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RHR: SIBO Update—an Interview with Dr. Mark Pimentel


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Dr. Pimentel, associate professor of medicine at Cedars-Sinai Medical Center, discusses some unanswered questions about small intestinal bacterial overgrowth. Find out how he defines SIBO and what is on the horizon for testing and treatment.

Revolution Health Radio podcast, Chris Kresser

Dr. Pimentel has been very active in research and served as a principal investigator or co-investigator for numerous basic sciences, translational and clinical studies in areas like IBS and the relationship between gut flora composition and human disease.  He is widely known and sought out for major scientific developments that he’s pioneered, including the discovery that IBS is a condition of altered intestinal microbial

In this episode, we cover:

7:36  What is small intestinal bacterial overgrowth?
11:20  Testing for SIBO
18:42  The future of SIBO treatment

Chris Kresser:  I’m Chris Kresser and this is Revolution Health Radio.

Hey, everyone.  Chris Kresser here.  Welcome to another episode of Revolution Health Radio.  I’m really excited about our guest today.  We have Dr. Mark Pimentel, a global expert on small intestine bacterial overgrowth, and I’m going to talk to him all about some unresolved questions and problems or issues with SIBO, the SIBO hypothesis, diagnosis and treatment of SIBO, and I’m really looking forward to this, and I hope it’s going to be useful for you as well.

Mark Pimentel is an associate professor of medicine at Cedars-Sinai Medical Center in Los Angeles, California.  His medical training includes a fellowship in gastroenterology at the UCLA Affiliated Training Program.  He’s been very active in research and has served as a principal investigator or co-investigator for numerous basic sciences, translational and clinical studies in areas like IBS and the relationship between gut flora composition and human disease.  Dr. Pimentel is widely known and sought out for major scientific developments that he’s pioneered, including the discovery that IBS is a condition of altered intestinal microbial balance, which we’ve talked about before; the recognition that antibiotics improve IBS, irritable bowel syndrome, and this officially legitimized IBS because before these discoveries, IBS was often considered to be a psychosomatic condition; the discovery that methane produced in the gut by specific microbes produces constipation, which we might talk about today; and then his work linking SIBO to IBS and other conditions.

So again, I’m really, really excited about this episode, and without further ado, let’s get to it.

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OK, now back to the show.

Chris Kresser:  Dr. Pimentel, thanks so much for being here.  I really appreciate it.

Mark Pimentel, MD:  It’s my pleasure.  Thanks for inviting me.

Chris Kresser:  Maybe you could start by telling us a little bit about how you got interested in SIBO in the first place.  I’m always curious to hear how people get involved in their field.

Mark Pimentel, MD:  Well, it’s interesting.  I mean, when I was in residency and planning my fellowship and my career, obviously IBS was not on my radar.  I think what I learned very quickly when I started to learn gastroenterology is that IBS was an area not too many people were interested in, and as I started to see these patients, I was fascinated by the fact that they all had distention and bloating, and it seemed to me that bacteria and fermentation in the gut could be an important aspect of that.  I also began to notice under the tutelage of my mentor that these patients often had positive breath tests, and we began treating them with antibiotics, and we got some remarkable results, and so this really was the beginning of a long journey into trying to help a group of patients that really were outcasts in medicine.  Doctors just didn’t want to see them, didn’t know what to do with them.

Chris Kresser:  Right.  For all the listeners, at that time, IBS was largely considered to be a psychosomatic condition, right?  Antidepressants — or maybe no treatment at all — was what was offered at that point.

Mark Pimentel, MD:  Yeah, I mean, in some of the early days and some of the early patients that I saw, I remember distinctly this one retired lady who had IBS.  She brought out a paper bag full of six different psychotropic medications, and she said, “I no longer need these medications,” but that was the therapy she was given, to no avail, and it didn’t help her.

Chris Kresser:  Yeah.  You were definitely ahead of your time now because I would say it’s pretty universally recognized — well, maybe I’m getting ahead of myself! — but at least within the scientific community, that altered intestinal microbiota is a major player in not only IBS, but a whole range of other diseases, both gastrointestinally and even extra-intestinally.  Things like fibromyalgia and even depression now are being linked to altered intestinal microbiota, so you were a real pioneer there, and I just want to thank you for your contribution to that.

Mark Pimentel, MD:  Well, it’s humbling to actually see this evolution because even before the term ‘microbiome,’ we were kind of yelling in the wilderness and saying, “You know, microbes may be important in some of these functional disorders.”  It wasn’t very well accepted, obviously, in the beginning, but it’s really nice to see the evolution of the science, and really it’s come such a long way.  Very exciting.

Chris Kresser:  It has, yeah.  We were chatting before.  Most of my listeners know that I struggled with a long chronic illness that started with an infection in Indonesia, and I saw you at some point early on in that journey, and that was enough to convince me that some alteration of the gut by a viral infection or a parasitic infection or antibiotic use — all of which were actually historically present for me — was something that could create so-called IBS or potentially even IBD.  There wasn’t much research on that at that time, but my own personal experience of it was enough to convince me!

Mark Pimentel, MD:  Yeah, it’s very interesting how a lot of these patients are describing exactly the scenario you had, and we’re learning a lot from that, actually.  I have to say just briefly, my largest group of researchers are my own patients because they teach me the answers.  You have to listen to your patients because they’re telling you what they’re feeling and their experiences.

Chris Kresser:  Yeah, I feel the same way.  I’m so glad to hear you say that.

So let’s move on to SIBO.  This episode, since we have Dr. Pimentel here, I really want to focus on, not some of the basics of SIBO, which we’ve already covered at some length, but I want to talk to Dr. Pimentel about some of the unanswered questions, at least in my own mind, and get his take and opinion on those.  But before we dive in, maybe we can just start with what should be or would seemingly be a straightforward question but maybe is not, which is, what is SIBO?  How are you defining it now?

What Is Small Intestinal Bacterial Overgrowth?

Mark Pimentel, MD:  I think the term SIBO is evolving in a sense because initially we used the term small intestinal bacterial overgrowth based on breath testing, and I think breath testing has a lot of merit, but SIBO does not equal SIBO does not equal SIBO, and I think both from a breath testing standpoint and even a microbiology standpoint we know there are different forms.  But essentially the bottom line is that it’s an overcolonization of specific bacteria, usually the colon bacteria, into the small intestine, where they don’t belong.  Ruminating animals, for example, like cows and sheep and horses, they have a lot of bacteria through their small bowel in order to help them absorb and digest grass, which they don’t have enzymes for.  Humans don’t need that.  Our small bowel is almost sterile — on purpose — because we’re sophisticated, we can digest many different things, and we have all the enzymes for that.  And when all this bacteria builds up in the small bowel, then you get this bloating, gas and distention, and a lot of changes in bowel function.

But the reason I started by saying, “SIBO is not SIBO,” is because as we move forward, we’re seeing that if you have methane type of organisms in the small bowel, you’re getting constipated, and if you have hydrogen type, you get more of the loose bowel movements or mixed IBS.  And it’s going to get even more complicated because we think that the type of bugs may be associated with different diseases.  Maybe fibromyalgia has a different type of overgrowth than, say, just simple IBS.  So those complexities are emerging.

Chris Kresser:  Right.  And I’ve seen some studies that show that apparently healthy controls — and of course, I always wonder about that because the definition of a healthy control has certain assumptions that I’m not sure are correct, but let’s just assume that they are healthy — up to 20% can have SIBO, at least according to breath tests or other testing methods, so what do we make of that?  Is it possible to have SIBO and be completely asymptomatic, in your opinion?

Mark Pimentel, MD:  That’s a great question.  The breath test, of course, has its limitations, and that may be part of the reason why some of the healthies are positive, but I like where you’re going, and you’ve obviously put a lot of thought into this, because healthy is not healthy.  Even the definitions of what is a normal bowel habit in textbooks were based on studies that didn’t exclude IBS patients.

Chris Kresser:  Right.

Mark Pimentel, MD:  The range is three times a day to three times a week as a normal bowel function, but after treating overgrowth in thousands of IBS patients and all of a sudden they’re having a perfect bowel movement every day, some of the IBS patients are better than healthy people that I’ve seen.

Chris Kresser:  Right!

Mark Pimentel, MD:  So it really speaks to the question, OK, so what is true normal?  And if we don’t know what true normal is, then it’s really hard to define healthy and then to compare breath tests between healthy and unhealthy.  So it’s complicated, and the answer to your question is, if we take super-healthy people who are spot-on perfect, the chances of having an abnormal breath test are very low, less than 5%.  But people might critique that and say, “Well, super-healthy is not normal either.”

Chris Kresser:  Well, yeah.

Mark Pimentel, MD:  It’s splitting hairs.

Chris Kresser:  Yeah.  It may not be common, but I would like to think it’s normal for humans.  It’s, perhaps, our default state if we don’t get in the way of that.

Mark Pimentel, MD:  Right.

Chris Kresser:  And certainly everyone listening to this show is looking for that super-healthy state, so I appreciate that distinction.

