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Gastroenterologist Mark Pimentel discusses his article, “SIBO and IBS: the hidden link keeping millions in pain.” Mark explains how small intestinal bacterial overgrowth (SIBO) is frequently misdiagnosed or overlooked due to its symptom overlap with other GI conditions, particularly irritable bowel syndrome (IBS). He outlines the evolution of diagnostic tools like hydrogen, methane, and hydrogen sulfide breath tests, the clinical relevance of new ICD-10 codes, and the FDA-approved treatment rifaximin. Mark emphasizes that the most effective treatment remains the elemental diet—now made more palatable thanks to food science innovation. He urges increased awareness, clinician education, and research to bring this hidden condition to light and improve patient outcomes.
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Transcript
Kevin Pho: Hi, and welcome to the show. Subscribe at KevinMD.com/podcast. Today we welcome Mark Pimentel. He’s a gastroenterologist. And today’s KevinMD article is “Small intestinal bacterial overgrowth and irritable bowel syndrome: the hidden link keeping millions in pain.” Mark, welcome to the show.
Mark Pimentel: Oh, it’s great to be with you, Kevin.
Kevin Pho: Thank you. All right, so briefly tell us a little about your story and then talk about the KevinMD article that you contributed for those who didn’t get a chance to read it.
Mark Pimentel: Oh, for sure. So my name is Dr. Mark Pimentel. I’m the executive director of a program called the Mass Program, which is sort of a biotech development program at Cedars. I’m a gastroenterologist, so I study the digestive system, but I focus on the movements of the gut and the microbiome and how they affect the gastrointestinal tract. So that’s my research area of focus, and I have a few claim to fames, one of which is the topic we’re talking about today.
Kevin Pho: Wonderful. And let’s get everyone on the same page. What is small intestinal bacterial overgrowth? And then give us a brief definition of irritable bowel syndrome.
Mark Pimentel: Sure. So small intestinal bacterial overgrowth is a situation where the small intestine, normally relatively clean—a nice low level of balanced microbes—and then all of a sudden, for reasons we can get into later, you get an accumulation of specific types of bacteria, which are like Ferrari in the gut. They’re just aggressive at fermenting and digesting your food and sharing your meal, giving you a lot of symptoms: diarrhea, bloating, etc. Irritable bowel syndrome is probably the most common gastrointestinal disorder worldwide. If you want to put numbers to that, it’s about a billion people worldwide who have irritable bowel syndrome. So that’s a big viewership of people who have this condition, and it’s traditionally characterized based on symptoms because nobody understood what the cause of IBS was. So you have pain, you may or may not have diarrhea, you may or may not have constipation, and bloating is part of that. And what we’ve been able to do is to connect the dots between the two—that probably 60 percent of IBS is SIBO. And that’s a pretty exciting discovery.
Kevin Pho: All right, so obviously they have some symptom overlap, right? So, in the primary care setting, what I do—do you find that these diagnoses are often confused with one another?
Mark Pimentel: All the time. And I think in the primary care setting—and you’re probably very familiar with this—if a patient comes in and they’re 25 years old and they have constipation, most primary care docs are not stressed. They’re going to handle it. They know what to do with constipation. When the patient comes in with diarrhea in a primary care setting, the primary care doctor is maybe a little worried. Could it be celiac? Could I be missing Crohn’s disease? Could I be missing a parasite? And you tend to work those patients up more vigorously, even though the most common or most likely diagnosis will end up being IBS anyway. So there’s a reluctance to make that connection to IBS without spending money doing tests, maybe even referring to a gastroenterologist for a colonoscopy, which is very expensive.
Kevin Pho: All right, and tell us the reason why we need to differentiate these diagnoses in terms of the treatment course for each.
Mark Pimentel: Well, so it’s a little complicated because if you think about irritable bowel syndrome, traditionally IBS was thought of as many diseases in medicine when you don’t understand it: stress, anxiety, or depression are the cause. I mean, I read a news article in the New York Times from 1972 about a CEO of a company who had a heart attack, and the doctor says, your job is killing you. The stress of your job caused the heart attack. And of course, we know it wasn’t the stress of the CEO job. It was that he was smoking cigarettes, eating at a steakhouse every night, and drinking alcohol, etc., that was leading to that risk, which we now know. But I think IBS suffers the same thing, in that we’ve attributed it to stress. Because of that and because IBS was always pigeonholed as a symptom disease—you have pain, you have diarrhea, you have constipation—if we can put a Band-Aid on each symptom, we make you better. So we spent a lot of time in the pharmaceutical industry developing laxatives for the constipated IBS patient, or developing antidiarrheals for the diarrhea side. But the only drug that actually treats the full package is rifaximin, which was FDA-approved in 2015 on the basis that IBS is, in fact, in part due to the changes in the microbiome, which we now believe is this SIBO phenomenon.
