SIBO & IBS Research Update with Dr Mark Pimentel - Part 1
Today I'm speaking with Dr. Mark Pimentel and of course, he's no stranger to anyone in the SIBO community. He's been really instrumental in many IBS and SIBO studies and a lot of research that's been happening over the last few years. I learned about Dr. Pimentel through his book, The New IBS Solution, about 10 years ago. He is the executive director of the Medically Associated Science and Technology program at Cedars-Sinai. He's a professor of medicine at Geffen School of Medicine and associate professor of Cedars-Sinai Medical Center in Los Angeles. He's very active in research and has served as a principal investigator or co-investigator for numerous clinical studies. And of course we know him as the developer or discoverer of the anti-vinculin and anti-CdtB antibodies that predict whether or not you have SIBO or autoimmune IBS. He also discovered the use of Lovastatin for methanogens.
Nirala Jacobi: Welcome SIBO Doctor practitioners to another episode of the SIBO Doctor. I'm Dr. Nirala Jacobi and today finally after years, I'm speaking with Dr. Mark Pimentel and of course, he's no stranger to anyone in the SIBO community. He's been really instrumental bringing up a lot of issues and a lot of studies and a lot of research that's been happening over the last few years. And really I learned about Dr. Pimentel through his book, The New IBS Solution, about 10 years ago, but he is the executive director of the Medically Associated Science and Technology program at Cedars-Sinai.
Nirala Jacobi: He's a professor of medicine at Geffen School of Medicine and associate professor of Cedars-Sinai Medical Center in L.A. and he's active, very, very active in research and has served as a principal investigator or co-investigator for numerous clinical studies. And of course we know him as the developer or discoverer of the antibodies, so the anti-vinculin and anti-CdtB antibodies that predict whether or not you have SIBO or autoimmune IBS and also discovered the use of Lovastatin for methanogens. And that's ... Definitely, I want to ask you about that a little bit more and lots and lots of other accomplished research studies. And we really want to talk to him today about some of the new developments that's happened in this past year. So welcome very, very warmly, Dr. Pimentel.
Mark Pimentel: It's my pleasure to talk to you. Thank you for that very humbling introduction.
Nirala Jacobi: Okay, so let's dive right in. I mean you've been involved in SIBO research for so long. What actually started it out for you?
Mark Pimentel: I wanted to do what we call motility, which is a part of branch of gastroenterology or the study of the digestive system and it's the branch that people tend to ignore. People didn't want to do research in that area because there was a perception that motility disorders or some of them, particularly irritable bowel syndrome, was a psychological disorder and that discouraged gastroenterologists who wanted scope from doing that field, but I saw an opportunity in two ways.
Mark Pimentel: Number one, I felt I could make a difference in people's lives and number two, I felt like the research may be [inaudible 00:03:41] going in a direction that needed more work. I mean there was a lot of room for improvement or a lot of room for trying to figure out the cause of disease. Imagine IBS is 1 billion people worldwide, 40 million just in the U.S., so 10% of the population which is a lot of people that was a mystery as to what was causing their illness.
Nirala Jacobi: And we've sort of kind of ... not watched you, but been involved in kind of seeing how this whole thing unfolded and some of the research that's come out and have been using breath tests for a long time now for the past, myself, for the past nine years. And understanding the sort of mechanism behind it in terms of hydrogen dominance and methane dominance and so it's interesting to see what's coming out with the new research that really looks at sequencing the small intestine. And I remember years ago, you talking about this at probably SIBO Symposium in Portland where you talked about the differences between small and large intestinal microbiome and it looks like we're finally getting there with some of the data that's coming out of your own study with a REIMAGINE study. Can you talk a bit more about that?
Mark Pimentel: Yeah. I'm so thrilled to have gotten this REIMAGINE study off the ground. I think one of the challenges that we have with ... Microbiome was a phenomenal movement in terms of the discovery in science because in 2007, the Human Microbiome Project said that, "Wow, look at all these microbes in the stool and how amazing would it be to study them all and maybe connect them to human disease?" The problem is fast-forward 10 years, there's been no smoking guns. They haven't found one bug, one disease, but the problem with stool is that it's a mess of material that isn't really in an area that's important. You don't need your colon. You need your small bowel. That's where absorption occurs.