Testing for SIBO

Let’s talk about breath testing next because that’s something I really wanted to go into some detail on.  As some listeners will know, there are different kinds of breath tests.  There’s a lactulose breath test and a glucose breath test, and I want to talk to you about some of those distinctions.  At this point, do you look at breath testing as being kind of the best compromise available, in the sense that other test methods are invasive and if you’re sampling a part of the small intestine, if SIBO is patchy, you may miss it because you’re getting a portion of the intestine that doesn’t have the overgrowth?  Tell us just kind of in a general sense where you’re at in terms of looking at breath testing as a whole category.

Mark Pimentel, MD:  Well, I think this is where is gets confusing for patients because, for example, Mayo Clinic doesn’t like breath testing, so they do a lot of aspirates.  They tend to want to take the sample.  Taking a sample is very expensive.  The validity of that is questionable, too.  I mean, we don’t really know what part of the bowel to culture for your best result.

Chris Kresser:  Right.

Mark Pimentel, MD:  You hit the nail on the head.  It could be patchy.  We don’t culture everything, so maybe we should be doing PCR or sophisticated genetic techniques to look at the bacteria.  Mayo Clinic doesn’t do that for their aspirates.  All they do is culture, so they’re missing stuff.  So there’s no perfect technique, but I have to say that what we’ve seen in the papers and in our own experience is that breath testing is kind of a compromise.  It’s extremely easy to do.  Patients can do it even at home, in some circumstances, with some of the kits that are available, and it’s convenient.

But what I will say is that when the breath test has methane in it — and I suspect we’ll be talking about that a little bit later — that’s super accurate.

Chris Kresser:  Yeah.

Mark Pimentel, MD:  So in that context, when you have methane on the breath test, that’s extremely predictive.  Hydrogen is a little bit more challenging.

Chris Kresser:  OK.  Let’s talk a little bit about methane detection now.  I know this is an area where you’ve made big contributions, and up until fairly recently, a lot of commercial labs weren’t even offering methane as an option.  Methane has some specific effects and characteristics compared to hydrogen, so maybe you could tell us a little bit about why it’s important to test for methane overgrowth and if you’re still using 3 parts per million at baseline as the cutoff there.

Mark Pimentel, MD:  Yeah, so methane is intimately related to constipation.  In fact, there’s now a large series of studies, various investigators around the world proclaiming the same results, and a meta-analysis.  But essentially, if the methane is present on the breath test at greater than 3 parts per million at any part during the test, the association to constipation is over 90%.  The other very interesting aspect of methane is that methane is proportional.  So the higher the area under the curve on the breath test for methane, the greater the patient’s constipation severity is.  And we know from animal studies that giving methane, just the gas itself, constipation or slows transit remarkably by about 60%, so getting rid of the methane is key.  The breath test is very accurate at picking up methane, and I think, to be honest with you, there’s almost no argument about methane and breath tests in terms of the utility of breath tests in that particular circumstance.

Chris Kresser:  And is it the same difference there between lactulose and glucose in terms of detecting methane?  Is lactulose more likely to detect it for the same reasons?

Mark Pimentel, MD:  The interesting thing about methane is that methane is not driven by the lactulose or the glucose; it’s driven by the presence of hydrogen, because hydrogen gas from fermentation of other bacteria fuels —

Chris Kresser:  It’s the food for the methanogens, right?

Mark Pimentel, MD:  Right, exactly.  I would say more than 90% of the time, just at baseline, the methane is already elevated, whether you’ve given the glucose or the lactulose or not.  So it really doesn’t matter which breath test you use because the methane will be there, and you don’t see, necessarily, a rise in methane all the time.

Chris Kresser:  OK, I have a bonus question for you, and this is just selfish clinician-to-clinician from a test result that I saw the other day.  It might be a little over everyone’s head, but we have a patient, and we treated them for SIBO.  They had high hydrogen levels and methane levels.  Then on the retest, their hydrogen was actually zero at nearly every time interval, but their methane was still a little bit elevated.  How is that possible since the methanogens require hydrogen to produce the methane?

Mark Pimentel, MD:  There are different methane profiles, and this gets a little complicated.  There are methane profiles where methane is elevated throughout the test and hydrogen is zero all the way across the board.  The only way that can happen is if the methanogen organisms are colocalized precisely where all the hydrogen organisms are.  In other words, the methanogens are eating up every bit of hydrogen that you find on a breath test because they’re sitting beside each other throughout the gut.

Chris Kresser:  Interesting.

Mark Pimentel, MD:  When you see hydrogen on the breath test, it means that the methanogens are not all localized to where the hydrogen producers are, and we call that ‘hydrogen escape.’  It’s kind of a term we made up.  Let’s say there’s 3 or 4 feet of bowel where there are hydrogen producers, but there are no methane producers in the area, so you’re getting this hydrogen release and you’re picking it up on the breath test.  So maybe you’ve gotten rid of the hydrogen in that area and therefore you’re only left with areas with some methanogens colocalized with hydrogen.

Chris Kresser:  Yeah, that makes sense.

Mark Pimentel, MD:  That’s kind of hypothetical.  It makes sense, but of course, you can’t dissect humans to prove that.  You can only kind of theorize how it works, but that’s how we think it works.

Chris Kresser:  It’s a reasonable theory, yeah.

OK, great.  Before we move on to treatment,  let’s talk a little bit about what’s on the horizon in terms of testing.  I’ve read a few papers that talk about electronic nose or metabolomics.  Is there any methodology that you’re aware of or excited about that might help us to have more accurate testing without being invasive or costing too much money?

Mark Pimentel, MD:  Well, I think that there are a number of people looking at volatiles in the breath for detection of cancer, for detection of getting bacterial signatures.  There’s a lot of excitement around that.  The problem is I haven’t seen anything that is kind of an aha moment yet.

Chris Kresser:  Right.

Mark Pimentel, MD:  I think it’s a matter of time because so many people are working on this, so I’m very excited, but I’m waiting for the aha moment that somebody says, “OK, this is very predictive of X, Y, and Z, and this is how you treat it.”  And I think those are the connections that will be made in the next few years.

Chris Kresser:  Maybe we’ll have SIBO-sniffing dogs.

Mark Pimentel, MD:  No doubt!

Chris Kresser:  We have cancer-sniffing dogs, mold-sniffing dogs now.  I wouldn’t be surprised!

Mark Pimentel, MD:  With YouTube, it’s only a matter of weeks.

Chris Kresser:  Right!

The Future of SIBO Treatment

All right, so let’s talk a little bit about treatment now, and specifically, along the same theme here, not the treatment that goes well and works perfectly as advertised, but some of the issues that we see with treatment.  The first thing I want to talk about is some of the studies that have shown recurrent rates of up to 45% in people that have been successfully treated.  They go breath test negative, and then almost half of those people are getting SIBO again.  Do you accept that number, is that your experience, and what do you think is happening there?

Mark Pimentel, MD:  The TARGET 3 Study, which is the latest rifaximin study, is the only study, really, that’s blinded and controlled for treatment and retreatment.  And what I was shocked at when I saw the results of the trial is it almost mirrors what happened in my clinic back when I started using rifaximin.  You can’t say that in my clinic now because I basically see the patients that fail, because everybody in the community is using it this way, and so I’m seeing the tougher cases.  But back when I started using rifaximin, this was exactly the rate.

We see about 72% of people have some response to rifaximin, for example.  Using the FDA endpoint, the patients who responded by FDA criteria, over 18 weeks 36% of them never relapsed, and they just dropped out of the study because they were done.  They didn’t relapse.  And then the 64% who did relapse then were randomized into the double-blind phase of the trial and responded again and again versus placebo, which was good.

But the point is that pretty much mirrors what I see.  I see about 70% of patients with IBS or SIBO — however you want to frame it — but definitely with the breath test, more than 70% respond to rifaximin.  What we then are looking at is relapses, and I think for sure I’m seeing about a third of patients that I don’t see them for months and months and months, and they never have a relapse, maybe more than a third.  But then the rest of them, they will have relapses.  And it depends.  Some of them relapse in six months, some of them relapse in three months, and some of them relapse in a week, and those are the tougher cases.

Chris Kresser:  So what do you think is driving the relapse?  I know you’ve done a lot of work on intestinal motility and impaired motility and its contribution to SIBO and relapsing SIBO, so maybe you could talk a little bit about that and if there are any other factors that you are investigating right now in terms of the propensity for relapse.

Mark Pimentel, MD:  Well, this speaks to kind of food poisoning triggering everything because this starts to get into that area, but we think food poisoning causes some kind of neuropathy or motility disturbance of the intestinal tract, and then you get stasis or slowing, and then the bacteria start to accumulate.  I would say that probably 70% or 80% of patients who come to me with overgrowth, that’s the mechanism of action, or at least that’s what we feel is the mechanism, and that it’s a reduction in the migrating motor complexes as a result of some insult in the past.

Where it gets tricky is that depending upon how bad that is or how bad the motility is will probably predict how quickly the bacteria will return.  The problem is we don’t have a good grading system for how bad the motility is, so I can’t tell a patient, “Look, you have this test; you’re going to relapse in two months.”  We don’t have that kind of sophistication yet.  I’d love to see that come.

