Gas, bloating, constipation, diarrhea – caused by bacterial overgrowth – part 1 – Podcast 2

In this episode, Dr. Ruscio discusses the symptoms, causes, testing and treatment in part one of this series on Small Intestinal Bacterial Overgrowth (SIBO).

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Symptoms of SIBO…..1:47
Causes of SIBO…..3:12
Mechanisms of SIBO…..5:26
Testing for SIBO…..8:43
Testing for other GI infections…..13:59
Treating SIBO – killing phase…..14:45
Treating SIBO – prevention phase…..27:08

Show Links:

  1. (2:49) As much as 84% of IBS may be caused by SIBO
  2. (3:56) “The odds of developing irritable bowel syndrome are increased six-fold after acute gastrointestinal infection.” –
  3. (8:48) NCNM SIBO breath testing –
  4. (10:09) Genova Diagnostics Organix Dysbiosis Profile Urine –
  5. (15:13) Antimicrobial herbs are as effective as the prescription medication Rifaximin –
  6. (18:01) Elemental diet has shown an 80% success rate in clearing breath test –
  7. (18:47) Dr. Siebecker’s homemade elemental diet formula –
  8. (23:04) Rifaximin study showed 49.5% with one round.


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Gas, bloating, constipation, diarrhea – caused by bacterial overgrowth – part 1 – Episode 2

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

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

Now, let’s head to the show!

Susan McCauley: Hey everyone this is Susan McCauley certified nutritionist from So, today we’re going to talk about small intestinal bacterial overgrowth.

Dr. Michael Ruscio: Yes, and I’m sure many people have lots of questions about it and definitely something I think is going to be helpful for a lot of our listeners, so I’m excited to jump in.

SM: So, it sounds like an awesome topic for today. But before we get started I’d like to remind people that if they have questions or comments about today’s discussion they can head over to where they can ask questions or leave comments on the blog post for today’s podcast. Okay, Dr. Ruscio, so tell us more.

Symptoms of SIBO
All right, well, there’s a lot that I want to cover, and so I’m thinking we’re probably going to have to break this down into two sections. And, we got a lot of questions on Facebook and a lot of the questions are more advanced level questions. So, I think the way we’ll kind of navigate this whole topic is we’ll do a part one today of more of the foundational issues and SIBO, and then the next recording we’ll do will be, kind of like, your more advanced concepts, where we’ll also go into the listener questions. So then, to start for today: “What are the symptoms of SIBO?” If you’re listening, how, you know, how might you know if you have SIBO? Well there are classical symptoms like: Gas, bloating, abdominal distention, diarrhea, constipation or an oscillation between diarrhea and constipation. Those are some of the, kind of, classical textbook symptoms. And then there’s also your non-textbook symptoms, meaning the symptoms that you can see when you have a gut problem that don’t manifest solely in the gut manifest and other symptoms. So things like: skin condition – like breakouts, brain fog – other neurological issues, uh, weight loss etc. So, there can be a fairly wide array of symptoms but, definitely, if you have gas, bloating, abdominal pain, or distention and either constipation/diarrhea or an oscillation between the two, then you very well might have SIBO.

SM: So if you get an ambiguous diagnosis from your Gastro, such as IBS, it sounds like that could be pointing to SIBO.

DR: Absolutely. And, there was a study published (and we have the reference for this so we’ll try to include as much of the links to the references in the show notes as much as possible) but the highest prevalence I’ve seen is as much as 84% of IBS has been shown to be caused by SIBO. So, pretty significant.

SM: That is very significant. So, what causes SIBO?

Causes of SIBO
 Well, there’s a couple theories and predisposing factors for SIBO. One that is the most well studied would be, what we call, post infectious IBS or post infectious SIBO. And we can almost use SIBO and IBS interchangeably — not quite, but they’re almost synonyms of one another. But the post infectious theory is you, essentially, get a bout a food poisoning, and that food poisoning causes damage in the intestines, and the intestines… then the intestines are more prone to harbor bacterial overgrowth. In fact, one study found that if you’ve had a bout of, what they call, acute gastroenteritis (or just like an acute bout of food poison) let’s say you have really bad diarrhea, or really bad throwing up, that usually self-resolves in a few days– you have a six-fold increase chance of contracting, or having, IBS afterwards.