Mark Pimentel: That's where chemicals bacteria produce would get into your body and influence you. So we'd always have the philosophy that the small bowel is important. We always knew because of the bacterial overgrowth, small intestinal bacterial overgrowth work, that getting the specific bugs from the small bowel was going to be critical. But at the time, we were preaching about it, but the resources weren't there. There's not a lot of money, not a lot of work being done in that area because nobody was putting the money in. The NIH wasn't either. But we finally scrapped money together and Cedars-Sinai also helped us with the MAST program creation and our flagship project is this REIMAGINE study.
Mark Pimentel: So briefly everybody who gets a scope from above and doesn't get a colonoscopy, we're taking juice, blood genetics, questionnaires. You name it, we're taking it from the patient and biopsies as well and we're creating an archive of material and from that archive we're nearly at a 500 patients now already. We were able to perfect the techniques for the small bowel because the small bowel is very different from stool and the techniques that are used to get DNA from stool weren't right for the small bowel. And we've perfected those, those are coming on publications in the next month and we're finding stuff already, really cool stuff. Single bugs, single diseases that were missing from stool. So that's just a flavor of the trial. From my point of view, this is ... it's amazing, so very excited.
Nirala Jacobi: Can you talk about some of the single bug single diseases discoveries other than SIBO or-
Mark Pimentel: What we have published ... I can talk about what we have published already. One of the most impressive publications that have come of this so far where we presented as an oral presentation at DDW, which is the big GI meeting. It's an international meeting here in the U.S. And what we showed for the first time and this is super important because there are skeptics of breath testing and there are skeptics of CBO out there, but there are less and less skeptics because of the accumulating data, but I think, again, a nail in the coffin for the skeptics is this study we just finished sequencing.
Mark Pimentel: So we also culture, culture and sequencing correlated. So we were able to show that SIBO is greater than 10 to the three, not greater than 10 to the five like the old dogma. Number two, we were able to show that breath testing was lactulose and 90 minutes time point, 20 minute rise was the ideal cutoff for finding SIBO by culture and deep sequencing. And in that same study we showed that the pathways that were elevated in patients with SIBO were hydrogen production pathways in the bacteria that we found there.
Mark Pimentel: And finally, all of that, all those things I just mentioned, correlated with gas, bloating and diarrhea. So for the first time, everything lined up and converged that what we were doing in breath testing was correct. Sequencing was able to identify this and prove this. And we also found the bugs, so it's E. Coli, it's Klebsiella, it's Aeromonas. These are the three sort of most important characters, bad characters that are elevated in SIBO. So the closer we get to the exact bugs, the closer we get to better treatments.
Nirala Jacobi: Right. So basically you've confirmed what we've suspected all along about this proteobacteria phyla or phylum that is overrepresented in SIBO.
Mark Pimentel: Absolutely. But now we're getting down to specific species and then we can start to tailor our therapy accordingly.
Nirala Jacobi: Do you think that some of the discrepancies in other studies are due to just other sampling techniques?
Mark Pimentel: So it took us almost 18 months to perfect the sampling technique. So nobody has this sampling device. We haD to create a new sampling device where it's protected or capped on the end, so it's a catheter within a catheter so you don't get contamination as you go through it. The other thing is that when you take juice from the small bowel, it's very mucusy and the DNA that's stuck in the mucus and the bacteria, the bacteria that live in the mucus, they don't come out.
Mark Pimentel: So if you don't treat the sample in a particular way, you get 10 times less bacteria, even for the culture part. So everything everybody was doing for small bowel was not optimized. So we had to do all of that first because we want to make sure we're doing it right before we start doing it. And that's the part that took about a year and a half. So now, that paper is coming out in another six or eight weeks, how to do it correctly in the small bowel so that the world can do it right.
