Small Intestinal Bacterial Overgrowth with Dr. Ben Weitz: Rational Wellness Podcast 351

Dr. Ben Weitz discusses Small Intestinal Bacterial Overgrowth.

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Podcast Highlights

1:14  SIBO, Small Intestinal Bacterial Overgrowth, is believed to be the cause of 60-70% of cases of Irritable Bowel Syndrome, IBS, according to research published by Dr. Mark Pimentel.  IBS is the most common gastrointestinal condition, occurring in up to 15% of the population.



Dr. Ben Weitz is available for Functional Nutrition consultations specializing in Functional Gastrointestinal Disorders like IBS/SIBO and Reflux and also Cardiometabolic Risk Factors like elevated lipids, high blood sugar, and high blood pressure.  Dr. Weitz has also successfully helped many patients with managing their weight and improving their athletic performance, as well as sports chiropractic work by calling his Santa Monica office 310-395-3111.



Podcast Transcript

Dr. Weitz:            Hey, this is Dr. Ben Weitz, host of the Rational Wellness Podcast. I talk to the leading health and nutrition experts and researchers in the field to bring you the latest in cutting-edge health information. Subscribe to the Rational Wellness Podcast for weekly updates, and to learn more, check out my website, drweitz.com. Thanks for joining me, and let’s jump into the podcast.

                                Hello, Rational Wellness podcasters. I wanted today to talk about small intestinal bacterial overgrowth and IBS and give my take on this important topic in the world of functional GI disorders. Now, we have had and will continue to have a number of interviews with various experts, and the bottom line is even though there’s a science behind everything we do, there’s also an art, and there is a difference of opinion about what is the best strategies for treating many of these conditions. And so I wanted to give my take on SIBO.

                                Now, SIBO is believed to be the cause in a majority of cases, 60 to 70%, according to studies published by Dr. Mark Pimentel, of irritable bowel syndrome, abbreviated as IBS. Now, irritable bowel syndrome is the most common gastrointestinal condition occurring in up to 50% of the US population. Now, what accounts for the other, say, 30 to 40% of cases of IBS that are not caused by SIBO? Well, some of these are caused by SIFO, which is small intestinal fungal overgrowth. They can also be caused by dysbiosis of the microbiome.  They can be caused by parasites, food sensitivities, and a number of miscellaneous other conditions related to the health of the gastrointestinal tract. Now, what are the presenting symptoms for IBS? We have gas and bloating, or gas or bloating, stomach or abdominal pain, constipation, diarrhea or alternating diarrhea and constipation, as well as a host of secondary symptoms including nausea, fecal urgency, meaning you have to go to bathroom right away, skin rashes often described as rosacea or eczema, acid reflux, upper abdominal pain, fatigue, depression, brain fog, and a series of other symptoms that may or may not actually be related to SIBO.

                                Now, the best way to diagnose SIBO is with a SIBO breath test. Now, let me just explain what happens in SIBO so you can understand what is the benefit of the SIBO breath test is that the small intestine usually has relatively low levels of bacteria lining the small intestine, and there’s several reasons for this. One of the reasons is because the small intestine is where the majority of nutrients get absorbed. So if you had a large number of bacteria that could potentially interfere with absorption of nutrients and that would not be a good thing. Second of all, the large intestine, the colon, is a very extensible organ. It could expand quite a bit.

                                And so if the bacteria and this does happen, if the bacteria in the large intestine produce a lot of gas, that gas forces these large intestine to expand, and that’s not a problem. But the small intestine is a smaller tube, and it doesn’t have the extensibility that the large intestine does. So if a bunch of gas is produced in the small intestine, it will often lead to stomach abdominal pain because it’s uncomfortable to try to expand that. And also just a sense of uncomfortability about the gas and bloating, and patients often feel like they’re overly full, et cetera.