SM: And other causes? That people should be aware of?

DR: So, other causes are if you’ve had a re-sectioning of your small intestine where you can have, what is called, short bowel syndrome, that’s probably not going to be very common. Diabetes is also one, because Type II Diabetes, remember, can cause damage to nerves. And it can, in some cases, cause damage to the nerves and innervate the gut that allows for proper movement of food through the gut and that can cause SIBO. Acid suppressing medication like PPI use, Nexium, Prilosec — any of your PPIs or histamine antagonists and then also inflammatory bowel disease, because, inflammatory bowel disease you can have narrowing of the intestines which can impede the movement of food through the intestines, and when food…kind of gets… stuck, so to speak, you can have this overgrowth of bacteria and, so– I should mention, if people haven’t heard this before, what we think happens in SIBO is as food is moving through the small intestine, the upper part of the digestive tract, if food doesn’t move through at the appropriate pace, then bacteria can start to over grow. It’s just like… if water is running it doesn’t really encourage the growth of bacteria. But if water becomes stagnant, then you have all sorts of bacterial over growth. That’s why, if you’re ever camping, you don’t drink from stagnant water, but it’s safer to drink from running water. Same thing happens in the intestines. If food doesn’t move through at an appropriate pace then you can have bacterial overgrowth. So, the main theory behind the post-infectious SIBO is that you can track some kind of infection. The immune system comes in to kill that infection, but while it’s killing that infection it damages cells. Specifically, they’re called interstitial cells of Cajal– that regulate movement of food to the small intestine. And when the movement of food through small intestine becomes hindered then you can have bacterial overgrow.

SM: OK. So, if we want to paint a picture for everybody: the bacteria that we want when we talk about the good bacteria, we’re mostly thinking about the large intestine or the colon, correct?

DR: Yes, there’s significantly more bacteria in the colon then there is in the small intestine and they over grow into the small intestine and that can cause problems.

Mechanisms of SIBO
 And that’s what causes the symptoms. So, we think of the bacteria migrating either… the food’s moving too slow, and the bacteria’s growing, or the bacteria’s migrating from where it should be, in the colon, up to the small intestine where not as much bacteria should be.

DR: Exactly. And, probably, both of those mechanisms are a play.

SM: Ok. So, if we think we suspect we have SIBO– we have some of the symptoms or we’ve had food poisoning or any of the things we’ve talked about today, how do we get a definitive diagnosis of SIBO?

DR: Well, to diagnose SIBO– well, you know what, there’s one thing I wanted– as you’re asking that question– that just shot into my mind that I want to mention, cause some people have asked: “Why is it bad to have more bacteria in your small intestine? Because, isn’t bacteria good? Aren’t we supposed to have a really rich and diverse microbiota? Haven’t many different studies shown that people living in 3rd world countries have more bacteria, and that’s good, and that makes them healthy? So, you know, why is more bacteria bad, in this case?” And the reason, again, is how the bacteria get de-compartmentalized. Where they should be, in the large intestine, and they shouldn’t get into the small intestine. And the main reason for that is the protective mucosal membrane in the small intestine is significantly thinner than it is in the large intestines, so you have less protection. And, also, the tight junctions– The little doorways that regulate how much stuff can move from the intestinal lumen into the bloodstream– the tight junctions are much more permeable in the small intestines. So you have… it’s easier to have leaky gut, I guess you could say, in the small intestine because of the thinner mucous membrane and because of more porous tight junctions, and that’s one of the main reasons why you don’t want these bacteria in the small intestine. So, I just wanted to mention that. But, then, to your point about testing… I think the easiest test, and the test that we use routinely, is the lactulose hydrogen methane breath test. So, this is a test where you drink a lactulose solution and then you collect breath samples, usually, every 20 minutes for three hours and then based on the reading of that test you can diagnose SIBO.

SM: The lactulose: is that a specific type of carbohydrate that reacts with the bacteria?