When the patients relapse in one week or two weeks, then we start to be concerned that it isn’t just a motility disorder, that maybe it’s an adhesion or some other mechanical cause for the overgrowth to begin with and not just the motility disorder.

Chris Kresser:  When you say ‘impaired motility,’ is that always clinically evident, like delayed transit time, or is it possible to have a defect in the migrating motor complex, but still have regular bowel movements?

Mark Pimentel, MD:  The migrating motor complex is responsible for cleaning the gut — or the small intestine, specifically — when you’re not eating.  The intestines have kind of like two computer programs.  One is eating mode, one is cleaning mode, and usually it’s the cleaning mode that goes bad in terms of the bacterial overgrowth.  If you were to ingest a meal, for example, and you measured stomach emptying, stomach emptying is perfect.  But that’s not telling the whole story, so if we really want to know what the patient has, we do a manometry of the upper gut.  We put a tube in that detects motor function, and we’re able to see how many migrating motor complexes, what happens when they eat, how are the mechanics of the gut working, and we can diagnose these things.  But if you have no migrating motor complex in 6 hours, is that severe, or do I have to do it for 24 hours to know how severe it is?  The patients don’t want to have a tube in their nose for 24 hours, so it’s really hard to grade these things.

Chris Kresser:  Mm-hmm.  What do you think of the idea that dysbiosis or changes in the microbiota in the colon could be a predisposing factor to SIBO and SIBO recurrence?

Mark Pimentel, MD:  I can’t discount changes in colon in terms of a response to antibiotics, although I will say with rifaximin, specifically, I think this has probably convinced some of late critics who were saying, “Well, maybe it’s the colon, maybe it’s the colon,” the stool study that we did and microbiome work that has been described at meetings but will be fully presented at the ACG meeting in Hawaii, there really is no change in the flora of the colon in these patients with overgrowth or IBS after rifaximin.  So rifaximin is not doing anything to colon bacteria, at least in stool.  I can’t tell you the cecum or the higher parts of the colon.  And no increases in yeast and other things in the case of rifaximin — in the stool, again, specifically looking at that area.

Chris Kresser:  Right.

Mark Pimentel, MD:  We think that all along, as we’ve been saying rifaximin dissolves in bile, will work mostly in the small bowel, not in the colon when the bile is gone, rifaximin crystallizes — I think we’re all on the same page with that now.  But I can’t totally dismiss the possibility that it is a dysbiosis in the colon.  We’re going to require more work there.

Chris Kresser:  Right.  OK.

Mark Pimentel, MD:  One more point on that, though.

Chris Kresser:  Sure.

Mark Pimentel, MD:  I will say in our animal models where we give food poisoning, Campylobacter, to the rats and then we follow them over time, they develop overgrowth.  But when we do PCR of the colon, we see absolutely no differences between the colon, the cecum, or any part of the colon in the rats who got Campy and the rats who never got anything and are normal.  It’s all in the small bowel, the detrimental events.

Chris Kresser:  Yeah, that’s really interesting and would definitely seem to support your argument there.

Mark Pimentel, MD:  Yes.

Chris Kresser:  Let’s talk a little bit about diet.  Within the, let’s call it, allied health professional world, functional medicine, alternative medicine community, it’s common to prescribe a low-FODMAP and even low-starch or no-starch diet during treatment for SIBO, and the thinking there is that these are carbohydrates that are poorly absorbed and can become food for the bacteria that are overgrown in the small intestine.  We ourselves at our clinic have been doing that for some time, but I have a couple of questions about that in my own mind, and I’m curious to get your take on it.

Number one is I saw a study recently — I’m sure you saw it — that showed that rifaximin plus partially hydrolyzed guar gum was more effective than rifaximin alone, and that’s essentially a prebiotic that would seemingly be expected to feed the bacteria in the small intestine, but yet this study showed that it significantly improved the treatment.

And then the second thing is that, as far as I know, there’s been no study yet that has examined the efficacy of a low-FODMAP or low-residue diet during treatment other than an abstract that was presented at Digestive Disease Week a couple of months ago, and I haven’t been able to track down the full paper, so I’m curious to hear your thoughts on that.

Mark Pimentel, MD:  Well, I can say you’re extremely well read because, yes, these are issues, and these papers are very, very interesting and hard to put into the context of this.  You’ve opened up a lot of things to talk about, and I’m just trying to figure out where to start, but let me start with the guar gum aspect.  I have told my patients from day one of rifaximin or treating with antibiotics — and this goes back to the 1980s; this is an old microbiological concept — happy bacteria, happy and well-fed bacteria, are more sensitive to antibiotics and are easier to kill.  What that means is that most antibiotics work on the replicating cell wall of bacteria.  When bacteria are in hibernation, starving, distressed, they wall off, don’t replicate, and they just sit there, waiting for conditions to improve.  That’s a survival mode.  So when the bacteria are in survival mode, antibiotics won’t penetrate and won’t work as well.

Chris Kresser:  Mm-hmm.  I have heard you say that.

Mark Pimentel, MD:  If you give guar gum or you augment their eating — so now you’re feeding them, they’re thrilled, they’re enjoying all that food — they’ll be more sensitive to rifaximin.  So when I treat with rifaximin, or antibiotics, in general, for these IBS patients, I don’t want them to be on a low-FODMAP diet simultaneously or any kind of carbohydrate restrictions.  I want those bacteria happy and fed because they’ll respond better, in my experience, and the guar gum study kind of supports that notion.

Now, speaking to low-FODMAP diets, for example, it’s kind of a joke I tell patients, and I don’t mean to be flippant, but it you don’t eat any food at all, the bacterial overgrowth will be better.

Chris Kresser:  Right!

Mark Pimentel, MD:  Looking at the entire spectrum of people publishing papers and/or books about diets for SIBO or for digestive health, the more restrictive you make the diet, the less the bacteria is going to be happy, or you’ll starve the bacteria out, but you want to do it within a rational and a reasonableness for the patient because we all want a relatively normal life, we all want to walk with our friends into a restaurant and at least be able to get something and not be so difficult, so that’s kind of how I start my conversation in the clinic.  The low-FODMAP diet works.  I mean, there’s no question.  Studies show it works.  I’ve experienced its benefit.  It’s just difficult for patients to maintain in the long term.

Chris Kresser:  Mm-hmm.  I’ve also seen some studies — I’m curious to get your take on these — that the low-FODMAP diet over the long term may actually decrease bifidobacteria production in the colon, which would make sense, given that that’s the substrate that those bacteria use, and therefore, there may be some disadvantage to doing a really strict low-FODMAP diet.  Maybe it’s helpful for SIBO or IBS recurrence, but maybe it’s not great for the colon.  What do you think about that?

Mark Pimentel, MD:  I agree.  Sometimes I think the paleo folks have it right because when we think about how we evolved, we didn’t have potato chips and various refined carbohydrates back then that we have now.  And eating whale blubber and seal meat and so forth, those were the staples, and a few berries off of the plains or whatever.  It was a very different time, and the question is, is our digestive tract honed into that type of diet more than it is to what we’re currently doing?  It’s so hard to know, but what I tell my patients is carbohydrates feed bacteria.  You can leave the bottle of oil on the counter for cooking, and it will never become contaminated because bacteria cannot live on oil alone.  You can leave your protein powder in the cupboard, and for the most part, it’s going to be fine.  As soon as you put carbs in something, if you take a teaspoon of sugar and put it in that olive oil, that olive oil’s done in 24 to 48 hours.

Chris Kresser:  Right.

Mark Pimentel, MD:  It’s carbohydrate related.  Now, I don’t tell my patients zero carbs.  I tell them try to eat the carbs that humans easily absorb and digest, so white bread, of all things.  It sounds like I’m telling them to eat Wonder Bread, but French, sourdough, and Italian bread are white breads, and they’re a little bit better than just Wonder Bread or the off-the-shelf, in-the-bag bread.

Chris Kresser:  So you’re talking about higher glycemic carbs that would be absorbed further up in the digestive tract and less likely to feed bacteria.

Mark Pimentel, MD:  Kind of like a glucose breath test versus a lactulose breath test.  You want to feed them less, as less as you can, and patients tolerate that well.  I call it kind of our low-fermentation diet as opposed to low-FODMAP.

Chris Kresser:  Yeah.

Mark Pimentel, MD:  But everything becomes individualized over time.  Patients will come in and say, “Well, yeah, that diet works great except for onions,” and they’ll tell me, but at least they can go to any restaurant in the country and get a meal and not feel so socially isolated.

Chris Kresser:  Right.  It seems so tricky because I totally get how that diet is better for SIBO recurrence possibly and even symptomatically.  I’ve seen that in our patient population.  But I do get concerned about the longer term.  You mentioned paleo, and it’s definitely true that our ancestors ate a lot of fermentable carbohydrate, like starchy plants and non-starchy vegetables and all kinds of stuff that would provide food for that beneficial bacteria in the colon, so my dilemma is, in fixing one problem, are we causing another one?  That’s what I’m always worried about.  It would be helpful if we had any studies at all to guide us in this area, but as far as I know — and correct me if I’m wrong — there haven’t been any studies specifically about a low-FODMAP or low-fermentation diet related to SIBO.  I know there have been a ton with IBS, but nothing that actually characterizes, does a low-FODMAP diet reduce the recurrence of SIBO after it’s been successfully treated? for example.  I’d love to see that question answered.