Kevin Pho: So if someone comes in with symptoms that could be suggestive of either SIBO or IBS, tell us about the diagnostic pathway that we could certainly elucidate SIBO from that.
Mark Pimentel: Right. And this actually is a significant cost savings. Imagine the patient—I’ve had a patient who is 25 years old and has had three colonoscopies, each of which was normal. So why were two further colonoscopies needed if the first was normal? But you know, it’s this desperation of trying to find an answer for some of these patients. But it’s a simple path to get to the diagnosis of SIBO if you have IBS, and it’s to get a breath test. A breath test can be done in a doctor’s office; it could be done at home now with new home kits. So there’s a lot of easy ways to get breath tested.
Kevin Pho: So what exactly are we testing for in a breath test?
Mark Pimentel: So the most recent breath test, which is probably the most validated breath test in history—and I was part of the development path of that, so just full disclosure—measures hydrogen, methane, and hydrogen sulfide. Basically, the patient gets a kit, they drink a sugar, and then every 15 to 20 minutes after drinking the sugar, they do a breath sample. And as the sugar encounters the bacteria in the gut, the gases rise, they end up in your breath, and you’re able to say where the bacteria are, how much they are, and if it’s too much. But what’s super important is that we now know that methane on breath test corresponds to constipation, and in fact, the methane gas itself slows the gut down. So if you have methane on your breath test, you get rid of the methane, your constipation goes away—you go to normal. It’s not a laxative; you just stop being constipated. And we now know the third gas that was never part of the breath test, hydrogen sulfide, is the driver of diarrhea. And so hydrogen sulfide has become really critical in terms of understanding the patient and understanding their diarrhea, and it does guide your therapy. For example, what we do with methane is we give rifaximin with neomycin together. If they have hydrogen sulfide, we give rifaximin plus bismuth. If they have just hydrogen, we give rifaximin alone. Maybe that’s too many details, but that’s how we use the breath test. But if you just do that upfront, in the majority of these patients, you’re going to save a lot of costs because patients are going to get their answer, get better, and if a patient responds to these antibiotics and your breath test was positive and they’re feeling normal, you don’t need a colonoscopy, you don’t need other tests, you don’t need celiac testing—celiacs don’t respond to antibiotics. So it really kind of allows and empowers the primary care physician to be able to get to the answer for these patients without all the expense.
Kevin Pho: So I definitely want to talk more about rifaximin, but before we do that, are there any risk factors or demographic characteristics that would lend themselves to developing SIBO?
Mark Pimentel: Well, so we think we know what causes SIBO. We know this based on animal studies that we’ve done over the last couple of decades. You may have heard of post-infection IBS. You get food poisoning—I was fine until I ate at that buffet, or I went on that trip to some country, and then I got sick there. And ever since then, I’ve had IBS. So we now know that the food poisoning, let’s say Campylobacter, contains a toxin that then causes you to react to the toxin, creating autoimmunity to the nerves of your gut. That then slows the gut down for an indefinite period of time because those antibodies are there forever almost, and then that slowing allows this bacteria to grow, and that’s how this all comes together. So the risk factor for developing IBS is really food poisoning and travel. And so you’ve got to be careful when you travel so as not to develop IBS to begin with. That’s something we’re very interested in trying to achieve as well.
Kevin Pho: So let’s say the primary care setting that I practice in, what would be some typical presentations that patients would come in with that would make me suspect potential SIBO and potentially order a breath test?
Mark Pimentel: So classically, the patient will have some degree of abdominal pain, they will have a change in bowel function, and sometimes it’s very mild. So you know this in your own practice probably: a patient comes in, you say, how are your bowel movements? “Oh, they’re fine.” And then you ask them, well, what does it look like? “Well, it looks like pudding.” But it’s always looked like pudding for the last five years. But they complain generally of bloating, and the bloating’s worse after eating. Two of the bugs that we find most characteristic of overgrowth are E. coli and Klebsiella. And when they’re in the small bowel, your small bowel’s fermenting capacity is 63 times faster than a normal person. So imagine you’re eating a meal, and your patients say, oh, I eat a meal, and 10 minutes later I’m bloated. And you’re saying, well, that’s too fast. That doesn’t make sense. But when you’re 63 times faster at producing gas in your gut, it does make sense. And so bloating is really the key. If you have a patient with postprandial bloating, a breath test should be done. That’s how I feel.
