smithii is undetectable. It’s attached to the bottom of the range. But every now and then when we see a methane-producing SIBO, when you look at the stool test, you see both. The smithii is also sitting there above the baseline, OK? So at least it’s now becoming detectable.

DrMR: Interesting, because I haven’t noticed that association, and I run SIBO testing on almost every patient. I use the National College of Naturopathic Medicine’s SIBO Center breath test, and then I’ve tandem tested that with the Genova GI Effects profile, and I’ve found maybe the opposite association, which it’s always interesting to hear these different experiences that we have, but I’ve found that in maybe 50 percent or more of the cases that we find SIBO we haven’t found the PCR testing to be high.

DrFSR: You’re absolutely correct, but remember with the PCR the load of bacteria has to get to a level to be able to show.

DrMR: Sure.

DrFSR: You may have a methane scenario of 5 parts per million, and you may see nothing, it is true, but if your methane production goes to a higher level, you’re going to see more numbers in the stool being positive. It is not a 1:1 association, you’re 100 percent correct, but you’re going to find many times the higher the methane level is, more chance to be able to detect the smithii in the stool, and I think it just has something to do with the cutoff level as how at what point they’re going to call this detectable or not.

And also remember Dr. Pimentel reports that the upper level for methane is less than 3, and until recently, everybody was going by 5 or 10, but once he announced it — and he actually published it — that 3 may be the magic number — and this is a very, very small amount of methane production and the load of bacteria in the stool may not be enough to show itself on the stool analysis, the GI Effects.

DrMR: Sure. I certainly agree. I certainly don’t question methane overgrowth or methanogen overgrowth being present if we see a positive on a breath test, and you are absolutely right that the normative ranges for the breath tests have changed, and I think we know far less about what the PCR technology looking at a more microbiotal analysis should be in terms of what’s normal and what’s not normal. There’s so little we know about what a normal value for a microbiotal finding is that I think we’re really in our infancy there.

DrFSR: Absolutely.

DrMR: So, yes, I’m not surprised to see some disagreement there.

DrFSR: Yes, the jury is still out on that, and we’re going to see what comes out of all these stool analyses. One thing is interesting because since the month of May another laboratory in Massachusetts is now performing the IBSchek, which you might have heard, and this contains two tests. One is the vinculin antibody, and the other one is the cytolethal distending toxin antibody, and we thought we were going to see a lot more positive on the methane-producing patients, and those patients would turn out to have a tick-borne illness based on the criteria that I presented, and many of them did not have the vinculin or the CDT antibody.

DrMR: Interesting.

DrFSR: So it seems to me that the mechanism of injury from what we call post-infectious IBS and the patients who may be suffering from this tick-borne illness, it doesn’t seem to be the same. Now, I haven’t done a formal analysis of this, but by just going through the tests I’m seeing more negative of these antibodies when the patient has really bad SIBO with methane and a documented tick-borne illness.



IBSchek test

DrMR: I’d love to get your perspective on the IBSchek. As I understand it, the IBSchek has its prominent utility for an early screening tool to differentiate chronic diarrhea IBS from potential IBD. Would you agree with its use there, and/or how are you finding it to be most clinically useful, for the people listening who are thinking about using this test?

DrFSR: Well, I’m going to have to be honest with you about how I use it!

DrMR: I appreciate the honesty!

DrFSR: I personally don’t need that test to separate IBS and IBD, and most patients end up having you look, anyhow. I use it because I want to understand the mechanism. I want to understand, is there an antibody against the body’s protein, vinculin, that may be interfering with motility and movement? I want to see if we’re dealing with an autoimmunity-type problem, which might have been triggered by a previous infection. Now, food poisoning is one thing, and as part of food poisoning, one gets the release of biological toxins, and the biological toxins through the molecular mimicry, they create an antibody against vinculin, and if you have an antibody against the toxin itself, you even have further confirmation of that concept.

But let’s ask the question, is it possible that there are other biological toxins in nature that can trigger the same autoimmune type of reaction? And my theory was that perhaps these other tick-borne illnesses may actually somehow produce a biological toxin — whether we understand it or we don’t understand it — that triggers the vinculin antibody concept, and by having a vinculin antibody then you have some confirmation that they body is being attacked. Interestingly, as I said, so far when I’ve looked at the last two months of data, we have seen more negatives of the IBSchek in these tick-borne illnesses. So the mechanism of the problem and growth of the smithii in the stool is probably other than the vinculin antibody.

DrMR: Now, outside of using the IBSchek for maybe more so academic purposes of trying to understand the underlying mechanism, has it been something that’s had a lot of clinical utility for you? The reason I’m asking this is I know there are people listening who are potentially debating about spending out-of-pocket money on testing, who are trying to enhance the SIBO care that they get, and I’m wondering if you feel like that test has clinical utility or is more of an observational tool, the way you’re using it.