Mark Pimentel, MD:  Yeah.  It’s not been answered, but if you want to add another layer of complexity to this whole thing, just to touch on methane briefly for a second, the highest population of methane colonization in the world is Sub-Saharan Africa.  And methanogens, it turns out, based on the microbiome work that’s being done on that particular organism, are super important to help liberate calories from nondigestibles.  So let’s say you have a high-fiber diet.  Humans generally can’t eat fiber.  Cows and ruminating animals have a lot of methanogens because the methanogens help facilitate digestion of fiber.  So what does that mean?  That means that you can get more calories from a meal if you’re a methane producer because you’re liberating calories from things that people who don’t have methane can’t get.

So where am I going with this?  What I’m saying is if you take a population from Africa and immigrate them into the United States, and those folks, for genetic reasons or environmental reasons, have methanogens flourishing in their gut, which is an evolutionary advantage for getting and harvesting nutrients, it’s not an advantage when food is abundant and food is so processed and easily digested that you get more calories, and we’ve seen signals between methane and obesity.  The question then becomes, does one diet fit all?  And the answer is, no, it’s not going to be that way, and maybe it does have to do with your microbial profile benefits from this diet, and your microbial profile benefits from that diet, and it’s not as simple as one suit fitting all.

Chris Kresser:  Yeah, I completely agree with that.  I’ve often said there’s no one-size-fits-all approach, and it’s really interesting to hear you say that about Sub-Saharan Africa because I know Jeff Leach and some other people who are down there studying the Hadza hunter-gatherers and looking at their gut microbiome because they’re one of the last cultures on Earth that is really still living a paleolithic lifestyle.  They’re down there trying to sequence the microbiome.  It’s the last kind of intact, normal human microbiome.

Mark Pimentel, MD:  Right.  At least for that area.

Chris Kresser:  Right, and what they’ve found are some really interesting things, which is that some of the bacterial species that we associate with ill health in the West are actually quite prevalent there in healthy populations, and vice versa.  Bifidobacteria, which is kind of universally considered to be a beneficial species in Western people, is virtually absent in those people.  So I think that really just supports what you were saying, that a great microbiome imprint for someone living in Sub-Saharan Africa could be a total disaster for someone living in the industrialized world.

Mark Pimentel, MD:  Which is probably why probiotics have been challenging to prove effectiveness in certain diseases, is because it isn’t all that simple.

Chris Kresser:  Right.

Mark Pimentel, MD:  I think probiotics are the way of the future, but it’s just trying to find the right key for the right lock.  Science is on to this.  This is a very exciting time in terms of the microbiome, and I have a great deal of optimism for the future in terms of characterizing it and then finding the key and locks for populations.

Chris Kresser:  Yeah, exactly.

I want to step back to something you mentioned when we were talking about eating prebiotic fibers during rifaximin treatment to kind of make the bugs come out to play so that they will be killed.  Different antimicrobials work in different ways, for the listeners’ benefit, and rifaximin appears to work when the antibiotics are multiplying or splitting.  Is that correct?

Mark Pimentel, MD:  That’s always the way antibiotics are best effective, is when the bacteria are happy.  For example, some bacteria form cysts or they sporulate, and once they’re sporulated, it’s done.  You can’t get an antibiotic to go into the cell or do anything.  Those are the kinds of concepts I’m talking about, is that stress or starvation will force those events in bacteria.

Chris Kresser:  Spore forming.  Right.

Mark Pimentel, MD:  Yeah.

Chris Kresser:  Given that, I suppose the same would be true for some of the botanical antimicrobial protocols.  I know there’s been at least one study, which you may have seen, that compared the efficacy of rifaximin with a botanical protocol and found that they were roughly equivalent.  We use both in our clinic.  We will tend to start with a botanical protocol, and if that’s not effective, we’ll go on to rifaximin, or rifaximin plus neomycin if it’s methane.  But would you guess the same thing is true for the botanicals?

Mark Pimentel, MD:  You’re referring to the study from Johns Hopkins?

Chris Kresser:  Yeah, they had the four different botanical supplements.

Mark Pimentel, MD:  Yeah, that’s the one.  I think botanical supplements have some benefit, and I’ve seen some of the studies like that one which show some interesting results.  I’ve done a couple of programs for the naturopathic college, and what I’ve learned from them is incredible because — you know, the funny thing is the naturopathic physicians are giving rifaximin, and when I first met them, it kind of befuddled me.  It would seem counterintuitive, but the scientists in their group — because they have a scientific core — they say, “Well, natural antibiotics are still antibiotics.  Bacteria still get resistant.  That’s where we get our penicillins:  from the plants.”  So the plant effects and side effects are identical to the pharmaceutical effects and side effects, and that really spoke to me in a way.

So I think, yes, there are botanicals — garlic, for example — that can have effects or anti-methanogen effects, and they’ve been studied.  I think the big challenge with the botanicals is not their lack of efficacy; it’s a lack of funding and ability to get good studies out in the public domain and prove their efficacy.  I think the Johns Hopkins study is a great study, it helps to demonstrate that these things are possible, but we need more like that.

Chris Kresser:  Yeah, I would agree.

Let’s talk a little bit about methane treatment.  I believe it was one of your papers that showed rifaximin alone is only effective about 45% of the time — I could be getting numbers wrong — but when you add neomycin, it goes up to 80-something percent.  Is that your current treatment of choice for methane, still the rifaximin-plus-neomycin combo?

Mark Pimentel, MD:  Right.  With methane, rifaximin alone or neomycin alone are relatively ineffective or modestly effective, and with then the combination of the two both in vitro, meaning in the lab, and in humans, we see a dramatic effect.  That is the cocktail we’re using now.  We sometimes substitute the neomycin for metronidazole, although that’s not published, so that’s mostly anecdote.  The neomycin-rifaximin combination was a small double-blind study we published about a year and a bit ago.

The new kid on the block, although it’s not available yet, is we’re in phase II trials of a product that just inhibits methane production.  It doesn’t kill the bacteria — or I should say ‘archaea’ in the case of methane.  It doesn’t kill them.  It gets in and shuts down the machinery that makes methane, because we think the methane it what’s causing the constipation.  You don’t need to get rid of the bugs.  Just stop them from producing methane.

Chris Kresser:  Right.

Mark Pimentel, MD:  In preliminary work, that’s highly effective.  We should have some top-line results in the late fall, so you can look forward to hearing that.  I don’t have results yet.  The study is halfway through.

Chris Kresser:  Right.  Yeah, I definitely will.

Since you mentioned that, any other future avenues that you’re looking into or excited about?  Prokinetics, we haven’t really touched on that yet, but what have you been looking at doing lately in terms of prokinetics for people with the impaired MMC, migrating motor complex, and who are highly likely to relapse?

Mark Pimentel, MD:  There’s a variety of prokinetics on the market.  I don’t like to use domperidone because of the side effects with the heart.  Generally we resort to two potential prokinetics.  One is erythromycin at a very low dose.  It has prokinetic properties at a very low dose and no antibiotic properties at that does, so that’s what we use.  Sometimes we get Resolor, which is prucalopride from Canada, a very potent prokinetic based on serotonin.  It doesn’t have any real side effects except for headache in some patients.  Those are the two.

The problem with prokinetics is we’re kind of hitting a wall.  The circuitry of the gut is not connected well, and you’re kind of forcing it to do something that — and again, it depends on how severe that is in a patient, as to whether the prokinetic will work well enough, so we’re shifting gears almost entirely.  We’ve spent the last six years kind of trying to figure out, well, why is this happening from food poisoning?  And that led to the next blood test for IBS that was just launched about eight or nine weeks ago.  Are you familiar with that?

Chris Kresser:  Yes.

Mark Pimentel, MD:  There are two antibodies that get created after an infection like you described in Indonesia, and these antibodies, when they go up, they’re the ones that are causing the damage of the nerves.  We, in fact, did a study in animals where we just gave the CdtB toxin from food poisoning, not the food poisoning, and the rats get bacterial overgrowth, so we know the toxin that causes bacterial overgrowth and IBS, and we can measure the antibodies in the humans now to that toxin.

So what does that mean?  First of all, it will tell us why you have the overgrowth, what the mechanisms are, and that it is likely this neuropathy.  Two, the antibodies, the higher they are, the worse the patient is.  Three, our entire focus now for the next two years is trying to get that out of the bloodstream and make the nerves come back to life, so really kind of essentially curing the disease.  Will it mean a drug in two years?  Drug development takes time.  But can we prove that that will reverse the disease?  I think in two years we’ll prove that that will reverse the disease, which means drugs will be developed around that concept.  That’s the exciting part, and then you don’t have to worry about whether you’re disturbing the microflora.  We’re basically treating it at the root.

Chris Kresser:  Right.

