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

SIBO and Methane – What’s the Connection?

by

Last updated on

Revolution Health Radio podcast, Chris Kresser

A lot of people might not be familiar with the term methanogen, but it is something that people should be aware of, especially if you have SIBO or suspect you may have SIBO.  We’ve talked about SIBO a lot.  For people new to the show or new to this work, this stands for small intestinal bacterial overgrowth.  It’s defined as a pathological increase in bacteria in the small bowel.  As a reminder, we have a lot of bacteria in our gut.  In fact, the bacteria and other organisms in our gut outnumber human cells by 10 to 1, but the location of that bacteria is really important. 

Note: The Prescript-Assist supplements discussed in this article are no longer available. Please click here to learn more about a substitute, the Daily Synbiotic from Seed.

In this episode, we cover:

1:29 What Chris had for breakfast
4:44 The role archaea play in gut health
7:50 What’s the big deal about methane?
14:38 How to address SIBO in methane-producing patients
23:56 Gut healthy treatment recommendations

Jordan Reasoner:  Hi.  Welcome to another episode of the Revolution Health Radio show.  The show is brought to you by ChrisKresser.com.  Steve is off today on a meditation retreat.  I’m your guest host Jordan Reasoner, from SCDlifestyle.com.  With me is integrative medical practitioner, healthy skeptic, and New York Times bestselling author, Chris Kresser.  Chris, welcome.

Chris Kresser:  Jordan, I’m happy you’re here.  And I’m happy Steve’s off walking the talk.  It will be interesting to hear about his experience when he gets back.

Jordan Reasoner:  I’m excited.  He’ll be back tomorrow, so I’m looking forward to it.

Chris Kresser:  This was his first 10-day Vipassana, is that right?

Jordan Reasoner:  Yeah, it’s his first one.

Chris Kresser:  It should be really interesting to hear about.

Jordan Reasoner:  All of our friends are just coming back from Burning Man, and Steve’s coming back from a meditation retreat.

Chris Kresser:  Yeah, other side of the spectrum.  Hopefully, you haven’t been getting any text messages from him in the last 10 days.

Jordan Reasoner:  No.  It’s been radio silence.

Chris Kresser:  Good, good.

Jordan Reasoner:  So he’s been a good boy.

Chris Kresser:  All right.  Cool.

Jordan Reasoner:  Before we dive in, let’s talk about your breakfast, because I know we always get a lot of flak from the listeners if you don’t tell us about your breakfast, right?

What Chris Ate for Breakfast

Chris Kresser:  Okay.  So let’s see, I had some chorizo. We buy half a pig from a local rancher a couple of times a year, and then a butcher in Santa Rosa, Willowside Meats, butchers it and gives us a whole bunch of different cuts.  One of the things they do is make this really amazing chorizo.  So we had some of that, some scrambled eggs, some sauerkraut, beet kvass, and some plantains fried in expeller-pressed coconut oil.  That’s pretty standard breakfast around here.  It’s a good one.  Sylvie loves it.  We all like it.  It’s pretty easy to make.

Jordan Reasoner:  I love your breakfast because it always has like five to seven parts to it.

Chris Kresser:  It’s all about the diversity, right?

Jordan Reasoner:  Yeah, exactly.

Chris Kresser:  Feed those gut bugs.

Jordan Reasoner:  You grew up on Lucky Charms.  It’s a nice transition, right?

Chris Kresser:  Thankfully, I didn’t grow up on Lucky Charms.  As I get older, I have more and more appreciation for my parents, and the way that my mom fed us when we were young.  I mean, certainly, she wasn’t feeding us Paleo.  That wasn’t really part of the understanding at that point.  But she fed us, really, a pretty healthy diet overall, so I’m happy about that.  We have a good question today from Simas I think it is.  I’m not sure how to pronounce it, but I think that’s the right way.  Let’s give it a listen.