                                So, in SIBO, you have an excess amount of bacteria lining that small intestine. And when you eat foods that contain fermentable fiber, those bacteria produce gas. Depending upon what type of bacteria or microorganisms are lining the small intestine, you can get hydrogen gas. You can get methane gas or hydrogen sulfide gas. And there are different microorganisms that account for each of those gases, with the methane gas being created by archaea, and archaea are actually primitive microorganisms there. They’re actually not bacteria, though they’re similar to bacteria.

                                And so we often refer to the type of gas produced as a way to explain what form of SIBO, which tells us about the type of microorganism, which helps guide our clinical judgment as to how we can treat these conditions because different antibiotics, antimicrobial herbs, other substances that can help to reduce the population of bacteria that produce hydrogen or hydrogen sulfide or the archaea that produced the methane. We also now recognize that the methane is produced… could be produced in other parts of the intestinal tract, including the large intestine.

                                So we now describe that the… we now describe methane SIBO as IMO, intestinal methanogen overgrowth. So the best way to test for SIBO is to use a lactulose SIBO breath test. Now, there are different substrates that can be used, and there are some practitioners that recommend glucose or fructose. And one well-known practitioner I’ve interviewed typically recommends all three lactulose, glucose, and fructose to be used. So the patient has to complete the SIBO breath test three times. Now, originally, we would do the SIBO breath test for three hours. Now, it is often recommended to do it for two hours, but a lot of practitioners still feel that doing it for three hours is more beneficial.

                                I prefer to do the newer Trio-Smart 3 Breath Test as compared to the older two-breath tests that measured hydrogen and methane. The Trio-Smart 3 Breath Tests also measures hydrogen sulfide, and I feel if we don’t do that, we’re missing out on 10 to 15% of cases of SIBO that are caused by hydrogen sulfite. Now, the old way was to do a two-breath test, and if you had a flat line of methane and hydrogen all the way through, that was considered positive for hydrogen sulfite. I don’t believe that that was really validated as an accurate way to test for hydrogen sulfite. And I think that some data comparing that with the results from the Trio-Smart 3 Breath Test indicate that that’s not an accurate way to do it.

                                However, there’s still still controversy. There are people who don’t believe in the effectiveness of the 3-Gas Breath Test at Trio-Smart, but I feel that there’s been enough research by Dr. Mark Pimentel and others to show that that breath test actually is the most accurate. And I also don’t think there… Since the reason for doing a two-hour breath test only is that anything after 90 minutes, at most a hundred minutes, certainly anything more than 120 minutes is going to be testing gas that’s produced past the small intestine in the large intestine. And we’re trying to just measure the gases in the small intestine. So I think that we only need to use the two-hour SIBO breath test. And I also believe that the lactulose is by far the best substrate to use.

                                For one thing, the glucose is not that beneficial because it’s usually absorbed in the proximal part of the duodenum, which is the first part of the small intestine. And very few patients have SIBO in that part of the small intestine. SIBO is way more common in the distal part of the ileum, closer to the large intestine. For most patients, fructose is also not needed, though there are a percentage of patients who have fructose intolerance, but that’s different than using fructose as a substrate for the SIBO breath test. The data shows that the lactulose is the most effective, and I think that’s the one that has guided me with my patients and been the most helpful.

                                Now, I also feel that most patients that see me for gut symptoms, like the symptoms related to SIBO, should also have a stool test so we can examine the microbiome and also look for parasites, fungal overgrowth, dysbiosis. And the stool test that we use also gives us some information about whether or not they’re secreting enough pancreatic digestive enzymes, whether or not they’re breaking down their fats, whether there’s inflammation in the gut, and how well the gut immune system is working as measured by Secretory IgA levels in the stool. And these are very helpful because they can help with part of our treatment as well.

                                For example, if the patient has low gut immune system function, then it’s going to be difficult to eradicate the SIBO even if we use the right agents that kill the bacteria or methanogens because we need the immune system to be participating in that. Anytime you have an infection, you need your immune system to participate in that, as well as whatever you do externally to stimulate the immune system. And also, when we think that the form of SIBO related to methane gas is now described as IMO or intestinal methanogen overgrowth, part of that explanation is that it doesn’t just exist in a small intestine.