I’m kind of skipping back here.  There’s a question I wanted to ask you before we finish up.  I saw a study recently that suggested that the length of treatment with rifaximin should be correlated with the severity of the breath test results.  I believe in that study, they used a course of treatment as long as 12 weeks with no adverse effects.  What do you think of that notion, and are you using longer courses of rifaximin in people who have very severely elevated breath test results?

Mark Pimentel, MD:  I’ve seen various groups or research groups around the world trying different cocktails for their patients with overgrowth.  I think that in my experience, and again, I haven’t studied longer-duration therapies, except I will say just in the phase II studies of rifaximin, there was a longer arm, and the longer arm did not work well.  It was really short-term therapy.

I don’t have a problem with longer therapies.  Again, this will be described at the ACG and was briefly described at DDW.  Rifaximin does not cause microbial resistance of any magnitude.  In fact, if there’s any resistance whatsoever, it disappears within a week or 10 days after stopping the rifaximin, and so rifaximin really doesn’t create any kind of superbugs or any kind of resistance, and this was epic amounts of culture, stuff that even Cipro and other antibiotics that are true antibiotics didn’t have to go through.  Rifaximin did.  And it’s not apocalyptic on the microbiome, rifaximin, compared to, like, Cipro.

Chris Kresser:  Yeah.

Mark Pimentel, MD:  But what I was saying is that I think using these longer therapies is fine, very experimental.  I haven’t seen the need for it in my practice so far.

Chris Kresser:  Right.  I’m mostly a natural medicine guy myself, but I’ve always felt like my standard is whatever works and causes the least harm, and if that happens to be a drug, then I’m all for it, and rifaximin certainly does seem to fall into that category.

Mark Pimentel, MD:  Yeah.

Chris Kresser:  Well, is there anything else, before we finish up, that if you could tell folks — let’s say we have folks out there listening to this who have SIBO and it’s recurrent, any words of wisdom or advice or even just a way for them to frame it in their mind that is helpful for them to think about?

Mark Pimentel, MD:  Anything specific you want me to?

Chris Kresser:  Well, part of it for me is just educating patients about the things that we’ve already talked about, so I think that this will help a lot, that SIBO is not necessarily a one-time thing.  I think it helps patients.  It’s not easy to hear that, right?  Most of us would like to be able to just treat it and move on.  But once they do hear that and they accept that, I think it helps with the outcome because then they know that they have to stay a little more vigilant and it’s something that they may have to treat repeatedly, and if they understand the safety profile of rifaximin, that’s a little bit easier to accept as well.

Mark Pimentel, MD:  Right.

Chris Kresser:  So nothing in particular.  I guess the question was more like, is there anything else you want to say?  We’ll put it that way.

Mark Pimentel, MD:  Well, I think I know exactly what you’re getting at.  Let me give you an example of something that happened in one of the clinical trials which kind of speaks exactly to your point.

As a patient in phase II studies of rifaximin, you take rifaximin, if you got better, you move on and get followed through the whole trial.  If you didn’t get better, you’re out.  One of my patients went into phase II.  She got rifaximin, it turns out, after the unblinding, and she came to my clinic, and I said, “Well, it looks like you didn’t do well in the trial.”  At the time, we thought she got placebo.  It turns out she got rifaximin.  She says, “No, no, I’m doing great!”  I said, “Well, what do you mean?  If you did great, you’re supposed to stay in the trial.  How much percent improved are you?”  She says, “Well, I’m 80% better.”  I said, “Well, that’s terrific,” and I said, “Why aren’t you in the trial?”  She said, “Well, they asked me if I’m all better,” and she interpreted it as, “If it’s an antibiotic, I should be cured.  I should be 100%.”

Chris Kresser:  Right.

Mark Pimentel, MD:  And 80% wasn’t like her urine infection in the past.  That’s a point for your listeners to kind of appreciate, that rifaximin is going to make you better when it works, it’s going to make you a lot better than anything we’ve had before, but it’s not like a urine infection where you’re cured, because the motility disorder underlying this is still there and you’re still going to have a little bit of gas and you’re still going to have poor clearance of the bowel, and it’s a bit of a lifestyle change until we have something that gets at the root.

Chris Kresser:  Yeah, that’s really helpful.

Well, Dr. Pimentel, this was certainly educational for me, and I think my audience is really going to appreciate it as well, so thanks so much for joining me.

Mark Pimentel, MD:  Thank you for your time.  This was a lot of fun for me as well.

Chris Kresser:  That’s the end of this episode of Revolution Health Radio.  If you appreciate the show and want to help me create a healthier and happier world, please head over to iTunes and leave us a review.  They really do make a difference.

If you’d like to ask a question for me to answer on a future episode, you can do that at ChrisKresser.com/PodcastQuestion.  You can also leave a suggestion for someone you’d like me to interview there.

If you’re on social media, you can follow me at Twitter.com/ChrisKresser or Facebook.com/ChrisKresserLAc.  I post a lot of articles and research that I do throughout the week there that never makes it to the blog or podcast, so it’s a great way to stay abreast of the latest developments.

Thanks so much for listening.  Talk to you next time.

We have even more SIBO information for you to learn more about its causes and symptoms.


Join the conversation

  1. Kris,
    What about using manual therapies such as Cranial Sacral Therapy and Visceral Manipulation to enhance gut motility and the brain’s awareness and ability to assist in such motility?
    Visceral Manipulation is an Osteopathic treatment that is quite validated for all kinds of digestive disorders, and pelvic and spinal pain. I think of it as like Physical Therapy for the viscera…like if you were on bed rest and needed to relearn to walk and balance again you would be sent to a physical therapist. If your gut stops working due to illness or disease for a period of time then using physical manipulation specific to the part of the gut affected would help the body to relearn to restore its function. Just like neuro muscular re-education for the knee or hip, the gut also has the ability relearn. The visceral homunculus is just under the cortex. Just like the development of fuzzy brain maps that occur in persons with chronic pain due to immobilization, the same would be likely for the gut.
    There are a few excellent Visceral Manipulation PT’s here in Phoenix and they have waiting lists up to 3 months for people who want treatment….because it works!

    • Which also brings up the question of neural and brain re-training techniques (not just the gut), ranging from neuro feedback to guided mediation to Functional Neurology.

    • Lesley
      Could you please give me the information of the 3 PT? I am in Phoenix and would like to make appointment with them. My email is pham_mai2005@yahocom. Thank you!

  2. Thanks Chris, for another fascinating podcast!

    I have a question/comment that I hope you’ll see amidst all this wonderful commentary. For five grueling months I had the worst case of SIBO. I lost a lot of weight because I couldn’t eat due to chronic distended belly/belching (not to mention general trauma from food due to how it made me feel). However, I have managed to overcome this in an unusual way. Apart from a strict healing/nourishing diet with lots of fermented foods, my most important intervention has been physical therapy and breathing therapy (no antibiotics or anti-fungals). I don’t mean superficial postural correction such as straightening up one’s shoulders, but intensive muscle development so that my back is naturally strong and straight, my hips are aligned properly, my psoas muscles are actually involved in functional activities such as walking and sitting, etc…it’s been a lot of work but the results have been astounding. My TMJ is resolved, my hearing impairment is improved, my vision is improved, back, neck and foot pain ceased….and SIBO has been thoroughly resolved.

    Which brings me to my question: Is it possible, given how digestive disorders such as SIBO are reaching unprecedented levels in our society…that if we take a step back and see the body holistically, we notice that everyone’s posture is also deteriorating at the same rate, with folks hunched over looking down at their phones, slouched at the computer, sticking their necks out as they commute long distances…that THIS could be a majorly overlooked cause of digestive distress? Perhaps the ribs are applying inappropriate pressure into the pancreas, for example, compromising gut motility? (I’m not an expert in that regard so wouldn’t know if this example makes anatomical sense, but you get the idea). Could it be that we’re focusing so much attention on the gut, and on fixing it because that’s where the symptoms manifest, when really in many cases we might be missing the boat in terms of the greater cause of systemic distress….which is why recurrence of SIBO is so common…because the underlying cause has still not been addressed? I would love to hear your thoughts on this, thank you!

    • YES!!! That might also explain those of us with high breath tests and few symptoms, or why Sub-Saharan’s can have lots of methanogens, but no illness symptoms. Perhaps the bacteria themselves are not the root cause.

      Bacteria in the mouth are commonly blamed for cavities, yet traditional cultures, with no tooth brushes, had lots of mouth bacteria and no cavities. Turns out the bacteria invade decaying teeth, rather than causing them – it’s the diet which causes the decay. Maybe SIBO bacteria are a similar red herring – showing up as an indicator of other problems.

    • Dear Ana – If you are still participating in this blog, I’d love to know of how you restored your alignment. How did you start? What did you start with? How much time each day do you need to devote to restorative movement (while hopefully retaining good alignment awareness the rest of the time.)?

