A streamlined stack of supplements designed to meet your most critical needs - Adapt Naturals is now live. Learn more

Unanswered Questions About SIBO


Last updated on

SIBO continues to be one of the most challenging conditions to treat. Treatment efficacy is often quite low and recurrence rates are high. In this podcast, I’ll discuss the questions I think still need to be answered about SIBO diagnosis and treatment—and maybe challenge a few “truths” in the process.

Revolution Health Radio podcast, Chris Kresser

In this episode we will discuss:

  • Is lactulose breath testing an accurate way to diagnose SIBO?
  • Is SIBO always pathological?
  • Are our treatments effective?
  • Is SIBO always the underlying cause?
  • Should probiotics and prebiotics be avoided during treatment?
  • Does a long-term low-FODMAP diet help prevent recurrence?

Hey, everybody, it’s Chris Kresser. Welcome to another episode of Revolution Health Radio. This week we’re going to do something a little bit different. Rather than answer one specific question that was sent in, I’m going to answer a bunch of different questions that I get all the time regarding a very popular topic, which is SIBO. As a matter of fact, I have many questions about SIBO myself, and that’s actually how I want to frame this podcast. I get more questions about SIBO than probably any other health topic. I’ve been treating it now for many years, and I’ve learned a lot about it in that time, and yet it seems like the more I learn, the more questions I have. Certainly, if you look on internet forums and blog comments, you look at summits and podcasts in our entire field, you can see that there’s still a lot of questions about SIBO and misunderstanding and things that we really need to figure out in order to be able to appropriately diagnose and treat this condition.

I think the best way to dive into this is just to say that I’ve started to doubt many of the standard assumptions or beliefs around SIBO that many of you are probably already aware of. I just want to go through five or six of these assumptions and tell you what my current thinking about them is, and this might be a little bit of a frustrating podcast to listen to because I’m not necessarily going to give you answers. I’m just going to tell you what the questions are, where my doubts are, and what further research or exploration or investigation I think we need to do.

Question #1: Is Lactulose Breath Testing an Accurate Way to Diagnose SIBO?

Let’s start with assumption number one, which is that lactulose breath testing is an accurate way of diagnosing SIBO. As many of you know, the standard way of diagnosing SIBO in an outpatient setting is using lactulose breath testing. There is another way, which is an endoscopy, where they put a tube down your throat and take a sample of bacteria from your small intestine, but that’s never used in outpatient settings because it’s invasive and expensive. It’s just not done. There are actually a lot of problems with that method as well, which leads us to probably the biggest issue of all from a 30,000-foot-view perspective with SIBO, is that in order for a test to be accurate, it needs to be validated against something that’s a gold standard, and we have no gold standard way of diagnosing SIBO. The endoscopy, which I just mentioned, has been used as the gold standard test against which breath testing is validated. But what if the gold standard test itself is not accurate? That obviously creates some pretty big problems in terms of developing another test like breath testing and then validating it against a test that itself is not very valid. That’s the biggest issue.

The problems with SIBO diagnosis and treatment

I’m not going to go into all the nitty-gritty details on why breath testing isn’t necessarily as accurate as some people may believe. But in this context, I’ll just say that—and this is a guess, I haven’t done any rigorous study—but I would estimate that over 90 percent of the patients we test for SIBO test positive. Now this is using the former criteria and I’ll come back to this in a second, but if you just use the machine-generated criteria that are printed on any of the SIBO breath testing labs, I would say over 90 percent of our patients test positive. Now, that alone should be a red flag. When more than 90 percent of your patients test positive for a condition, that should raise some eyebrows.

Certainly SIBO is common, but do we really expect that 90 percent of patients, even people who are sick and dealing with chronic health issues have SIBO? I’ve never seen any research suggesting that over 90 percent of people with any particular conditions also have SIBO. The exception might be acne rosacea. I think I saw one study of 42 patients where 100 percent of patients with acne rosacea had SIBO [Correction: study I was referring to found that SIBO was 17 times more prevalent in patients with rosacea than in controls.] This doesn’t mean for sure that the test is inaccurate, but it definitely raises my eyebrows. It makes me wonder whether we’re over-diagnosing SIBO.