Simas:  Hi, Chris.  I just wanted to ask, what would be the best way to deal with methanogens in people with SIBO?  I know Dr. Siebecker says that it’s best to use allicin, but it seems that I have a negative response, extreme fatigue and things like that, after taking it.  Thanks.

Chris Kresser:  All right.  So let’s jump in here.  That’s a great question.  A lot of people might not be familiar with the term methanogen, but it is something that people should be aware of, especially if you have SIBO or suspect you may have SIBO.  We’ve talked about SIBO a lot.  For people new to the show or new to this work, this stands for small intestinal bacterial overgrowth.  It’s defined as a pathological increase in bacteria in the small bowel.  As a reminder, we have a lot of bacteria in our gut.  In fact, the bacteria and other organisms in our gut outnumber human cells by 10 to 1, but the location of that bacteria is really important.  They should mostly be in the colon, the large intestine.  We do have small amounts of bacteria all the way through the digestive tract, from the mouth to the anus, but the majority of the bacteria should be in the colon.  Very little should be in the small intestine, because the small intestine is where we digest and absorb food.  If you have a lot of bacteria growing in the small intestine, that’s going to interfere with the assimilation of nutrients from food, which is one of the major adverse effects of SIBO.

The Role Archaea Play in Gut Health

So most of the research that you’ve probably heard about has focused on the role of bacteria in the gut, but recent evidence suggests that archaea also play a role.  That’s A-R-C-H-A-E-A.  Archaea are actually a completely different class of organism than bacteria.  They’re pretty ancient, single-celled organisms with no cell nucleus and no membrane-bound organelles.  They were originally classified as bacteria, but they’re now classified as prokaryotes, which again are a completely different class.  They’re considered totally unique from the other two major domains of life, which are bacteria and eukaryotes.  Some of the archaea that you might have heard of in the news, in the mainstream media are halophiles and thermophiles.  So these are archaea that live in extreme environments like salt lakes or hot springs.  But we now know that archaea are present in pretty much every habitat where you see biodegradation of organic compounds occurring, and that includes animal guts and human guts.

When you go to get a breath test for SIBO—which is one of the major ways of testing for SIBO that we talked about—they’re going to measure the presence of, and the production of, methane and hydrogen gases at baseline.  Then they’re also going to measure the increase in hydrogen and methane production that occurs after you drink a sugary solution that they give you as part of the test procedure.  So typically, if you have a significant increase in hydrogen or methane after drinking the sugary solution, it means you have an overgrowth of bacteria in your gut.  To be more specific, when you have an increase in methane after drinking this solution, or if you just have high levels of methane at baseline, that indicates an overgrowth not of bacteria, but of these methane-producing archaea.  Unlike bacteria, which primarily produce hydrogen, the archaea are what produce this methane, and they do this actually not by fermenting carbohydrates.  So bacteria produce hydrogen and the way they do that is by fermenting fibers.  The methane production works differently.  The archaea consume the hydrogen that’s produced by the hydrogen-producing bacteria, and then they produce methane as a by-product of that process.  So this is actually one of the ways that excess hydrogen in the gut gets metabolized, is by these methanogenic archaea converting that hydrogen into methane.  And another way that hydrogen gets dealt with is by bacteria that convert hydrogen into sulfites.  That’s probably a little more detail than you needed, but it’s kind of interesting to see how this all works.

What’s the Big Deal about Methane?

Methane production begins at about three years of age.  You don’t see any methane production in infants, for example.  This suggests that methane production has everything to do with how the gut is colonized initially, because there are no archaea initially in the gut.  And it peaks at about 10 years of age, when adult levels are reached.  So by the time a child is 10, they’re typically producing the adult amounts of methane that they would produce for their whole life.  But here’s the thing—not everybody produces methane.  Depending on the studies that you look at, the numbers I’ve seen range from 30 percent to 50 percent of adults being methane producers.  So anywhere from a third to half of people have significant amounts of archaea that produce detectible amounts of methane.  That’s something important to understand—this is not an issue that affects everybody.