      Myself I am newly exploring The Psoas Book by Liz Koch, Alignment Matters by Katy Bowman and Pain Free by Pete Egoscue. I’ve just begun making myself move again with the Garipoli’s Qi Gong for Detox routine. I’m also doing the Egoscue ‘static back’ position using gravity to align my pelvis. Its simple and effective. – thank you

      • Hi Doris,
        I am following the comments on this article. I saw that you have found the Egoscue Method. It is the only intervention (after trying everything) that helped me with my chronic knee pain and the occasional back spasm. I cannot recommend it enough. After being introduced to it via ‘PAIN FREE’ I went to an Egoscue Clinic and began working with a therapist. My improvement went even faster. I do not know where my body would be without it. Pete Egoscue has started making videos with Sonima Fitness. They are on youTube. A lot of them are very advanced workouts, but some of them are therapy too. From my opinion, his best book is ‘Pain Free for Women’ it gives exercise menus for all the stages of a womans life. Best wishes.

      • Doris,
        I am very ill and haven’t been able to restore many things as a result of having much trauma in my life, a tick infection, blastocystis hominis, working in a toxic work environment. Being given many antibiotics and never told to take probiotics. I have candida that spread so bad its into my tissues feeding off of the heavy metals. Every day is a blessing. Medicine and technology wasn’t there for me 28 years ago when I came down with Candida and IBS (which was a parasite no one checked for or understood) Chronic adrenal exhaustion from stress from no one understanding what was going on has been detrimental to my recovery.
        I don’t really have anything to say further other than to offer others help through my struggles and research.

  3. Thank you for a wealth of information on SIBO. Would it be possible to post references to the studies you discussed? It would be very helpful for the scientists in your audience to get additional information, and quite time saving versus a complete literature search on pub-med.
    Thank you.

  4. Really interesting talk here!

    I got an idea – one of effects of the diabetic drug Metformin is alteration of the bile acid pathway – the acid is no longer re-absorbed in the terminal ileum and continue down to the colon. So, just maybe, combining Metformin with Rifaximin could mean that the antibiotic would also have effect in the colon. IMHO, this could be either good or bad, depending on the goal.

  5. Fantastic webcast Chris. Very informative. Great to hear MD and functional practitioner speaking so respectfully and intelligently to each other.

    As someone who recently received Rifaximin treatment for SIBO and saw great benefits and more recently some set backs, it was helpful to hear that SIBO treatment may take time and won’t necessarily be cured with one course of Rifaximin.

    Thanks for doing such a great webcast

  6. Would you agree that the autoimmune disease of Ankylosing Spondilitis (supposedly caused by overgrowth of the gram negative Klebsiella bacteria) is a form of SIBO ?

    I have never heard of Rifaxamin recommended/used for this, and it is not available in the country where I live. Nor are the methane breath tests available here.

    I have had no improvement on implementing Dr Sibecker’s botanical protocol, nor any long lasting improvement with Bactrim. Only a constant strict no starch/no lactose diet seems to keep it “manageable”, along with supplemental magnesium. Can’t say that I notice any improvement with LDN, nor probiotics. Any insights please ?

    • I just did a round of the rifaximin and still feel terrible. I combined this with visceral therapy which helped for about a day and then I would feel bad again. I have only added the boulardii – but so confused on what type of probiotic to take and how to find these single strain probiotics that are free of all the allergens – soy, dairy.

      • I had to take rifaximin for 18 months before I believe it was killed off. 2-550mg per day for 10 days, then wait a month then repeat. I did fell better off and on but sometimes even worse during treatment . I thought of it as all those toxins from killing bacteria were more concentrated until the body could be rid of them. I ignored diet except to eat as I felt I could. I avoided probiotics, since I did not know which bacteria I was trying to kill off, and I did not want to be adding more of it! good luck.

      • I am taking VSL3. very expensive, but it is what my dtr has me on WITH the Xifaxin. I was taking boulardii, but she preferreed VSL3. Still working on the entire protocol….so cant give you more than that!

  7. Hi Chris,

    Thank you for the great interview. I was expecting to hear something about fecal transplants in this discussion but it was never mentioned.

    Is this a treatment that is still being considered for SIBO? I’d be interested to hear Dr. Pimentel’s take.

    Thank you!

    • I got the impression that Dr. Pimentel feels that the status of the microbiome plays a significant role in SIBO pathogenesis. (I could be wrong, so please correct me if that’s the case Mark!)

      I’m not so sure, however. We know that antibiotic use is a predisposing factor to developing SIBO, and one of the primary effects of antibiotics is to alter the microbiome.

      With this in mind, I’m definitely interested in how FMT might help with SIBO prevention. I’m less certain or confident that it will help with SIBO treatment, but only time will tell.

      • If you visit the FMT boards on facebook, you almost exclusively see those with severe and debilitating SIBO/Dysbiosis almost strictly from antibiotic usage. Many of us can hardly eat or function. I am extremely disappointed that this is NEVER discussed amongst practitioners treating SIBO. I imagine more than 50% of their patients have SIBO due to antibiotic usage. If this is the case, antibiotics to resolve it seems extremely risky and further life-altering for the patient. This subject desperately needs to be brought to light, despite Dr. Pimentel’s claims that Xifaxin has a high safety profile. Antibiotics destroy the microbiome. Xifaxin is STILL a broad-spectrum antibiotic and the microbiome is too diverse to say it will not cause a number of other overgrowth’s that may be life threatening.

  8. I thought the interview was excellent in every way….minus one point. I felt a bit duped upon finding out immediately after listening, that Dr. P. Created the blood test that he referred to. I wish there had been more discussion and transparency on that vital point. This would have felt more honest and might mitigate common beliefs that someone is “out to gain or advertise” on such medical webcasts.
    Thank you for your work.

  9. Implied from this interview is that intermittent fasting is a bad idea pre-treatment or during treatment because one of its otherwise touted benefits is starving bad bugs, and doing so could help send them into hibernation mode? Whereas it seems like IF might be a good strategy post-treatment? Thoughts?

  10. I have methane SIBO and have a few questions after listening to this OUTSTANDING interview (thank you both!!!):
    1) At first it sounded like Dr. P said that only some people’s cause of SIBO was due to damaged MMC, but at the end, in his wrap-up about Rifaxamin and a patient being 80% better, he said to remember that it kills the bacteria/archaea but doesn’t cure the root cause — for me that implied that ANYONE with methane type will not be “cured” and have recurrence. Is that correct? I’d previously heard Siebecker say that only SOME people react to the food poisoning toxin in an autoimmune type of way that results in damage to the MMC, so I’m confused about that. In other words, if I have methane SIBO, does that automatically mean that I have a damaged MMC?

    2) So carb restriction should only happen for a precautionary period following treatment and a negative retest? And what about probiotics, when do they start?

    3) Re existing CCFM patients: will you be recommending guar gum during treatment going forward? also will you be recommending the new blood test that he mentioned to test for the antibodies in order to determine severity/damage to the MMC?

    4) Does methane imply hydrogen bacteria also? In other words, if I’m testing positive for methane but not for hydrogen, does that imply that I have BOTH archaea and hydrogen, and that the hydrogen just isn’t showing up because it’s all being consumed by close neighbor colonies of hydrogen-producing bacteria?

    In all of the online summits, podcasts, etc, it’s the first time that I’ve seen Dr. Pimentel featured, so again, thank you Chris!

    • Sorry, my question 2 should have read ” prebiotics ” (not probiotics) and question 4 should read “BOTH archaea and bacteria” (not hydrogen).

    • NCNM’s (National College of Natural Medicine) annual SIBO symposium always features Dr. Pimintel. I believe you can purchase recordings – not exactly sure how, but contact them or their SIBO Center to find out.

  11. I was just diagnosed with SIBO and want to take rifaximin, but am currently breast-feeding my infant twins. Do you know if this antibiotic is safe to take when nursing?

    • Call the Infant Risk Center (google it) & ask them.

      Per LactMed:
      Drug Name:Rifaximin
      Rifaximin is poorly absorbed orally and used only for gastrointestinal infections. It is not likely to reach the breastmilk or bloodstream of the infant or cause any adverse effects in breastfed infants after maternal use. However, no published experience exists with rifaximin during breastfeeding; therefore, an alternate drug may be preferred, especially while nursing a newborn or preterm infant.

  12. Just wanting to confirm that Xifaxan doesn’t lead to increased fungal/Candida growth in the intestines. The implication from what Dr. P said is it shouldn’t because it’s not disrupting the rest of the bacterial biome (unlike Cipro, etc), but I’d love a confirmation and am curious if that is something you’re seeing in your clinic. I was treated with Xifaxan on and off for a year and developed a difficult Candida gut infection I had always blamed on it.

    • Yes, you are correct. That is a big component of the Small Intestine that is overlooked. SIFO is also quite common, which includes yeast. Wiping away the bacterial SIBO will allow the yeast, if present, to thrive.

  13. Hi,

    Very informative material, thank you!

    For someone with very high methane (150 PPM) SIBO, and MARCoN’s in nose, on Thyroid medication (Hypo), constantly constipated, suffering from “severe” insomnia most likely due to high cortisol (or MSH effects), and currently testing for CIRS (but most likely positive and a result of MOLD exposure), are there any special considerations in the treatment plan to ensure one doesn’t interfere with the other? (i.e. treatment for SIBO or CIRS/MARCoNs might affect thyroid meds)

    Also, looking to understand the root cause. Is it more likely that SIBO caused CIRS and lowered resistance to mold effects, or is it more likely that exposure to mold triggered CIRS (due to gene) and in turn caused the SIBO?