Nirala Jacobi: Well that's exciting because it's really frustrating as a clinician when you're reading the papers and they're very conflicting very often when it comes to microbiome sequencing and studies. So that'll be good to have some sort of ... Hopefully, a little bit more overlap or at least studies that concur about their findings.
Mark Pimentel: Well what I will say though is that, first of all, the whole point of that study is to standardize the methodology, to validate it and standardize it. But I'll say one thing though, that to my knowledge, almost every culture study of the small bowel in IBS particularly, has been showing abnormalities and almost always consistently proteobacteria being elevated. They're not large studies for the most part, but for example, the Posserud study all the way back in 2006 by Iris Posserud, she showed that there were elevated coliforms in IBS. So I think we're just advancing the story with more sophisticated techniques and better, more validated techniques. I think stool is a bit of a mess still. All studies are different. So I think I agree with you on that.
Nirala Jacobi: Yeah. I was thinking of this other study that came out in May 2019 in Nature about just ... The authors concluded that SIBO was really just a state of dysbiosis rather than an overgrowth. But anyways, I think that that's the sort of conflicting results that we sometimes see, but maybe it's the sampling.
Mark Pimentel: Yeah, no, I mean certainly that study from the Mayo Clinic that you're referring to, in one sense, it confirms that there is dysbiosis in IBS. So you could say that it has ... It is suggesting that there are abnormalities. So I won't take it as negative, but they weren't able to find SIBO because ... and here's the trick. Most of the proteobacteria live in the mucus. So when we got 10 times more bacteria, when we liberated the bacteria from mucus, what was augmented more than any other organism was proteobacteria. So again it speaks to, when you do something, you've got to validate the technique before you start. And that's the deficiency in that Nature communication paper.
Nirala Jacobi: That's really interesting because that mucus in the small intestine is so difficult to sample, isn't it? I mean that's why you had to create this new technique because it's so adhesive and very difficult to actually get a little sample of it.
Mark Pimentel: Right. And we've gone one step further, we have another catheter that we developed that isn't out there yet, that is a capillary-based catheter because the mucus is so thick, it takes so long to get a good sample that ... With this capillary system, it takes 10 times [inaudible 00:13:34] time because it's [inaudible 00:00:13:37]. So anyways, you'll see more about it. We presented it at the EGW in Barcelona about two weeks ago. Sorry no, we presented it at ACP just last week. We were at two meetings almost at the same time it felt like.
Nirala Jacobi: It's exciting times for the gut microbiome. As naturopathic doctors and integrative practitioners, I think we've been so fascinated about this topic for so long because we've known about it for a long time or at least this whole concept of microbiome health. And so it's been so rewarding to see some of these research papers come out that validate what we've been thinking all of these years. But when I was a practitioner in Montana, basically, I would treat patients with IBS for dysbiosis and there were always this subset of people that just didn't respond even though I got good results with IBS, but those were the SIBO patients.
Nirala Jacobi: And so that part is just so validating to us practitioners in a way that we now have an understanding a little bit more about SIBO and the differences between small and large intestinal microbiome. Now the question I had that was going to follow up with that was ... Well first of all, I wanted to clarify about this lactulose breath test validation that you talked about. Did you find the same thing with glucose as well?
Mark Pimentel: So we only do lactulose breath test here at Cedars, generally speaking, so we were able to validate with a lactulose breath test. I'll give you ... not a sneak peek because we've already presented the data at a meeting, so it's really public information, but soon to be available for you to read as an actual journal article is, we showed that in the target three trial which was a Rifaximin study, that when breath tests were positive and then became negative with Rifaximin, 76% of those patients met really difficult FDA endpoints.
Mark Pimentel: So in other words, breath tests do predict the response to Rifaximin. The reason I'm saying that is that breath testing in general in IBS is only positive in about 30% if you use glucose. If you use lactulose, about 56 to 70% are positive. So if you used glucose, you would miss about 30% of patients who could benefit from an antibiotic approach, for example. And my point is that, glucose is very specific, more specific than lactulose because when it's positive, you really have overgrowth. I believe that.