Changes in criteria

Now I mentioned the criteria, so up until pretty recently the idea was that if you see an increase in 20 parts per million or more of hydrogen in the first 120 minutes of the test, that would indicate a positive result, and the criteria were an increase in 12 parts per million for methane, but those criteria recently changed; there was a consensus statement issued in the spring. A bunch of SIBO experts got together and talked about how to update the breath-testing criteria to make it more accurate and ensure that the criteria were modified to, on the one hand with hydrogen, the changes would lead to fewer diagnoses, less overdiagnosis of hydrogen-predominant SIBO. But in the case of methane, they’re going to lead to a greater number of diagnoses because those criteria, instead of becoming more strict, became more liberal. The new hydrogen criteria are increasing 20 parts per million within the first 90 minutes, and then with methane, it’s any value over 10 parts per million at any point during the test, including during the third hour. That’s a pretty big difference, and that’s going to lead to a lot more positive results for methane.

It’s also worth pointing out that there are a lot of different studies that are critical of lactulose breath testing that suggest that there is a very high potential for false positives, especially using lactulose instead of glucose. With glucose breath testing, the opposite problem is true. There’s a high potential for false negatives. If there is a positive, it should be positive. But if there’s a negative, you can’t rule out that SIBO might be present. Again, I’m not going to go into great detail here, but let’s just say that there is a lot of uncertainty about breath testing as a way of diagnosing SIBO.

Question #2: Is SIBO Always Pathological?

The second assumption is that SIBO is always pathological. The idea is that if SIBO is present, it’s always causing the patient’s problems, whatever they are, but that’s not sound thinking, of course, because we know that correlation is not causation. It’s possible that SIBO could be present, but it’s not actually driving whatever the patient’s symptoms are. We know that early studies suggested that up to 20 to 30 percent of healthy controls have SIBO but don’t have symptoms. Of course, I have to offer a side note here, which is, I don’t know where these studies are finding these so-called “very healthy controls with no symptoms.” I haven’t met that many of those people, but let’s assume that that’s true. That could mean that 20 to 30 percent of the population has SIBO, but it’s not causing any problems for them.

In many cases, we treat SIBO, and the numbers improve, so the patient goes from being breath-test positive to breath-test negative, but their symptoms don’t necessarily improve. That would suggest that maybe SIBO was present, but it wasn’t causing their symptoms. It’s possible that the testing is accurate as far as what it’s measuring, but what we call SIBO as a condition is not always pathological. It’s also possible that SIBO might be present in a patient and might be causing some issues, maybe a mild nutrient deficiency or something like that, but it’s not causing the main complaints.

The reason I bring this up is that I see some patients just getting hyperfocused, almost obsessed about SIBO, at the expense of everything else. And clinicians—there is that saying, “If you’ve got a hammer, everything looks like a nail”—I see both clinicians and patients becoming over-focused, I think, on SIBO, and the risk there is that you actually miss other pathologies or underlying mechanisms that are really actually driving the condition in those cases if we’re just myopically focused on SIBO.

Question #3: Are Our Treatments Effective?

The third assumption is that our current treatments are effective and optimal. The typical treatments for SIBO are antimicrobials. Initially, there were prescription medications. Rifaximin is the most commonly used, especially for hydrogen-predominant SIBO, and neomycin is also added at times when methane is present. Metronidazole is another medication, or Flagyl is used in some cases for treating SIBO, as well as other antibiotics, but rifaximin certainly has become the drug of choice. But then there have been some studies recently that have found that botanicals, herbs, are as effective as rifaximin treatment or even more effective and cause fewer side effects. In general, the approach is if SIBO is there, then you use antimicrobials to reduce the growth of bacteria in the small intestine.

The problem with this approach is that the efficacy is often quite low. I’ve seen some studies that we use rifaximin individually that show as low as 40 percent efficacy. Of course, there are other studies that show higher efficacy, and then if you combine other agents in the treatment, you can make it more effective. There was one treatment where the researchers speculated that using partially hydrolyzed guar gum would improve the efficacy of rifaximin, and in fact it did. It increased it significantly. In our clinic we use a combination protocol that uses a bunch of different things together, all of which are designed to maximize the efficacy. It also depends whether it’s just hydrogen alone that’s high, or methane alone that’s high, or both hydrogen and methane, and each of those scenarios requires a different approach.