Kevin Pho: All right, so we get the breath test. It’s positive for small intestinal bacterial overgrowth. You mentioned rifaximin. Tell us a little bit about that medication itself.
Mark Pimentel: Yeah, so rifaximin is a non-absorbed antibiotic. It doesn’t get absorbed because it’s what we call hydrophobic—it reacts to water; it doesn’t dissolve in water—and so it really just dissolves where there’s bile and other chemicals in the small bowel. It acts in the small bowel, doesn’t do much to the colon, doesn’t hurt your microbiome, but gets rid of those bullies, the E. coli, the Klebsiella, and some of the other organisms that cause hydrogen sulfide or that produce other hydrogen sulfide. So rifaximin is very effective at improving the symptoms of IBS and only needs to be taken for two weeks, and then you’re good for months. Now, if you go back to something we said earlier, the food poisoning and the damage to the nerves of the gut, that’s still there. So what ends up happening is that you might need to take rifaximin a couple of times a year just to tidy things up again because the bacteria will start to accumulate again in some patients. But rifaximin is extremely safe. We’ve done safety studies on it. The number needed to harm for rifaximin is over 8,000 patients before one person even stops the drug because they feel a side effect. So it’s extremely safe.
Kevin Pho: And is this a lifelong phenomenon? Like you mentioned that if you stop the rifaximin, the symptoms may come back later on in a year. You have to do this several times a year. So is this something lifelong a patient may have to deal with?
Mark Pimentel: Well, for now it’s lifelong. One of the—and now we’re going into sort of advanced discussions about what the future therapies might look like—we now know the antibodies in the blood that are driving this poor motility, and so if we can get those antibodies out of the blood, we might be able to cure IBS. But that’s a future thing. We are working on that, and that is something that’s going to happen in the next couple of years, and then it’ll take five years for the FDA to approve it as you go through that process. But there is hope that we don’t have to do this forever. But for the time being, this is sort of a pattern.
Kevin Pho: Any worries about those bacteria becoming resistant to the rifaximin if it’s being used so often?
Mark Pimentel: So rifaximin has been around for now 30 years, on and off in Europe, and here in the United States for at least 20, and there has been no described resistance except a recent paper saying that daptomycin resistance could happen in patients taking rifaximin if they’re like a bone marrow transplant patient and they’re in extreme situations where they get these multi-resistant organisms. But then a paper just came out yesterday saying no, they’re not seeing that in cirrhosis patients who take rifaximin every single day for the rest of their life. So it’s up in the air. But generally speaking, the resistance studies that had to be done for the FDA didn’t show stable resistance at all.
Kevin Pho: So we have the rifaximin. Is there anything patients could do from their standpoint, from a dietary standpoint perhaps, that could reduce the incidence of attacks?
Mark Pimentel: Yeah, so what we generally recommend—there’s a diet called low FODMAP, which has been around for a while. Low FODMAP is highly restrictive, and even before low FODMAP, our clinic had developed what’s called a low fermentation diet. Now, low fermentation eating is the way we designed it for lifestyle. So you could go to any restaurant in this country and order a meal, because there should be something that fits our diet on the menu. Because one of the problems with IBS is I can’t eat this, I can’t eat that. You go to a restaurant with your friends, you spend 10 minutes talking to the waiter to see if there’s this, that, or the other thing in the composition of the meal, and we wanted to simplify that so these patients don’t have to suffer that kind of embarrassment. And so the diet is more socially acceptable and allows you a little bit more liberty. But there is also another diet that is a full treatment for IBS or SIBO, and it’s an elemental diet, and one of the newest ones is Enbióta, which tastes good. The old elemental diet tastes like battery acid, but the new one tastes very good. And if you do that for two weeks, you starve the bacteria out, so you actually can get a better response from the Enbióta than rifaximin because it so comprehensively reduces the bacteria. Again, the problem is it can recur. The diet is cash pay; it’s not covered by insurance. So those are things that patients and doctors have to consider.
Kevin Pho: So what exactly does an elemental diet comprise of? What’s that like?
Mark Pimentel: So an elemental diet is basically all the food in this powder that you mix with water. It’s completely broken down, so it’s just the amino acids, the fundamentals, and they all get absorbed so quickly by you because you don’t have to do anything. You don’t have to digest it. It just comes in, so you get fed—there’s nothing left for the bacteria, and they just starve over two weeks, and then they kind of recalibrate down and patients do better. It’s highly effective at getting rid of overgrowth, at least temporarily. And we use it quite a bit more now because it tastes better.