Mark Pimentel: But because it's absorbed so quickly, you're missing a whole bunch of patients who could respond. So I'm more of the inclination that you want to get as many people as possible that are positive in order to get that ... to get them on the right treatment. So I'm more and more and more disinclined to recommend glucose as the main substrate. I know there are doctors out there who swear by glucose and they don't want to give it up, but I think the data are really now compelling that lactulose is preferable.
Nirala Jacobi: Yeah, I would definitely agree with that. I usually recommend it in patients that we're negative on a lactulose, but I really suspect that they do have SIBO and sometimes I do lactulose followed with a glucose and many of the practitioners do that and we can capture or catch some people that were negative on a lactulose. I've had a number of patients that tested positive, very positive on a glucose and negative on lactulose, but it's certainly not the norm, but we do see that.
Nirala Jacobi: So would you say that your study then finally put this to bed, this idea that lactulose cannot be used as a ... in some circles? There's some research circles that definitely still deny the usability of lactulose and just think it's basically a ... well more or less, a laxative and will affect motility and therefore you shouldn't be using it. So do you feel like that study really put the nail in the coffin on that one?
Mark Pimentel: So in my opinion, yes. But of course, the way research is, one center does not a gold standard make. So I cannot be so arrogant as to assume that my data's better than somebody else's data. But what I will say is that this is extraordinarily compelling and I think that the sequencing data, I don't know if anybody's sequencing the small bowel, so it's going to be hard to find another study from another center anytime soon. But I think this suggests that lactulose absolutely should be your first choice and validates the reason we chose lactulose and continue to use [inaudible 00:18:18].
Nirala Jacobi: Great. Now one last question on the small intestinal microbiome before we move on to methane, I have a lot of questions about methane. I'm fascinated with it. But my particular question is really about now that we are getting closer to really understanding a healthy microbiome in the small intestine versus an altered one, should we not be concerned also with repeated uses of antibiotics disturbing that level of ... or that balance that is in a healthy microbiome in the small intestine. We know that Rifaximin doesn't really affect the large bowel, but as you mentioned, you don't really even care about the large bowel. You care about the small intestine. But for people that let's say have ... need repeated courses of Rifaximin, are we also thinking to start studying the effects of Rifaximin on that particular microbiome?
Mark Pimentel: So we've done some of that. We have an animal study that we published that shows that ... the principle things that go down in the small bowel and the colon. And so we looked at animal's duodenum, jejunum and ileum, the three sections of the small bowel and then we also looked at colon and stool. And Rifaximin really, in the animal study, in human studies, doesn't affect stool microbiome much. But it does have an effect on the small intestine and principally, Rifaximin reduces proteobacteria, which are the E. coli, Klebsiella and the culprits in SIBO.
Mark Pimentel: What we don't know is what happens to all the other organisms as we reduce those. Do they go off? Do they result in any kind of long-term consequence? We've been using Rifaximin for more than a decade here in the U.S. for IBS. And to my knowledge, we see nothing in terms of ... We don't see increased obesity from Rifaximin. These patients aren't recording weight gain or any unusual symptoms. So we're not really seeing an adverse effect clinically, but I take your point seriously. I understand that there are consequences or potential consequences to overuse of antibiotics and it needs to be checked and monitored.
Nirala Jacobi: Okay. So time will tell and we'll find out more as you continue your studies. Now before I move on to methane, you also were involved in a study that showed that Campylobacter jejuni was actually the main cause of acute appendicitis. How did that come about?
Mark Pimentel: So our lab is very creative. I can't take all the credit and we've got some superstar PhDs in the lab that take some of the ideas, crazy ideas that I have and make them materialize. And a couple of the folks in our lab discovered a way to determine what the microbiome is in tissue from 10 years ago. So you take samples of appendix that were taken out, a normal appendix and patients with appendicitis and were able to compare the microbiome after scraping the tissue off of slides. It's amazing.