But the problem remains that efficacy is much lower than I certainly would like to see it. Not only that, in some cases, not only do patients not get better, they actually get worse after treatment. They might get worse right away or they might improve initially, but then the symptoms return and when they come back, they come back even worse. I’ve seen this actually happen in multiple cycles, meaning with each treatment and each return of symptoms, the symptoms get worse after each cycle, which is obviously problematic.

Then there’s the very high rates of recurrence for SIBO, which is related to what I just said. One study, I think, found a recurrence rate of 45 percent in patients who had been treated by rifaximin. In our practice, despite using all of the evidence-based methods and combining several different methods, we still see recurrence rates a lot higher than optimal, than I think is acceptable. That’s one of the main things that has led me to question many of these beliefs and assumptions because when the treatments are not that effective and the recurrence rates are very high, then I think that something is definitely wrong.

Like what you’re reading? Get my free newsletter, recipes, eBooks, product recommendations, and more!

Question #4: Is SIBO Always the Underlying Cause?

The fourth assumption is that SIBO was always the underlying cause of a particular condition. This is somewhat related to what I mentioned earlier, but a little bit different. In functional medicine, we’re always trying to get to the root of the problem, but sometimes that’s easier said than done, and it can be like peeling layers of an onion back to keep going deeper to find the deepest underlying issue. If a patient has SIBO, for example, and we treat their SIBO and it doesn’t go away, or maybe it does go away and it comes back, and we do that two or three times, then of course I start wondering, “All right. Well, is there some other deeper condition that is causing the SIBO?”

In this case SIBO is not necessarily a cause itself, but almost a symptom of a deeper underlying problem. In my experience, those problems can be things like:

  • mold or chronic inflammatory response syndrome
  • chronic infections like tick-borne illnesses
  • viral reactivation
  • other gut infections that have escaped detection
  • heavy metal toxicity
  • other types of toxicity
  • mitochondrial deficiency

And a range of other problems. But the point being that in those cases, those problems are the real thing that’s driving SIBO and then whatever symptoms the SIBO is causing. It’s like layers, and so you have to keep going deeper in order to identify and address those conditions, otherwise that patient is never going to get over SIBO. We’ll just keep treating it, it might improve a little bit or not, and then it just keeps coming back. Even though rifaximin and the botanicals are relatively safe compared to other antimicrobials, they’re still antimicrobials, and we still want to minimize our use of them.

Question #5: Should Probiotics and Prebiotics Be Avoided during Treatment?

Assumption number five is that probiotics and prebiotics should always be avoided when a patient has SIBO and shouldn’t be included in treatment. I think I’ve discussed this before and I’m not totally sure where this belief or assumption came from. It’s pretty prevalent within the mainstream SIBO community, if you want to call it that. But all of the studies that I’ve seen, I think, without exception, have found that when you use probiotics, either along with antibiotics or as a separate distinct treatment for SIBO, they are effective. They’re either effective as solo treatment, or they increase the efficacy of SIBO [treatment protocols]. Even the studies that have used prebiotics have shown positive results, which might be a little counterintuitive because you would expect prebiotics to feed the bacteria that are present in the small intestine. I think there are still quite a few questions here. Certainly, I have seen probiotics and prebiotics make patients with SIBO worse, but in other cases, I’ve seen them make patients with SIBO significantly better. We do include very specific types of probiotics and even prebiotics in our SIBO treatment protocol. We’ve done that for many years because of the research I’ve seen on this, and I do think it is effective in most cases.