DR: Exactly. It’s a non-resolvable prebiotic that travels through the gastrointestinal tracks.

 Testing for SIBO
And some tests use glucose, but glucose has been criticized because it may not make it all the way through the small intestines. It may get absorbed before it reaches the end of the small intestine– and small intestine’s about 24 feet so if glucose can’t make it all the way through that entire 24 feet… lets say it gets absorbed by the 15th foot… then you don’t have any way of testing the end part of the small intestine. Lactulose, however, seems to be able to make it all the way through, cause it’s not really absorbed and so it’s probably a better medium for testing.

SM: OK, so fear of getting your lab test done, you want to make sure it’s lactulose and not glucose.

DR: Yes.

SM: And are there any other tests that a practitioner might run on you?

DR: There’s also the urine test for dysbiosis markers that you can do through something like Genova. And I haven’t been a huge fan of that test, just because it’s not incredibly well studied. When I took some time to vet the literature belt in the test there… wasn’t really a whole lot of literature, whereas for the breath test it’s very very well studied. So I haven’t been really big on the urine test. However, just yesterday in the clinic we had a gal who came in and she had tested positive, previously, with urine. And she was negative for the breath test. She was treated with– she was treated for SIBO, she got better, and her urine test results got better, but she didn’t fully clear SIBO. And all the while her breath test was negative. So, essentially, her breath test was negative but her urine test was positive… so… I don’t see that often, but in her case, for some reason, breath testing was negative but urine testing showed positive. The reason why that may be is because there is one type of gas that we don’t get– we can’t capture, so to speak, on the breath test– and that’s hydrogen sulfide. And the liver, as I understand it, filters hydrogen sulfide because it’s considered a toxin to the body. So the body filters hydrogen sulfide so it doesn’t get into the breath. So, if someone has hydrogen sulfide producing bacteria and they do the breath test you won’t see it.

SM: Ok, so there could be a false negative on that one. So we should look for more of the symptoms as opposed to just say: the breath test negative, so you don’t have SIBO.

DR: Exactly, exactly… And that’s why I always recommend that people look at the entire clinical picture and don’t let labs be the “end-all be-all” because there are certainly some cases where you have to treat more so based on symptoms. So the urine test is something that I’m now considering as a fallback. Let’s say we tested someone for SIBO via breathe, they came back negative but it really looks like SIBO, we may then… repeat test, with urine test this time, to see if we can find out what’s happening. And, I just found out about a test in Belgium that will test hydrogen sulfide. I don’t know how well validated it’s been… but this may be an option for people who really suspect they have hydrogen sulfide and they want to get some kind of objective way of showing that. So, you can do a urine test through Genova– they won’t tell you if you have hydrogen sulfide– they’ll just tell you if you have bacterial dysbiosis. And there also is a test from Belgium that will tell you hydrogen sulfide specifically.

SM: Okay, and I know a lot of our listeners probably are wondering: does insurance cover any of these tests?

DR: So with the lab that we use which is the national college… or the… yeah, the national College of Naturopathic Medicine – it’s a side backers affiliate lab up in Oregon. They do bill to insurance. So that’s really nice option. There’s another lab that’s really popular for SIBO breath test, which is Commonwealth Labs. And I don’t know if they bill insurance or not. They were a little bit more difficult to try to set up an account with them and get everything started so I just ended up working with the national College of Naturopathic Medicine… so I’m not sure if Commonwealth does insurance testing. And then, for urine tests usually… not, as far as I understand.

SM: Yeah… I don’t think… yeah, Genova usually doesn’t take insurance. So you’ve got your test, you have your positive results… what do you do?

 Testing for other GI infections
 Well, the other thing that people should consider is also testing for other gut infections, because I would say in 30-40% of patients will find SIBO along with Candida or along with H. Pylori or along with Yersinia and I think it’s important to try to catch these because it can really help steer your treatment to make it more effective. So, just a word of caution, just because SIBO right now is receiving a lot of attention let’s not forget about some of the other tests that have been very successful. And, it may be a good idea to include those, or ask your doctor to include those, in the workup that he does.

SM: Okay, great information.