    Dr. Nett is fantastic by the way!!!

    • Good point Jeff, I believe that everything starts as a result of gut issues and it seems to be all related…for example acellular carbs may promote overgrowth and toxins from grains and other craps promote CIRS and it’s related with SIBO as well, together leading to mold sensitivity…
      the evolutionary clues together with the observations make think that everything is connected…of course when you already damaged, it can be possible that getting rid of junk foot might not be enough to fix the issue…I think that the Homo Heidelbergensis found in Spain was hardly sensitive to the mold in their cave…

  14. Hi, great interview. Adds more light to things. I have recently discovered Triphala to help restore gut motility and it seems to be working. I was wondering if maybe Statin drugs could be a contributor to the problem, since they are well know to hamper muscles, which has proven true in my life.

  15. I am an acupuncturist and mental health counselor and this topic is very interesting to me not only for personal reasons, but professional reasons as well. I believe I have SIBO and have had it for most of my life. I’d like to know if the breath tests for SIBO can be purchased somewhere or are they only given through a doctor to confirm what I suspect is SIBO?

    • You can order a test kit from Commonwealth online without a prescription, but there may be advantages to having the test done in-clinic, supervised by an experienced GE since there would be a lower margin for error. If you state where you’re located, one of Chris’s many readers with SIBO might be able to make clinic suggestions too. See siboinfo (Dr. Siebecker’s free website ) for lots of great info on testing and related.

    • If you have someone willing to order it, any physician can run a test through NCNM’s SIBO Center. The results will come back with useful interpretation info, so your practitioner needn’t know much about it, just be willing to order the test.

  16. My wife has been suffering for 15 months straight with severe neurological and psychiatric symptoms that started on day two of a 10 day course of rifaximin, which was prescribed for suspected SIBO. I’m a former Navy SEAL and have never seen anyone suffer as much or as long as she has. I am desperately looking for relief for her. We have seen many doctors (functional medicine, neurology, psychiatry, neuropsychiatry, acupuncturist, chiropractor, massage therapist, etc.) but they do not seem to have the skill set to handle this in a holistic way. Have you ever heard of anything like this, or know of anything that can be done? Any “Chris Kresser” type information would be greatly appreciated.

    • Sir, after reading Brain Maker by David Perlmutter, MD, (author of Grain Brain), you just might look into Fecal microbiota transplantation (FMT) options. Sounds gross, but seems quite helpful in desperate situations! Read his book if possible.
      Good luck!

      • We actually already review Dr. Perlmutter’s book, and tried to make an appt. with him last year but couldn’t get in before he sold his practice. My wife started doing the probiotic enemas (PEs) as suggests in his book, which seemed to be working this past May and June until she had an iron IV upon advice from one of her doctors. This reinitiated the worst parts of her symptoms after making so much progress with the PEs. We believe the iron may have feed the infections onboard which caused increased inflammation in the brain thereby increasing her symptoms. From then on she was unable to use the PEs in the same manner. They started to cause her symptoms to get even worse. As for the inflammation in the brain, she has some sort of genetic issue that prevents her from taking quercetin. When she has tried it, out of desperation in the past, it set off her symptoms. She is a very sensitive person, and reacts very differently to treatments than most people. As for the fecal matter transplant (FMT), we have already researched that long and hard. We even received info regarding Tamount in the UK from Dr. Perlmutter’s office. We brought it up to one of her functional doctors who said it was an option but that it could cause some issues (increased inflammation), especially with her sensitivities and unusual reactions to treatments. He also mentioned antivirals, antibiotics. The real issue is having someone to work with that knows other alternative (non-allopathic) ways to approach this without antiviral and antibiotics, and who knows in what order to attack this (order definitely matters). Would we need to heal and seal the gut before addressing the infections, would we need to address the infections before trying the FMT, etc? We have been working on healing her gut for the past year with the paleo diet, and trying to implement AIP, but really need knowledgable guidance from someone who can bring all these areas together. Any assistance is greatly appreciated.

        • I had some psychological issues after taking (not for Sibo) antibiotics that effected my flora and found that B12 and B6 supplements worked well along with various amino acids like l-theanine, insositol and oddly lysine. You may want to check out mythelation process and research more about the right type of B12 to take as you need to start slowly to avoid side effects. I think a good naturopath could offer specific recommendations. I wish you both the best in coping with this and hopefully getting past this challenging stage.

          • Thank you so much for the information and for the well wishes. I’m very sorry to hear about your issues as well. My wife understands your suffering. We have done a good bit of research on B6 and B12, along with mythelation and pyroluria. She had some benefit from the vitamin B’s, theanine and insositol (not sure about the lysine). However, they were short-lived. It seems that a lot of the things that are supposed to be “good for you” work for a day or so and then reverse on her and cause her symptoms to flare worse. One of her doctors talked to us about mythelation, and said she was under mythelating. However, on the next visit said she was over mythelating, which was quite confusing. He wanted her to follow the Walsh protocol, but with all of her issues (not to mention his Dx reversal) we’re not sure where to begin. The thought of setting her back from where she has slowly progressed to is extremely traumatizing to her. He also said she has pyroluria. Again, all well and good to be diagnosed with but is that even a factor in her symptoms when looking at all of them as a whole. I see them all as slices of a cake, which she has many. Some bigger than others and causing more suffering. Some, once removed, causing the cake to collapse unless removed in the proper order. It all comes down to the correct order of treatment. We’re lost without that. I’m rambling, but thank you again for the great insight and kindness.

            • Brad,

              My heart goes out to you and your wife in this difficult situation.

              I’ll offer a recommendation for Dr Schweig, Chris’s partner. I’m too early yet with him to vouch for results but so impressed with his caring and knowledge. (which tend to get good results!) I believe he understands methylation well enough and, a favorite quality in a practitioner, works collaboratively when outside his understanding.

              The sudden onset of neuro symptoms 2 days after antibiotic. Has she been tested for Lyme? Anything in history that might point to this? Tick bite, family or personal symptom history?

              Prayers for direction and healing.
              Thank you for your service to our country!

              • Thank you for these recommendations and for your compassion. We are considering making an appt. with Dr. Schweig. I agree with you about that being a good quality in a practitioner. She is not in the best space for traveling at the moment, but we will make it happen for the right doctor. We wanted to see Chris, as he sees things from a different perspective and the body as a whole instead of individual parts that can be divided up into specialties, but he only takes patients from CA (and I believe he’s not even doing that at the moment).

                As for Lyme, that is a hotly contested topic that we have been round and round with trying to determine if she actually has it and if so how much, if any, of the piece of the pie that makes up all her symptoms does it contribute. The question then becomes is it worth taking a chance on giving her more antibiotics, which pushed this freight train in motion to begin with and could very well make her situation excruciatingly more horrifying, in the off chance that it suppresses the Lyme (that she may or may not have) enough to lessen her symptoms measurably. It’s a risk/benefit analysis that we have conducted and due to her suffering, any addition beyond where she is would not be survivable.

                For now, we continue to look for a holistic doctor that will take in all her symptoms and determine the correct/best order to address them all.

                Thank you again for the suggestions and for the “service to the country” acknowledgement. You are very kind.

                • Brad,

                  I believe Dr Schweig and Chris have a similar style in their functional medicine approach. A (for fee) phone consult is available…might be helpful before investing.

                  There are objective ways to determine if TBD (tick borne disease) is an issue. And antibiotic treatment is not first or only option. Whatever is going on with your wife likely needs to start with addressing immune system.

                  Hope to hear a success story soon!

                • I will check on the phone consult. That definitely sounds like the way to go. Hopefully he can provide more of those objective ways of determining if TBD is an issue, and suggest alternatives to antibiotic treatments. We know of hyperbaric treatment as an option but it could cause some severe issues with her sensitivity according to the doctor that runs the facility and knows her situation. He has provided her with IV therapy in the past.

                  For now we have been shoring up her immune system by radicalizing her diet, which of course helps the GI lining and the microbiome, which in turn helps the immune system. This, along with all the other things, we are making some slight progress in her situation.

                  Thanks again for all the information and the kindness of your responses. We’ll keep you updated.

                • Dear Brad,
                  I agree with Rebecca and Ed that you might wish to check for both Lyme and its co-infections of Babesia, Bartonella, Erlichia and Mycotoxins, as the neuro symptoms may be caused by these multi-systemic microbacteria and be impacting the gut in insidious ways, without having been previously detected. IGenex Labs in California perform the gold standard labs in this area. Good luck in your most complex of tasks, very confusing and complex! Best Wishes from wife of someone in Class 116!

                • Thank you for your response and info re IGenex labs. I will see if that was the lab she used when previously tested. If not, we will definitely have one of our doctors get an account with them and go from there.

                  It was good to hear from someone like-minded from the frog family. I was class 162, then east coast 2 and 4.

                  Thanks again and good luck with your search for alternative health as well.