                                So if we’re going to have any sense of whether or not there is an increase of methanogens in the colon, a good stool test that includes looking at methanogens is… specifically Methanobrevibacter smithii in the colon is going to be helpful to help us diagnose that. So I do think that a stool test can be part of properly diagnosing IMO. Now, how do we treat IMO, or how do we treat SIBO in my office? Well, first of all, it depends on the form because we use antimicrobial herbs and other nutritional agents, and we typically find that there are different… antimicrobials are more effective for one type of bacteria than another.

                                And like I said, there’s different bacteria that produce hydrogen versus hydrogen sulfide. And then we have the primitive microorganisms known as methanogen that produce the IMO. And we, through trial and error and talking to other experienced SIBO practitioners, know which antimicrobials are likely to be the most effective, the most tolerable, the ones that have the least side effects, and the ones that can get the patients better as quickly as possible for each form of SIBO. I find in my office that we typically have to do two to four months of antimicrobials, and we like to rotate the antimicrobials monthly so the bugs don’t get use to the antimicrobial natural agents that we use.

                                We will often make some changes to the diet at the same time. I may recommend a full low FODMAP diet, a modified low FODMAP diet, a specific carbohydrate diet, or we may just remove certain foods like gluten, dairy, beans, et cetera. It depends on the person. But we typically will make some dietary changes, though not always. And there’s many things that go into that, but looking at the whole patient and trying to understand what’s going on and what’s best for their overall health.

                                Now, we also know that a significant percentage of patients with SIBO, and this is from Dr. Pimentel research, that the SIBO was caused by a lack of intestinal motility. Typically, what will happen is the patient ends up with a bout of food poisoning, meaning they get a bacterial like E. coli or Campylobacter jejuni that causes food poisoning. The patient has a immune reaction to those bacteria, forms antibodies. Those antibodies then cross-react, meaning the antibodies designed to attack the E. coli attack structural proteins in the intestine that look similar.

                                And those structural proteins help to control the migrating motor complex, which is the part of the small intestine that leads to what are called cleansing waves. So when you eat, you have peristaltic action. You get this wave of contraction that goes through the digestive tract that helps to move the food through as your body slowly digests it. But there are cleansing waves that occur when you have a need for at least three or four hours that are these peristaltic waves that help to keep excess bacteria from building up in the small intestine.

                                And when these get damaged, you’re more likely to end up with SIBO to have an increase in those bacteria. So we will often use a natural prokinetic, something that helps to reset the motility as part of the treatment protocol, and we may use certain nutritional agents that help us to break up biofilms. Now, what are biofilms? Well, we know that bacteria and other microorganisms, fungi, methanogens, tend to produce a biofilm. So if you’ve ever seen in a stream where you get this moss buildup, that’s like a biofilm.

                                And so the bacteria surround themselves with this biofilm, and it’s a way to ward off the gut immune system. The bacteria want to continue to thrive in your intestines whether we want them there or not. And so that’s part of how the bugs are able to sustain themselves, and we may need to break down that biofilm to help the antimicrobial herbs to get in to kill those bacteria or methanogens.

                                Now, another thing that helps to keep the population of bacteria down in our small intestine are hydrochloric acid, which is produced in the stomach, bile, which is produced in the liver, started in the gallbladder and released into the small intestine, and pancreatic enzymes, and all three of those can help reduce bacteria in the small intestine. So if we see on a stool test or we have a sense that one or more of those are depleted, then adding in some HCL, some pancreatic enzymes, and or some bile may be an effective part of our SIBO eradication program.