This sort of points to another question or concept, which historically a lot of SIBO authorities have claimed that SIBO is just really kind of a small intestine, it’s not really related to the health of the large intestine or the overall gut microbiome. That doesn’t make sense to me. There is a sphincter that separates the small and large intestine, but one of the prevailing theories about how SIBO got started in the first place is it’s an inappropriate transfer of bacteria from the large intestine to the small intestine. It’s entirely possible, and even likely, in my opinion, that one of the predisposing factors that can lead to that translocation of bacteria from the large intestine to the small intestine is an unhealthy large intestine. It may be that that’s one of the reasons that prebiotics and probiotics work in terms of treating and even preventing recurrence of SIBO is that they help to improve the gut microbiome. That, in turn, has a sort of upstream effect on the small intestine. Really, still a lot of unanswered questions here related to probiotics and probiotics, but I’ve seen enough now to convince me that the dominant idea that they should always be avoided is not true.

Question #6: Does a Long-Term Low-FODMAP Diet Help Prevent Recurrence?

Then finally, the last assumption, number six, is that a long-term low-FODMAP diet is always a good idea in order to prevent recurrence. I have discussed this and written about this before, so I’m just going to mention it briefly. But studies have shown that a long-term low-FODMAP diet can reduce the diversity and quality of beneficial bacteria in the large intestine, and for the reasons that I just mentioned, I think that that can be problematic. Even though the low-FODMAP diet can reduce symptoms, it may be setting patients up for recurrence if it’s leading to undesirable changes in the beneficial bacteria in the colon. Also, there was a recent study that just came out that found that patients with IBS are often able to reintroduce certain FODMAPs without any adverse effects. This study didn’t consider SIBO, but as you probably know, many patients with IBS do have SIBO. My guess is that they would have found a similar effect if they had done the study in patients that only had SIBO. It seems that even in patients who do have SIBO or IBS that reintroducing some FODMAPs not only could be potentially beneficial, but doesn’t actually lead to a return of symptoms. That’s what I’ve always encouraged my patients to do is reintroduce as many FODMAPs as they can without significant discomfort. I think that’s a wise approach because we want to keep our diet as diverse as possible, and especially when it comes to fermentable fiber, it can support our beneficial gut bacteria.

Okay. I’m going to stop there. As you can see again, this is a little frustrating maybe to listen to. I’ll tell you that it’s super frustrating for me as a clinician. This is again something I’ve been paying very close attention to for a long period of time, and I feel quite frustrated with the lack of answers around many of these questions. Certainly, not for lack of looking, experimenting, and exploring, but my commitment to you is that I will continue to do that.

I think it’s a very important starting place to just admit when we don’t know the answers to these questions at least, and to lay those questions out so we can start exploring what the answers might be, and of course that is the process of science. It’s not that we always have the answers and we always know what and we stop looking. Once we think we know the answers, we always question our assumptions and we continually re-evaluate them, especially in the face of evidence that contradicts our previous assumptions or beliefs. That’s the true application of the scientific method in the case of healthcare.

I hope that was helpful in some way. If you’re a patient out there and you’re frustrated with your lack of progress with SIBO, you’re definitely not alone. If you’re a clinician out there and you’re frustrated with your lack of progress with SIBO in terms of treating patients, you’re definitely not alone. I think we should … we need to get these questions out there more so that we can all work together to answer them. Okay, that’s it for now. Please continue to send your questions in at chriskresser.com/podcastquestion, and I’ll talk to you next time. Take care, everybody.

ADAPT Naturals logo

Better supplementation. Fewer supplements.

Close the nutrient gap to feel and perform your best. 

A daily stack of supplements designed to meet your most critical needs.

Chris Kresser in kitchen
Affiliate Disclosure
This website contains affiliate links, which means Chris may receive a percentage of any product or service you purchase using the links in the articles or advertisements. You will pay the same price for all products and services, and your purchase helps support Chris‘s ongoing research and work. Thanks for your support!


Join the conversation

  1. Isn’t it just possible that low stomach hcl is more the problem? I read in a paper (can’t remember name) that I found on google scholar, that suggested if hcl is not high enough, the various sphincters in the GIT do not close properly allowing leakage of bacteria into the small intestine. You can kill them with abx but they will be right back unless you increase stomach acid. It will kill more bacteria in the stomach, leakage stops before they are killed, and bacteria do not recolonise from the large intestines.

  2. What if I think that I might be sub-clinically hypothyroid and have tested positive for methane type SIBO after treatment. Should I insist on being prescribed thyroid meds or support?