Kevin Pho: Earlier on, you mentioned low FODMAP or low fermentation diets, so give us a sense of what kind of restrictions those particular diets have.
Mark Pimentel: So I generally tend to use these diets as a maintenance. I’ll treat whether it’s with antibiotics—rifaximin and the other combinations I mentioned earlier—or the Enbióta, and then after that, I ask them to do the low fermentation diet for an indefinite period of time, depending upon their relapse rates. Because the whole point is, if we can treat once, and we can get away with remission for a year or two years, that’s better than every three to six months having to take an antibiotic. And the diet essentially restricts foods that you don’t digest, so it’s very low in fiber, no non-digestible sugars like sorbitol or Splenda, even monk fruit. All of those things are non-digestible. And so the bacteria, these Ferraris that we talked about, they’re just burning through those sugars and creating a lot of gas, and then reducing cabbage and beans and some of the things that are highly fermentable. Those are the basic principles of it, but it’s a very well-balanced diet for low fermentation.
Kevin Pho: You mentioned a connection between food poisoning, specifically with Campylobacter, and bacterial overgrowth. Now, as you could imagine, a lot of people get food poisoning every year, right? So people who get food poisoning, do they have to worry in the back of their mind, oh my gosh, I am going to be at risk for bacterial overgrowth and lifelong recurring symptoms?
Mark Pimentel: Well, let me put it in perspective. There was a meta-analysis that was just published two months ago on food poisoning and the development of IBS, and it varies by the type of food poisoning you get. Of the bacterial E. coli, quite common, is the least likely to precipitate IBS, but Campylobacter, which is the most common cause of food poisoning in the United States, it’s one in five. If five people get food poisoning with Campy at a dinner at a restaurant, one of those people at that table is going to have IBS for an indefinite period of time. So this should raise a bit of an alarm that we should be much more careful in our food choices and/or treating the food poisoning right away to prevent the development of IBS, and those studies have not been done properly yet. So while we have animal studies that say if you treat food poisoning right away, the animals don’t develop IBS as much, we don’t have such studies in humans. But the data suggests we should do those studies.
Kevin Pho: And moving forward, do you feel like there is a misconception or perhaps a lesser-known awareness of bacterial overgrowth?
Mark Pimentel: I think it’s growing a lot lately. So awareness has increased, the research has increased. There are so many studies coming out on bacterial overgrowth, and new therapies are emerging for bacterial overgrowth. There’s a drug emerging right now that we’re going to present in a month that blocks methane production by the methanogens, which helps constipation. So you’ll hear a little bit about that in a month. So new things are coming because of all of this SIBO research, and so it’s going to get pretty exciting pretty quickly. And I think that patients should be optimistic, primary care physicians and physicians in general should be optimistic that they’re going to have a war chest of things they can use in these instances that can really benefit patients, rather than treating them as a psychological condition or just giving them Imodium or just giving them those types of therapies. I just want to say one thing: I don’t know if you read the ACG guidelines on ulcerative colitis, which is a diarrhea condition, or IBS in ulcerative colitis. You don’t see Imodium as one of the things they talk about in the guidelines. It’s an antidiarrheal; it can help ulcerative colitis symptoms, but it’s not in the guidelines. In IBS, it’s in the guidelines because we’re treating symptoms in IBS. It’s a bit of a shameful commentary, because we shouldn’t be focusing on symptom treatment in IBS. We should be focusing on treating the cause, and I think that’s where we’re heading. That’s my point of that comment.
Kevin Pho: We’re talking to Mark Pimentel. He’s a gastroenterologist. Today’s KevinMD article is “Small intestinal bacterial overgrowth and irritable bowel syndrome: the hidden link keeping millions in pain.” Mark, let’s end with some takeaway messages you want to leave with the KevinMD audience.
Mark Pimentel: Oh, thank you so much for having me on the program, but I think what I should leave with is SIBO is part of IBS. It’s probably 60 percent of irritable bowel syndrome. SIBO can be caused by other things—diabetes, etc.—so you’ve got to think outside the box. But if you have somebody with bloating after eating, consider a breath test. That’s a really important thing to do. There are lifestyle things you can do to help SIBO like diet. We’ve talked about those things. But new treatments are here, emerging, and I think what patients need to take away from this is a degree of optimism that a lot of new things are coming in the near future that are going to help them. And even though we have rifaximin now, better things are coming imminently, so stay optimistic.
Kevin Pho: Mark, thank you so much for sharing your perspective and insight. Thanks again for coming on the show.
Mark Pimentel: My pleasure.