So what’s the big deal about methane?  Simas’s question, “Is the presence of methane different?  Does it require a different approach?”  I think the answer is yes.  For what we see in the research and then what I’ve seen in my clinical experience working with patients.  Methane is a colorless, odorless, inert gas.  For a long time, it was thought that it didn’t really have any impact on human health, except for maybe causing a little bit of bloating and distention, if you had high levels of it.  But more recent evidence actually has linked methane production to various disease states.  And it’s still somewhat unclear whether that’s because of the level of methane itself, or whether it’s because of the removal of hydrogen from the bowel that happens when that hydrogen is converted to methane by archaea.  But we do know from studies that methane-producing archaea are present in 45 percent of people with SIBO.  In other words, a substantial percentage of people with SIBO have methane-producing archaea.  And the amount of methane that’s produced is significantly higher in patients with SIBO, compared with patients with fructose and lactose malabsorption, which are other gut issues.  So if you’re looking at a breath test, the presence of methane, to consider yourself a methane producer, you would have baseline methane levels of over 3 parts per million.  And I can tell you, from running a lot of these tests, that that’s quite common.  It’s more than 50 percent, I would say, in my patient population.  Then again, I’m testing people that mostly have SIBO and other gut issues, so it’s not necessarily a representative sample.

Jordan Reasoner:  Now Chris, if I’m a patient and I’m experiencing problems, I think it’s SIBO and I’m not looking at a test, are there symptoms that are different in somebody who is predominantly going to have methane-producing bacteria versus non-methane-producing?

Chris Kresser:  Yeah.  That’s a good question.  And it takes us right into the next section, which is, the answer to that is constipation.  Constipation, of course, can be caused by many things.  So it’s not to say that methane-producing archaea are the only cause of constipation.  But methanogenic flora, or archaea that produce methane, are significantly associated with chronic constipation in the scientific literature.  The amount of methane produced is correlated with colonic transit time.  So the more methane you have, the slower your transit time is.  In one study, if a breath test was positive for methane, they saw a 100 percent association with constipation-predominant IBS.

Jordan Reasoner: Wow.

Chris Kresser:  So yeah, it’s pretty strong in terms of association.  In other words, to put it in plain language, everyone who is positive for methane had constipation-predominant IBS in that study.  In contrast, the prevalence of methane was very low among patients with inflammatory bowel diseases like Crohn’s and ulcerative colitis, which typically present with diarrhea.  So you see that it’s much more common in people with constipation than it is in people with diarrhea.  I’ve also seen this correlation in my work with patients, people who have the really chronic, intractable constipation that doesn’t tend to respond well to a lot of different interventions.  I will often see really high baseline levels of methane and/or an increase in methane production after the challenge test.  A few other things you’ll see clinically are methane producers can have a higher prevalence of rectal hypersensitivity compared to non-methane-producing patients.  So sometimes, pain in that area or just a feeling of urgency can signal methane production.  This is not something that patients will be aware of, but if you’re looking at test results in constipated patients, the average pH of the colon will be significantly lower in patients with methane-producing flora.  So if you see a low pH on a stool test, it might be one potential sign of methane production.  Also, I think the other thing that’s important to know is that methane production seems to be much more common in women than it is in men.  That’s the only real demographic characteristic I’ve been able to find.  It seems there’s no age-specific distribution, other than the fact that you don’t get methane production until three years of age, as I mentioned before, and it will be lower in kids up to 10 years of age typically.  But other than that, the only significant association I found is that it’s more common in women than it is in men.

Jordan Reasoner:  In your research, have you seen any associations between being breastfed or vaginal birth versus C-section?  Have you seen any associations around that?

Chris Kresser:  No, I haven’t.  I don’t think that that means there aren’t any, but there are only a handful of studies on this topic.  Most of them are pretty recent; most of them were done by Dr. Mark Pimentel’s group.  He, as many people know, has been a pioneer in research on SIBO and has a research clinic at Cedars-Sinai down in LA.  It does a lot of great work.  So I think there’s still a lot to be learned about this.  My guess is there is possibly an association, Jordan, but we don’t really know for sure about that.