Treating SIBO – Killing phase
 Now, regarding treatment… I guess you can think of this in two phases. The first phase, would be your killing phase, where that’s… where we just want to get rid of the SIBO. In the second phase would be your preventative phase. So in the killing phase, I like to use a blend of herbal antimicrobials. Things like… oregano, berberine, grapefruit seed extracts, olive leaf… and they were actually used in a side-by-side comparison against Rifaximin recently (and we also have the reference for the study, we’ll put in the notes). In both the herbs and Rifaximin, were shown to have equivalent effectiveness. So, sometimes people think that the drugs are stronger and going to be better at killing bacteria, and I’m certainly open to that, but in this case it seems that they’re about equally as effective.

SM: So with the antimicrobials, why not start there instead of going for the antibiotics? You know… milder… more “whole food/whole herb” version?

DR: Right, and that’s most of the patients I work with like to start with the natural… the only time where we differ from the approach is if someone is really trying to be as financially conservative as possible and their insurance will cover Rifaximin… or Rifaximin and Neomycin the prescriptions, then they may do that. So there’s a little bit of a pro/con for each, but the major Pro for the antibiotics is if you have insurance coverage you have nothing to pay for. But my bias is herbal… but I have used antibiotics in some patients, and they do work well. One of the questions that I think most people are concerned about regarding antibiotics is will this create some kind of antibiotic resistance? And it doesn’t seem that Rifaximin will allow antibiotic resistance to occur. And Mark Pimentel who’s done a lot of work with Rifaximin and treating SIBO has found that when Rifaximin is used– even with other antibiotics, like Neomycin– it actually prevents what’s called plasmid resistance and it helps to prevent antibiotic resistance. So, that’s one thing that may be comforting to people, that being said some of the worst reactions I’ve seen have been with the antibiotics. So, there’s always a trade-off

SM: And, then in regards the antibiotics, how about: do they ever create further dysbiosis?

DR: That’s certainly a good question… that may be part of the reason why people tend to react a little bit more to the antibiotics. I don’t know of any studies that have really, kind of, quantify looking at the herbs next to the antibiotic. But, generally speaking, I think that herbs tend to be more selective and not disrupting your healthy bacteria, yeah.

SM: And then, as far as diet during the killing phase, what would you recommend?

DR: So there is a diet that can be used as a killing agent if you will. And this is the elemental diet… which is essentially just a liquid diet that you do for 14 days. And one study did show an 80% success rate in clearing SIBO from the breath test in using the elemental diet. It’s tough though, because you have to only drink a liquid for 14 days.

SM: I can’t imagine that!

DR: Yeah. (Laughter) Yeah, and it’s not… eh… I mean I haven’t tasted any of these personally but from what I’ve heard from feedback from patients they’re… they‘re not very palpable, so…It’s an option but I think that’s kind of a last-ditch option. But it’s an option. And there’s Avidemux and Peptamen-  are two of the premade versions and you can buy. And then there’s also… Allison Siebecker did a great job in creating a homemade version of an elemental diet that one can just buy with store-bought stuff. But, that’s kind of a tough one because a lot of people aren’t going to like that. So that’s kind of the killing phase. Regarding probiotics in the killing phase: we’ll oftentimes use a soil-based probiotic, like Prosypithcus. Oftentimes we might use Garden of Life, the Garden of Life Probiotic Primal Defense. We usually have people on the paleo or the omni-paleo diet while we’re treating. And then… I’ve been toying with biofilm or anti-biofilm agents, and I can’t say that I’ve seen it make a huge difference one way the other… but right now I’m just kind of tracking data and tracking patients and hopefully I’ll be able to report on this in, maybe, six months to a year and have some definitive numbers for people in terms of cure rate of SIBO with abiofilmation compared to without a biofilmation.

Why don’t we fill everybody in on what actually a biofilm is and what these anti-biofilm agents do?