Mark Pimentel: And that technique took about a year to perfect also, but the ramifications of that are, we can study all sorts of diseases that may or may not have been associated or was believed to be associated with the microbiome. But to basically cut to the chase of your question, we found that appendicitis in at least a third of cases of appendicitis, the culprit, the reason they had appendicitis might've been Campylobacter jejuni which is food poisoning.
Mark Pimentel: We know Campylobacter jejuni, when it happens it causes swelling of the tissue. And in the appendix if you swell the tissue up, you block the exit of the appendix and then it gets an abscess and that's appendicitis. So it looks like Campylobacter could be the cause of appendicitis which really means, Campylobacter could be treated with antibiotics and you don't need to take it out necessarily. Some people believe Campylobacter is very important.
Mark Pimentel: It's sort of a test tube that keeps the microbiome inside that little tube as you take antibiotics or other bad things happen to the gut and repopulates the gut with that magic mix that the appendix keeps for you. So I think the appendix is a more important organ than we used to think it was. And I liked to know that the appendix could be kept and this is an important start to that.
Nirala Jacobi: Yeah, like a reservoir of your own microbiome that's so unique to every human being. That's a really good thought that we have some way to keep ... I mean it makes sense. There's so many reasons why people had diarrheal diseases or food poisoning and you really do get rid of a lot of your microbiome I guess, flush it out with all the diarrhea and so that you have this little reservoir with which to repopulate yourself. But my question that follows up from that is, so if Campylobacter is the main cause of appendicitis, wouldn't we expect to see a bit more food poisoning symptoms? Like the cases that I've seen with acute appendicitis is not always at all like a food poisoning case. It's sort of ... It can even be smoldering. It kind of goes along for a while and all of a sudden, it can be pretty acute but it doesn't ... I haven't seen it to be similar to this acute food poisoning symptom.
Mark Pimentel: Well Campylobacter can present in many different ways. It doesn't always present with diarrhea. It can present just with pain and cramping and all of those sorts of symptoms. So it's tricky, but I'm convinced that at least a third of these cases is Campylobacter. But I understand what your point is.
Nirala Jacobi: Would it also be another sort of maybe red flag for somebody who has IBS like symptoms and who had an acute case of appendicitis, had their appendix removed as another potential for SIBO that could have also caused SIBO in terms of creating anti-vinculin antibodies and anti-CdtB antibody because that's also the consequence often of a Campylobacter infection. So do we see that, that people with appendectomies are more likely to also have SIBO?
Mark Pimentel: Yeah. So we haven't studied that, but now that we have this data, obviously, that's another very big question, so you're right. We now know that the number one cause of IBS is food poisoning and that food poisoning has a toxin CdtB and vinculin which we'll get into, that trigger IBS and trigger the bacterial overgrowth to begin with. And Campylobacter is the biggest culprit in all of that, so clearly appendicitis could be a trigger for IBS. Fortunately, it doesn't happen all as much as often as food poisoning, but that's possible.
Nirala Jacobi: Well let's talk about the anti-vinculin antibodies a bit more. So just for you listeners who are still after all these years, kind of unfamiliar with the concept, why don't I have the expert himself explain what we're talking about when it comes to anti-vinculin and anti-CdtB antibodies.
Mark Pimentel: This is, in my mind, a very exciting story. I won't get into all the nitty-gritty, but basically we've known for a couple of decades that some patients develop a chronic bowel disturbance after food poisoning, but there was always pushback that that's not really IBS. But the ultimate study was published in 2017. This was the Mayo Clinic study that showed that looking at 45 outbreaks of food poisoning ... No doubt, 2019 if you don't believe food poisoning causes at least a percentage of IBS and that percentage we believe is about 60% of IBS with diarrhea and mixed, then you're ... I don't know what you're reading because this is now believed to be a major cause of IBS.