                                Do we or do we not use probiotics for treating SIBO? Now, there is some data showing that certain specific strains have been found helpful in killing certain bacteria. And Dr. Jason Hawrelak from Australia, who runs the Probiotic Advisor, has cataloged some of these studies, and he feels that the use of specific probiotics is often an effective part of his protocol. There’s another popular podcaster in the functional gastrointestinal world. You may or may not know who I’m talking about, but he recommends probiotics as first-line for reducing SIBO, and he recommends three different types of probiotics, a lacto-bifido blend, a saccharomyces boulardii, and a spore-based probiotic.

                                And he finds that that’s very effective. I don’t. I have found that using some of those probiotics, specifically lacto-bifido blends, tend to increase the population of bacteria that we’re trying to eradicate. So adding more bacteria while we’re trying to reduce bacteria may not be the best strategy. And a number of the most prominent SIBO practitioners who I know and have spoken to, either at conferences or personally, also do not feel that using probiotics are helpful. Now, I have experimented with using spore-based probiotics during the initial killing phase for SIBO, and at some points, I feel they’ve helped. At other points, I feel they haven’t, or they’ve been neutral.

                                There are a number of people who recommend these spore-based probiotics, and one of the reasons for this is because these spore-based probiotics supposedly will not open up until they get through your small intestine and get into the large intestine, and that’s when they’re designed to open up. So, therefore, theoretically, they won’t contribute to more bacteria in your small intestine. But I have found that they don’t seem to be particularly helpful, and I’m already prescribing a number of natural agents for my patients to take during the initial phase of SIBO eradication, what we might call the killing phase or the remove and replace phase if we go with a Four R or a Five R Program that Dr. Jeffrey Bland came up with.

                                And I do think that, in general, that general strategy continues to make sense. And I know that’s controversial, and other practitioners have told me they don’t believe in that, but I have found that to be very helpful, and I think that that overall strategy continues to work. So I usually wait on probiotics till we get to the restore and reinoculate phase. So we may want to stimulate the gut immune system using specific type of non-dairy immunoglobulins. And as I mentioned, if the gut immune system is not participating, it’s going to be very difficult to eradicate these… the SIBO.

                                So not only do we need the proper antimicrobials, but we will need the gut immune system to be working. And so, we’ll use several strategies, one or another strategy, to help during this phase if the stool test seems to indicate that that’ll be beneficial, typically find that it’ll take two to four months of antimicrobials. I know other practitioners, say, one month, some will blast every possible natural agent all at the same time. Some will combine natural agents with prescription antibiotics like rifaximin. I prefer to use natural agents and to use two or three at a time and to rotate it monthly.

                                And I find that not only is that helpful… Now, of course, look, I wish we could eradicate it in a month. I have found that if we try to be too aggressive that too many of the patients come back with a lot of side effects and are unable to tolerate the treatment, and that’s not beneficial. So I would rather do it more gradually and give ourselves the amount of time we need, which is typically two to four months. Then, once we’re done with that phase, we go into the restore, reinoculate, and repair phase using prebiotics, gut repair nutrients, and probiotics, and often also using polyphenols. And we often will like to continue to utilize a pro natural prokinetic because we want to keep that motility going.

                                And for some reason, it takes in my experience and discussions with some of the other top SIBO practitioners, unfortunately, six to 12 months to restore that motility once it’s been damaged. Now, how do we know that motility has been damaged? In clinical practice, we don’t really have a good test for that. So there are some ways that clinicians have tried to have patients, for example, consume charcoal and see how long it works its way through the digestive tract. But until we get a good test for measuring intestinal motility, I think it’s safe to assume that most patients are having some issue with intestinal motility.

                                Prebiotics are specific nutrients that help the healthy bacteria in the microbiome to grow. Most of these patients have damaged guts. So we need to use typically a formula of gut repair and nutrients. And these will include one or more of the following nutrients, L-carnitine, zinc carnosine, and Acetyl-D-Glucosamine, L-glutamine, specific botanicals, typically what we call mucolytic herbs like deglycyrrhized licorice, aloe vera, slippery elm, marshmallow, okra extract, and cat’s claw. And I typically find two to four months of the restore, reinoculate, and repair phase is usually sufficient to get the patients feeling a lot better.