  3. Am I far off base here, or would it be reasonable to suggest that SIBO and it’s worsening recurrence could be suggestive of a much more sobering underlying problem such as missing key microbes that can’t repopulate?

  4. Chris Dr Satish Rao does EAGBT presented at DDW. Endo assited Glucose breath test and its super accurate as you know glucose is more accurate and done this was very accurate. While is done there he does cultures ofcourse and hopes they culture and checks for Bacteria, SIFO Celiace and other things so its a good way to test. having said that his protocol was not working for me so i moved over to Cedars and after one appt I am well a year now.

  5. Chris Dr Satish Rao does EAGBT presented at DDW. Endo assited Glucose breath test and its super accurate as you know glucose is more accurate and done this was very accurate. While is done there he does cultures ofcourse and hopes they culture and checks for Bacteria, SIFO Celiace and other things so its a good way to test. having said that his protocol was not working for me so i moved over to Cedars and after one appt I am well a year now.

  6. I believe Sibo is also related to laparscopic surgeries through/around your belly button. I had 2 different surgeries and the scar tissue blocks or pinches my small intestine. Abdominal massage helps. I really like Dr Ohiras probiotics- have helped me.

    • Wow. Now that you mention it, all my issues began shortly after fall 2014 after an appendectomy. I wonder if anyone else has looked into this? The bruising on my abdomen was significant and the doctor who did my follow up a couple weeks later was shocked, asked me what happened? I didn’t know it was unusual. I just said, “well, I had an appendectomy.” He said he was surprised how much bruising there was.

    • I haven’t been formally diagnosed with SIBO, but I started having SIBO-like symptoms (malabsorption, bloating, distension, hair loss, crippling insomnia, others) immediately after an EGD/Colonoscopy.

  7. If you want to get rid of bacterial overgrowth just take activated charcoal. My friends wife, got food poisoning, charcoal, took away her pain in 10 minutes.

    • I am taking Polisorb plus – which is 10 times better absorbent than charcoal and it is doing nothing for me – or at least i dont feel any difference.

  8. Chris,

    Your answer to question #5 needs to be proofed again….”probiotic” when you meant “prebiotic” in multiple places.

    Thanks for the info, though.

  9. I am so totally confused and frustrated with not knowing where to turn. I have had stomach bloating after eating – visible even with a small meal, since childhood. It’s worse at times – sometimes a small meal makes me look 7 months pregnant. I also get attacks of severe GERD that also make me feel like I’m smothering and recently sent to ER twice in two days. I take digestive enzymes, have tried probiotics of various types and generally eat a good diet although years ago that wasn’t the case. I took antibiotics daily (erythromycin, tetricycline and others) for 25 years for cystic acne and at age 67 still get an occasional breakout. I’ve also had 42 IV chelations for high levels of lead and cadmium and it didn’t get rid of it. I was recently tested for various “bugs” like CMV, epstein Bar, and such that cause autoimmune disease (have had Hashimotos and Graves for years) and i came back positive for all of them. Mild for candida. had stool test over a year ago which showed a bit of imbalance in gut bacteria and an inflammatory factor but with no real explanation – negative for H-pylori, parasites and such. I’m doing a round of homeopathic treatments because a Gene test tied to that showed candida, a “strep gene”, a Syphilis Miasm and showed most all my organs having low life force – especially the esophagus and gallbladder but everything was at half force or less except my lungs. Mainstream docs of course think the answer to the GERD is PPI’s which I took for a week out of desparation and they only helped slightly but causes sourness to come up into throat. I stopped them. I’ve tried every natural thing I can think of. This past month I lost 7 pounds because I could barely eat anything. It’s a bit better now but I’m scared. And I get so tired of looking pregnant and like I weigh more than I do (I’m high end of normal BMI and weight loss is very difficult – when I lost recently it was due to practical starvation) – so two different integrative doctors are trying to help plus I saw one for years before we moved. Some diet advice is contradictory – everything is. mainstream just limits their ideas to drugs and surgery and doesn’t even listen to most of what I say so I gave up on them long ago. I never know when the horrible GERD and feeling of smothering will return and no idea what the endoscopy is going to show or what they will try to push on me! I feel that I have SIBO – it’s the thing that fits and when the GERD was bad so was the stomach swelling – but then other times I’ll have one without the other – but I get little response when I mention SIBO to anyone. Now reading this article and how complicated it is makes me wonder if there is an answer at all.