DrFSR: No, I definitely believe it has clinical utility. If you have a patient with highly suggestive irritable bowel syndrome-type symptoms and the IBSchek comes back positive, that’s further affirmation of that. However, I think there’s also value if it comes back negative because that may explain that this may not be your typical IBS and you might as well proceed with additional investigation. Having said what I said earlier, by no means did I mean to devalue it, the value of the test that has been clinically checked and shown to have some role in supporting the physician’s decisions. If negative, I still would value it because it would tell me to do more workup, and the positive will support the diagnosis of the IBS, and I may want to hold off on doing additional testing.

DrMR: So if the IBSchek comes back positive, do you typically reflex to testing for SIBO?

DrFSR: By that time, I would have done the SIBO.

DrMR: Gotcha, OK.

DrFSR: Anybody who comes in to us with IBS-type symptoms, we will do the SIBO. The question is whether the patient needs a colonoscopy or more invasive procedure, but for something that is relatively easy, I would not need the IBSchek to decide on that.



Diagnostic sequencing

DrMR: OK. So when you’re finding SIBO and you’re finding a tick-borne illness, do you have a certain sequencing of starting with the gut and then working to the tick-borne, or tick-borne and then going to the gut?

DrFSR: As a general principle, the gut should be addressed always first. We work with other physicians who actually treat Lyme and tick-borne illnesses, and these are usually physicians we call “Lyme literate.” In our practice, I do understand the treatments, but because of the time constraints we cannot commit to full treatment of the Lyme and tick-borne illnesses. As far as the GI part, I definitely make sure that the intestinal integrity has been addressed as the patient is starting to enroll themselves into treatments that involve Lyme and tick-borne illnesses.

DrMR: Gotcha. That’s always been my general approach, is to start with the gut and then work our way out, and I’m certainly not a Lyme expert, but from the training that I’ve done in Lyme, that seems to be reflected in the Lyme community also: starting with the gut or even starting with co-infections and then working up your way up to Lyme, so I’m glad to see that we’re on the same page there.

DrFSR: Absolutely. Many times when you address those, the patients feel better, and it’s not just about treating the test. Eventually if somebody feels well, one may want to refrain from doing additional treatments.

DrMR: I couldn’t agree with you more there. One of the things that I’ve been trying to harp on with this podcast is just because there’s a positive marker doesn’t always mean that we have to treat that marker, and there are some patients — just to use a hypothetical example — they will start off with six positive markers, and then after a couple of months of therapies, they will only have two positive markers. They still have two positive markers, but all their symptoms are gone. For that person, I consider that, in a lot of cases, a clinical win, where no further treatment is necessary, so I’m really glad to see you kind of echoing that and having a little bit more of a conservative approach.

DrFSR: Absolutely.



Episode wrap-up

DrMR: In close, is there anything important that you want to leave people with in terms of closing thoughts or actions if there’s anyone who is listening to this and these things are resonating with them?

DrFSR: I’d like to say that patients should do their own research and they should be well educated. There are different schools of thought on this. The area is scientifically evolving, and I think part of the challenge we have is the cost of the testing and the validation of the testing.

DrMR: Right.

DrFSR: Many universities and university hospitals that work with the physicians do not necessarily accept or agree with this other alternative or expanded testing that we have discussed, but again, I always say that there’s a story behind it, and if you listen to patients’ stories, you will see that there’s a repetition of the same pattern, if you will. So patients need to be actively involved in this process. You cannot just go by one test or one book or one opinion, and eventually it’s going to be an interactive process between the patient and the team of doctors who work with the patient.

DrMR: I agree. I think that’s sound advice. And, Doc, where can people track you down if they want to read more from you or hear more from you or contact you?

DrFSR: Well, we don’t have a regular blog. Time hasn’t quite been there. We are making a presentation, as I said, in Fort Lauderdale in October. The ILADS Society may have some of that information in the form of a CD or some other material. I’m not sure how they do it. My information is available on our website at More or less, everything patients need to know about the practice, we have tried to keep it up to date on the website.

DrMR: OK, great. Well, Dr. Rahbar, thank you so much for coming on the show. I think people are going to get a lot out of this. And thank you for the research that you’re doing. I’ll be curious to follow you and see what findings continue to pour out of your practice, so thank you again for that.

DrFSR: Thank you, Dr. Ruscio. Thank you for inviting me. I appreciate that.

DrMR: Absolutely. My pleasure.

DrFSR: Thank you.

Thank you for listening to Dr. Ruscio Radio today. Check us out on iTunes and leave a review. Visit to ask a question for an upcoming podcast. Post comments for today’s show and sign-up to receive weekly updates. That’s


If you need help diagnosing and treating your SIBO, click here

What do you think? I would like to hear your thoughts or experience with this?


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!