DR: Okay so great question. When bacteria and fungus are in the body for a prolonged period of time, they form biofilms over them, and biofilms are protective coatings that help bacteria and fungus resist treatment with antimicrobials or antibiotics. So once a bacteria or fungus has been in the body for a while they kind of all team up and start building this protective fence over them, and that fence helps to shield out agents that are trying to kill them, like antibiotics and antimicrobials. So, one of the things that can be done is while you’re administering some kind of killing agent you can co-administer an anti-biofilm agent which breaks down this fence and it’s been most well studied with acetyl cysteine in the treatment of H. pylori and it’s been very effective in that application. We also know that biofilms do form the small intestines. And, we also know that the bacteria and even the archaea, which are different form of organism that can overgrow in SIBO, will form biofilms. So we certainly have a good case for it’s just, there’s no real data looking at “Okay we gave half the patients a biofilm agent and the other half we didn’t, what kind of difference does that make in the treatment outcome?” We don’t have that kind of data yet, but that’s something I’m tracking in clinic and hopefully we’ll have some specifics on the future.

SM: Have you ever heard any negative things about biofilm agents? Recently, somebody came to me and said that– because there’s biofilm in her mouth and her teeth– that they had had some teeth problems due to biofilm agents.

DR: Well, certainly biofilms… biofilms can be formed by good and bad bacteria, so that’s one of the things to be cognizant of. And biofilms definitely form in the mouth and they’re certainly something that’s well studied in oral– in dentistry or oral health. The way I look at this is if we can reduce the amount of times we have to administer an antibiotic or antimicrobial agent because we use a biofilm, then to me, that seems that the risks, or… I’m sorry, the benefits outweigh the risks. There’s nothing published to that regard but that’s just the way I look at it. So if we could cure your SIBO with one round of treatment as opposed to three because of a biofilm agent then I think we would be in a better position had we– then if we had not used it. But it’s a little bit of an unknown.

SM: Yeah, and financially as well. Cause, six rounds of herbal medications can get pricey after a while.

DR: You’re right, right, yeah… yeah…

SM: So I guess there comes the million-dollar question: so what is the “cure” rate? And, I’m putting “cure” in air quotes.

DR: Right, you have to be very very careful with the word cure.

SM: Yeah.

DR: So a study was published recently and we will provide the link for this reference too, it was a study on Rifaximin and the best… this is the best cure rate that I was able to find, and they showed a 49.5% cure rate of SIBO with one round of treatment. And, I was recently listening to a lecture by Dr. Pimentel and he estimates that 30% of patients can clear SIBO with one round of treatment. And, I’m starting to find that I agree moreso with Pimentel’s estimate then I do with that one Rifaximin study, but I think you anywhere between 30 to 50% cure rate with one round of treatment which I think is important for people to understand– because if you approach SIBO from a perspective of “If I don’t cure this with one round of treatment, then, you know, the doctor I’m working with sucks or I did something wrong or this treatment isn’t working.”  I would encourage people not have that mentality because if you… if you jump around and you try different doctors and different approaches, you may make it a lot harder to actually cure yourself of SIBO because sometimes you just have to keep doing the same thing a little bit longer to get over it. So, what I like to do is just retest and look and see that “Okay your methane levels were 100. We treated you. You’re feeling a little bit better, and your methane levels have improved a little bit, so now your methane levels are at, let’s say, 60.” And so then we’ll treat again. And now methane levels have dropped to 38 and you feel even a little bit better and so it’s a good way to just make sure that your treatment is on the right track, meaning that your symptoms are improving, the symptom improvement matches the lab improvements, you’re on the right track, and we’ll keep, kind of, proceeding.

SM: So patience is the key.

DR: Yes.

SM: Test, treat, test, treat… and hopefully at the same time as were going along this pathway the symptoms are… you’re getting little better… little better… a lot better… a lot better, as we go down the road.

DR: Exactly, yeah, exactly. And it’s just important that, to have patience and not jump ship or start chasing down some other potential diagnosis cause you think isn’t, you know, “Oh it’s not SIBO. It must be methylation. Let me go do a gene test and start treating the genes.” And I see patients that do that. They… they’re looking for results really quickly, and when they don’t get them, they want to do something else. And, just like you said, sometimes you just have to be patient and just be consistent and see the one item through to its completion.

Treating SIBO – prevention phase
 And how about a relapse rate? Does SIBO come back once you have it, or are you more prone to get it again? Does it come back?