    • Alexis,

      Try some blue cheese – you may be surprised by the results.
      Blue cheese = penicilinum – maybe better than rifaximin.
      Dont expect some practitioner to tell you the cure – cured patien is a lost client as they say in my country.

  10. It sounds like the test results are very confusing. In testing it was found that I have aeromonas sobria. I was also found to have methane that was pretty much off the chart after the 2 hour mark. The physician I was seeing basically stopped treatment because I wouldn’t take their brand of meds/orals. I find this happening way too often. So many meds have ingredients that I react to, so I wanted to separate out the main treatment ingredients (oregano, neem, and barberry) to make sure I wasn’t going to react to any of them or if I did, I would know immediately which one it was. No go for that physician. I react to many OTC meds and Rx meds negatively and I’m just very frustrated since I can’t seem to get a physician to work WITH me, not just tell me what they want me to do or they will kick me out. I’m not opposed to certain treatments but I have had issues for at least 50 years now and I’m tired of EVERYTHING. I sure hope that some of these studies and testing can help people down the road to find out the cause of their SIBO/pain/whatever. It’s debilitating to feel crappy all the time. Thank you Chris for asking the questions and for searching for whatever answers might be available! That’s the hard stuff!

  11. I’m wondering if you know anything about GOS. It’s a prebiotic that supposedly doesn’t cause the gas associated with inulin and fos?
    I read that for some reason it’s good for anxiety.
    Any opinion on the safety of GOS and whether it would be OK to take for someone who is sensitive to fos?

  12. I use garlic for it’s abtimicrobial effects. I eat one raw clove chopped up in Manuka honey with or just after dinner

    I’ve read black cumin seed oil can be helpful as well

    • Amy, how do you use it? I’m curious. I tried anti-microbials and they made no impact, and I’ve resisted using Rifaximin and neomycin (for methane type) because 1) it’s a hardcore drug and 2) nothing convinced me that the results were compelling and 3) very high recurrence rate. I just didn’t feel that the $ cost and physical cost of trying it were worth the odds of it helping. Los FODMAPs diet made it worse. But I’m open to wholistic methods if they are sensible.

      • Use a very small dose, 1/8 tbs and combo it with Berberine and Neem! Be sure to use a probiotic while you do this as it is super powerful. Don’t use it more than 2-3 weeks. Anything more, you’ll just wind up with worse issues. A safer option is Pomegranate powder!

  13. I don’t know how this is the first time I’m hearing about SBIO. I’ve been trying to get to the bottom of a recurring cramping/bloating issue in my abdomen that seems to be randomly occurring. It’s debilitating. Not accompanied by diarrhea, but BM’s aren’t consistent anymore. It started over a year ago and was shortly thereafter accompanied by joint and tendon pain in my feet. Not sure if they’re related, but I see now they could be. I have had a colonoscopy and endoscopy, blood tests, and CT scan. Nothing appears abnormal. I do a raw meal shake every morning that has probiotics but I’m wondering if there’s a “first line” treatment – perhaps a specific strain of probiotic – that practitioners might generally recommend first to see if it happens to work? So many of the symptoms I just looked up that I have could be SBIO. I just recently got off PPI’s (two months ago) and am dealing with trying to get some balance from that as well, treating with 450mg/day of ranitidine. Was hoping that was the cause of my foot issues (magnesium/calcium absorption), but it didn’t seem to help much.

    • I’ve had chronic foot pain off and on for 10+ years. I know it had gone away in the past but I couldn’t remember what worked. Recently it was super bad again. Just finished another round of PT, podiatry, orthotics, strengthening, etc, with some improvement, though still my feet were quite painful. I don’t know what your diet is like….I have been gluten free for 10 years. I just recently again cut out dairy and eggs, and my pain went to practically nothing! Like an inflammatory response? Hoping to heal my gut and slowly be able to eat some of these foods again. We will see. Best of luck to you.