Mark Pimentel: But the question all along this timeline of two decades was, how does that happen? What we did was we created an animal model using Campylobacter jejuni that number one cause of food poisoning by bacteria in the U.S. and worldwide usually and that organism has a toxin called CdtB. The reason we focused on that toxin was because Campylobacter, Shigella, salmonella, E. coli, they all share one toxin in common. It's the only toxin they all can have and that's CdtB because they can all cause IBS. So I was looking for something that unified why all these different organisms could all cause IBS.
Mark Pimentel: Anyways, we created an animal model and we were able to show that these antibodies go up and that these antibodies correlate with SIBO in these animals. So we were able to for the first time, show that this is potentially a cause of IBS, how this works. But the best study was, we took CdtB, just the toxin and we injected it in an animal study into the arm like you would get a vaccine and then did a booster about three weeks later. The animals formed antibodies to CdtB from being exposed to CdtB. That's obvious. But they also formed antibodies to vinculin and they also got overgrowth and they also got these weird cytokine changes and they got changes in bowel pattern.
Mark Pimentel: The point I'm trying to make is just that toxin alone was enough to create the dysbiosis of IBS and create IBS and SIBO and all of that. So we then went to humans and said, could we use measuring anti-CdtB and vinculin as a way of diagnosing IBS and that it's a dysbiosis from food poisoning and compare it to Crohn's, all sort of [inaudible 00:28:35] patients and celiac patients. And sure enough that first study show that absolutely the marker worked and that was in PLOS ONE. People were sort of complaining about the sensitivity of it, but we set the sensitivity low and the specificity high for two reasons.
Mark Pimentel: We don't think everybody with IBS was caused by food poisoning, so the sensitivity can't be perfect because not everybody with IBS had food poisoning. But more importantly, we realize these two proteins are weird. They have weird functions and when you make a test out of them, they don't behave normally. So we did sort of a very specific thing. It's called epitope optimization and I can't really talk about the methods because it's proprietary to a company, but it allows the epitope or the part where the antibodies bind to be exposed on the plate.
Mark Pimentel: The reality of that is that the test is more specific and more sensitive now in this second-generation test called ibs-smart. And now if you're positive on one or both markers, the specificity is over 90%. If you're positive on both markers, the post test probability of having IBS is 98 to 99%. So you get medical certainty because anything over 80% is medical certainty, plus it means you have a disease, not a syndrome. This is organics. You actually have a marker that says you're real. This is not psychological. This is caused by food poisoning and the test is positive in the IBS population in about between 56 and 65% of patients with IBS.
Mark Pimentel: So that's what we believe the percentage of IBS patients that food poisoning caused them to have the IBS. But it's really important because people say, "Well, so what? You have these antibodies, maybe a good doctor could diagnose it." That's not how it works because I see patients in my clinic who've seen good doctors, good gastroenterologists and they've had two or three colonoscopies that are all normal. So why are the doctors doing all these tests on patients that they already know have IBS?
Mark Pimentel: So we think if you just start with this and you get the answer, you get to treatment faster and you save a lot of money in health care. We've actually modeled this to be about $800 less per patient because you get the answer faster and you don't have to waste time with all these colonoscopies. And the final thing is, if you're positive on these antibodies, you're more likely to get food poisoning again. So we use it for prognosis and for educating patients around travel and around careful eating behaviors so they don't get sick again.
Nirala Jacobi: Do you find that there are patients who are positive for these antibodies who don't recall ever having had a case of food poisoning?
Mark Pimentel: Yeah, I get this question a lot because doctors think, "Oh I have to ... Patient has to say, "Oh, it all started from food poisoning." No, I mean you have diarrhea. You have mixed bowel movements. So you already have diarrhea, so how do you know the first day wasn't food poisoning? So I say that you test the patients with chronic diarrhea, you test them. Of course if there's blood in the stool and you're losing weight and all of that or you're over the age of 50, a colonoscopy is needed because you want to rule out cancer or Crohn's or ulcerative colitis because IBS doesn't have blood in stool and you don't have weight loss typically. So those things would make you want to scope a patient. But if you have a 25 year old woman who's had diarrhea on and off for six months to a year, that's the perfect patient do this first in my practice.