DR: SIBO can relapse, that’s one of the challenges with SIBO is preventing relapse. And, this is where pro-kinetic agents come in and so the reason people may relapse and how this ties into pro-kinetics, the reason people may relapse is because they don’t have that proper motility through the upper half of the small intestines, remember we talked about the water that gets stagnate and fosters bacterial growth?

SM: Mhmm.

DR: So, if you don’t have adequate ability to move food through the small intestines, if you kill the bacteria but don’t fix motility problem, then you may just have a relapse because you haven’t fixed interline cause of the problem. And that’s something I want to back more to… to the motility issue, in the second-half’s discussion, because we had some great listener questions to that regard. But, pro-kinetics can be really helpful in that regard and there’s two natural — or three natural that I like. But you know what, maybe we’ll save that for the next conversation.

SM: So after we do the kill phase what comes next?

DR: So, after we do the killing phase, there’s a few things we can do in our preventative phase. The first, and maybe most foundational thing, is food. So typically we segue someone from the autoimmune paleo diet onto the low-fodmat diet or a low fodmat combined with SCD diet.

SM: Okay, not specific carbohydrate diet, for those of you that are not familiar with the term SCD.

DR: Right, exactly. Both these diets, to a greater lesser extent, are diets that don’t really feed bacteria, so they have low prebiotic functioning, if you will. And, of course, if we’re dealing with conditional bacterial overgrowth then we don’t want to really feed bacteria too much.

SM: So, quick question though, I’ve heard this in the blog sphere and on different podcasts: if you have SIBO you’re not supposed to have fodmats. So why is your approach to take the fodmaps out towards the end instead of the beginning?

DR: The main reason for that is: if you start to really restrict a bacteria of its food supply they can go into a hibernation or a dormancy state, where they go into, where, what’s called a spore, and when they do this, again, they essentially hibernate and so they’re not really going through the process of really up-taking a lot of nutrition. And so if they’re not eating the stuff that you put in the gut, and you’re putting an antibiotic or antimicrobial in the gut to kill them then it’s going to be very hard to potentially kill that bacteria.

SM: Ah, we want to leave them alive and kicking so we can get rid of them all.

DR: Exactly and this same approach is sometimes used when people treat Candida. Where they… if they’re going to administrator an antibiotic or an antimicrobial herb, they don’t want… er… it’s not common practice to have people go on a super low carb diet. They leave a little bit of the carbon there so the fungus has little bit of food supply, they’re going to up-take that sugar and along with the up-take of that sugar will be the up-take of the antimicrobial agent.

SM: Okay and then once you’ve either done fodmap or fodmap SCD, then once your symptoms are gone and your test results are normal, then reintroduce the food that you previously taken out and see how you react.

DR: Exactly. Usually when someone has cleared their SIBO and they’re stable– I’m sorry, they’ve cleared their SIBO, we put them on the low fodmap or the low fodmap with SCD… Once they’ve been stable for a few months then we have them go through a reintroduction. Just like when you go on the autoimmune paleo diet after a few months you go through your food reintroduction. Same kind of thing: you just go through a fodmap or a SCD reintroduction and usually what I find is most people have a much higher tolerance for the fodmap and SCD foods but they also notice there’s one or two they’re really sensitive to and they have to be careful with.

SM: Yeah, for me cabbage is my sensitive food. I can eat cooked cabbage, but raw cabbage? My tummy does not like it.

DR: Yep, exactly, and that’s just one of the things that’s beautiful about the reintroduction approach. ‘Cause it just helps people really personalize a diet to them.

SM: Mmhm… Okay, so to wrap up, do you want to say anything in conclusion, we’re going to have a part two coming up soon, where we’re going to do an advanced module– we can call it the “advanced modules.”

DR: All right, yes, in Part 2 we’ll go into a little more detail about troubleshooting for kind of recurrent SIBO. We’ll talk more about pro-kinetic agents, and different strategies that can help restore motility. And we’ll take some listener questions, more about pro-kinetics, and some more listener questions about ileocecal valve issues, and then also some information about methane SIBO and obesity.


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