            • Brad:

              Have you looked at biotoxin exposure – mold, mycotoxins, and fungi – as a source of your wife’s issues? Have you done any testing for mycotoxin overload?

              • Yes, we are looking into that. We have not done the mycotoxin test yet to see if she has any overloads. That’s next. Great suggestion. Thanks.

        • Brad,

          Sorry to hear about all of your and your wife’s suffering. To address such an extreme case of sensitivities and symptoms, I would recommend Dr. Majid Ali. He is in NY and NJ.

          • Thank you for the recommendation. I will look into him and his practice. Bless you all for your kindness and responses. Hopefully we can make some good progress again.

        • Brad, if you have had genetic testing already, a 23andme saliva test can be very useful. If youf wife has MTHFR defects then it is necessary to svoid folic acid and to supplement with methyl folate and a B12, not Cobalamin. This test is a good start in determining what some issues are.
          Wishing you the best of health in this new year.

          • If you have 23&Me results, upload them on “Know Your Genetics” to turn them into a useful report on her genetic methylation capacity. If lots of stuff comes up, consider learning Dr. Amy Yasko’s protocol. It’s a lot of work, but it’s designed for people who are super sensitive to everything due to neuroinflammatory issues, and absolutely covers what to address first, and implementing super slowly, so as not to overwhelm the system. It has helped me tremendously (Lyme, methylation and detoxification defects, multiple food and chemical sensitivities, recurrent SIBO), along with a super clean diet.

    • When I read that your wife had a reinitiation of her worst symptoms after having IV iron, I recalled my functional medicine nutritionist telling me that iron is one of the most inflammatory things you can give an autoimmune patient. Have you heard of Cyrex Labs? They have an multi-tissue autoimmune panel. Perhaps she is dealing with autoimmunity. That certainly can make someone VERY sensitive to many interventions. When you research out a new practitioner, I would ask if they are familiar with Cyrex Labs and their offerings. I had very debilitating symptoms and I did not begin to get better until we began treating my symptoms as autoimmunity. The information on my food intolerances and on what kind of autoimmunity I have from Cyrex Labs, along with regular blood panels, has helped me make dietary adjustments and helped my nutrtionist reccommend supplements. Best wishes finding a practitioner or a team of practitioners who can help.

      • By chance does your wife have amalgam fillings? It sounds like she could be dealing with a case of mercury toxicity. With agitation, mercury leaches from the fillings in the form of vapor and absorbs in the soft tissues. Over time it can cause/exacerbate innumerable medical conditions, including digestive disorders like SIBO. There are many nutrients one can take to chelate the mercury from the soft tissues. Iron is definitely one of them. However, if too much mercury is released at once, or the cleansing organs are too damaged from long-term mercury exposure to keep up, the worst illnesses and symptoms can flare up as one gets re-intoxicated.

        • My wife used to have Mercury fillings but had them removed about ten years ago. Unfortunately, at the time she didn’t know, nor did the dentist she used, about proper protocol for Mercury removal. So I am quite sure she was tox’ed by the Mercury. You are very insightful to note the correlation between the iron and the Mercury detox symptoms. That would account for her flare up. As you can see from all my comments so far how different, difficult, complex and intertwined her case is. It’s like the game where you pull the sticks out without moving any of the others. The “others” in this case being the symptoms of each problem that you don’t want to set off while trying to correct another problem. Just as in this game, the order of removal matters. Right now we are trying to support her body by feeding it the best possible foods for gut and brain (foundational) support, while managing symptoms set off by either those natural foods that she desperately needs but apparently can’t tolerate, or by doing other things like an iron IV (a stick being removed out of order). So far we are seeing progress as we move forward. You are so kind and insightful to bring this to our attention. I hope others are helped by your observations as well. God bless you.

          • It sounds like your wife is still very toxic. This means that her cleansing organs are not working optimally (that will happen from so many years of trying to filter poison) or she does not methylate well, or both. Her priority right now should be bolstering her cleansing systems. There are seven, and she should maximize all of them to the best of her ability, focusing especially on the colon (daily coffee enemas are the most powerful remedy, as well as hydrotherapy if funds allow), the liver (castor oil packs and lots of fluids, especially cleansing herbal fusions such as dandelion root and burdock root), and the lungs (deep breathing therapy–oxygen needs to travel better through the body to support healing). She WILL get better if she follows this protocol. Email me if you’d like more information, [email protected]. Sending lots of healing warmth to both of you!

            • Thank you for all the info. I will pass it on to her. She is already doing castor oil packs here and there, drinking lots of fluids (water, herbal teas, etc. but no sodas or sugar drinks). Hopefully your additional info will accelerate her progress more. Thank you again.

          • Dr. Yasko believes that microbes hold heavy metals. As her body gets stronger and can start fighting microbe loads, the metals will come out on their own. To do so before then might work, or might cause bad backlash.

      • Thank you for this information. Yes, my wife is very familiar with Cyrex Labs. She has had testing done from them before but I do not know for what exactly. She does have Hashimoto’s, which she’s had for years, but we don’t know of anything else at this time. Probably a good ideas to run that multi-tissue autoimmune panel for verification. Many of her symptoms are indicative of autoimmunity. She has been on a modified Paleo/AIP diet but between her many food sensitivities and the restrictions of the diets themselves there are very few foods she can have (tolerate or afraid of). This makes receiving the proper nutrition a bit difficult. I’m sure she’s still eating some foods that are contribute to her symptoms but we’re making some good progress. We’ve been adding and subtracting foods as we good (modified elimination diet) to find the right foods that she can tolerate. It’s slow going and lots of ups and downs but at least it’s progress. Thank you again for the information and for your compassion.

        • Check for Celiac disease if you haven’t already. Gluten is everywhere and could be a piece of the puzzle.
          Best Wishes and God Bless

  17. I’m a little confused by the comments regarding diet and hope you can shed some light?

    On one hand, Dr. Pimentel says, “…I don’t want them to be on a low-FODMAP diet simultaneously or any kind of carbohydrate restrictions. I want those bacteria happy and fed because they’ll respond better, in my experience, and the guar gum study kind of supports that notion.” and a little later he says, “…The low-FODMAP diet works. I mean, there’s no question. Studies show it works. I’ve experienced its benefit.”

    So does he only not advocate diet changes because of the difficulty in maintaining them, or are the abx really more effective without diet changes?

    I’ve been taking herbal abx for over 3 months now, cycling through a variety of formulas, and strictly adhering to Dr. Siebecker’s SIBO diet, but am still completely unable to add starches or fibers without symptoms. I have not taken a followup breath test, but if my symptoms are any indication I have not eradicated my SIBO.

    I do not really have a problem sticking to the strict diet, but it is VERY difficult to get adequate carbohydrates on this diet and it shows in my failing T3 levels, and chronic fatigue. I would love to go off-diet for that reason alone, but if it causes symptoms I worry that it is also feeding the bugs and allowing them to flourish.

    I’m getting fairly confused at this point on the correct path to healing. I appreciate your clarification.

    • The point is that low FODMAP diets work in reducing symptoms by denying the bacteria their food source. But it’s unlikely to eradicate the bacteria (in any reasonable time frame, at least, and poses certain risks long term). When attempting to kill the bacteria, you do not want to deny them food, because they go into a form of hibernation that negates the efficacy of antibiotics. For that reason, Siebecker’s “SIBO specific diet” should not be adhered to when taking antimicrobial herbs. The most logical protocol I’ve seen is that outlined by Dr Michael Ruscio: a paleo AIP diet while being treated, followed by a low FODMAP/SCD/SIBO specific diet for 1-3 months when the breath test is negative, then a gradual introduction of FODMAPS to test for individual tolerances. The paleo AIP includes lots of FODMAPs, so you’ll be feeding the bacteria while taking antibiotics. But it doesn’t include inflammatory or cross-reactive foods that might cause symptoms in a damaged gut.

    • Here is where I think one needs to kill off the bacteria rather than accommodating it. It took a long treatment for me but I believe it is finally gone. I can eat as I wish now. It took 13 rounds of Rifaximin (Zifaxan) 2×550 mg per day for 10 days, then 1 month off, then repeat over 18 months. I just ate what I could during this time. At the beginning of each cycle I took Bromelain for a couple days which distinctly helped . Good luck !

  18. What about the use of LDN (Low dose naltrexone) for MMC? Also if they are finding antibodies in blood tests, wouldn’t LDN help?

    • Beg your pardon, but what I can observe is that Hadza are healthy and we are sick, thus it’s a big stretching claiming that we may have an healthy diet that fits for us choosing among neolithic food and even worse processed stuff like white bread. We are going on with “there is no evidence that something is wrong” mantra but it’s very different from “there is evidence that it’s right”…we have to exploit observations with studies and make a puzzle using the evolutionary sense. We have enough evidence to avoid cereal grains that I’m shivering at the idea to feed with bread a person with an apparent gut issue, when such food is reasonably on the culprit’s desk…from the evolutionary puzzle it’s very likely that most of the issues we have in the gut and in any other part of our body is due to a non species appropriate diet..if you inflame your body with toxins you develoo sibo, leaky gut and you are going to trigger diseases, there’s no need to find out the theory of the dark matter to understand it…