                                Now, what about some patient… Oh, another very important part of the restore, reinoculate, and repair phase is we want to bring back in most of those foods that we remove from the diet. So if I put the patient on a full low FODMAP diet, many of the low FODMAP foods are super healthy. Cruciferous vegetables like broccoli, cauliflower, brussels sprouts, legumes, other foods with fiber, many other healthy vegetables, avocado, et cetera. So I think it’s very important for people to be healthy to have a diverse diet with a range of different vegetables and nutrients.

                                So I very much encourage my patients to slowly test back in all the foods that they’ve taken out. Now, I also encourage them to test them in one at a time so we can test if that patient is still having a reaction to that food. And people do have reactions to certain foods, and this may just be their own immune system. But even if we’re unable to bring a food back in, in the future, we would like to continue to retest it because, ideally, we would like everybody to have no restrictions on what foods they need to eat. Now, it’s not a bad thing, I don’t think, to take a few foods out like gluten. I do think there’s a number of reasons to think that gluten is potentially harmful for many people.

                                Now, there may be a percentage of people… I do believe a percentage of people can tolerate gluten without any harm, but that’s one of those foods that I think it would be okay if you remove permanently from your diet. If you feel like you don’t react well to gluten, or you’ve had testing that shows that your body doesn’t react well to it. But otherwise, we would like you to have a very diverse diet, and we want you to have foods like legumes, which are such a great form of fiber, especially soluble fiber that helps to reduce your risk of certain diseases like colon cancer. And also, soluble fiber, we know helps reduce your risk of cardiovascular disease by helping to pull some of the unhealthy cholesterol out of your system, like oxidized LDL, et cetera.

                                So that’s basically the type of approach we will use with a patient. But everybody’s individual. It depends on many things. It depends where exactly what their symptoms are exactly what their testing shows. There may be other confounding factors. Do they have other conditions, autoimmune conditions? Do they have other gut problems, et cetera, et cetera? Patient could have an overgrowth of H. pylori. They could have a parasite. We may feel that that is the number one thing that we want to do is get rid of that parasite before we even try to address the SIBO.

                                And so it may take working through several layers of gut dysfunction, like using the metaphor of the onion where you peel off the first layer, then you get to the second layer, you peel that off, and eventually, you solve the problem. And I do think that there are a number of patients that have levels of gut problems, and we may need to work through each of those. And that’s another reason for doing a good functional medicine-oriented stool test as well as a SIBO breath test. Sometimes, an organic acids test, which may be better for picking up candida and fungal overgrowth than the stool test.

                                Some practitioners recommend to get a better stool test to have the patient use biofilm-busting agents for a week or so prior to doing the stool test. But this has not really been tested out by the stool test company, and I, at the present time, don’t recommend that, though I would love to see a study on that to see if there’s some efficacy for it, and it certainly makes some sense, and I doubt it would be harmful. So anyway, I hope I’ve given you some insights into how I treat patients with functional gastrointestinal disorders like SIBO, which we believe is the main cause of IBS in my office. And thank you, and I’ll see you next week for another exciting episode of the Rational Wellness Podcast.



Thank you for making it all the way through this episode of the Rational Wellness Podcast. For those of you who enjoy listening to the Rational Wellness Podcast, I would appreciate it if you could go to Apple Podcasts or Spotify and give us a five-star ratings and review. If you would like to work with me personally to help you improve your health, I do accept a limited number of new patients per month for a functional medicine consultation.  Some of the areas I specialize in include helping patients with specific health issues like gut problems, neurodegenerative conditions, autoimmune diseases, cardiometabolic conditions, or for an executive health screen, and to help you promote longevity and take a deeper dive into some of those factors that can lead to chronic diseases along the way. Please call my Santa Monica, Weitz Sports Chiropractic and Nutrition office at 310-395-3111, and we’ll set you up for a new consultation for functional medicine, and I look forward to speaking to everybody next week.


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