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

How to Address SIBO in Methane-Producing Patients

Jordan Reasoner:  Chris, before we move on, what do I do about this in general?  If I’m somebody who, I find with a practitioner that I have more of these methane gases in my body, and I’m that type of a person with small intestinal bacterial overgrowth, how does that change your approach as a practitioner?  And how does that change what I do, as somebody who’s trying to recover from this?

Chris Kresser:  So it could change the medications that you take for SIBO, if you are going to take medications, and may change the way you treat it overall.  The first thing, taking even a step back before we get into that, is to determine—so far, we’ve been talking about associations between methane and constipation, but that doesn’t necessarily tell us that methane is causing the constipation.  It could be that constipation is causing the high methane levels.  There is actually some research that suggests that might be true.  There are studies showing that treatment with laxatives and bowel cleansing, like a colonic, can reduce or eliminate methane production in some patients.  So that would suggest that constipation, at least to some extent, may increase—methanogens may favor a slow transit type of environment, and when you’re constipated, you might get an increase in methane-producing species.

However, there are also a lot of other studies that suggests that methane directly causes the constipation in the first place.  For example, in animal models, they directly infuse methane into the small intestine.  You’ll see a reduction in transit time of 60 percent, compared to just infusing normal room air.  They suspect, right now, that this effect may be mediated by serotonin, which is a neurotransmitter—as I’m sure most people know—that is present in the gut in about 400-fold higher concentrations than is present in the brain.  So serotonin really, more than anything else, is a gut neurotransmitter, and it’s thought to affect intestinal motility.  Studies have found that methane producers have lower post-meal serotonin levels than people who produce primarily hydrogen.  So I think it is pretty reasonable to assume that methane does play a causative role in constipation.  Then there are also studies that show that the elimination of methane in treatment correlates very closely with symptom improvement.  That’s where your question comes in, Jordan.  So if you treat SIBO and you don’t address the methane production, even if you get rid of the hydrogen, the patient is probably not going to improve to the extent that they should, because you’re not getting rid of the methane.

So here’s the tricky thing—rifaximin, which is the drug that is typically used to treat SIBO, is not very effective against methane-producing species on its own.  For example, in a study with patients who all had baseline levels of methane above 3 parts per million—which established them as methane producers—10 days of rifaximin alone led to a clinical response about 56 percent of the time, so roughly half the time.  But it only led to a negative result on the breath test 28 percent of the time.  So about 70 perecent of the time, rifaximin was not clearing the methane from the breath test, and about half the time, it wasn’t leading to any clinical improvement at all.  Now, 10 days of another drug that’s often used to treat SIBO on its own, called neomycin, led to a clinical improvement in 63 percent of cases, which is a little bit better than rifaximin on its own.  And it led to a negative breath test result 33 percent of the time, which is again, a little bit better than 28 percent for rifaximin.  But it’s not great, right?  We’re still talking about two-thirds of the time that it’s not working.  But if you combine rifaximin with neomycin together and take them for 10 days, that led to a clinical improvement 85 percent of the time, and a negative breath test result 87 percent of the time.  So now we’re talking about some real treatment efficacy numbers here.  Actually, they don’t really understand why the combo of rifaximin and neomycin works better than either of these two drugs alone, but there are other examples where this happens.  For example, the H. pylori treatment, right?  That requires two different antibiotics, and if you use one alone, or the other alone, you don’t get the same efficacy than if you use the two antibiotics together.  So there is a precedent for this kind of thing happening.

The other thing to be aware of is that outside of rifaximin and neomycin, most methanogenic archaea are resistant to the majority of the antibiotics that are typically used against gram-positive and gram-negative bacteria.  So your ciprofloxacins and Flagyls and things like that that a lot of practitioners would use to clear out bacterial infection are probably not going to work for these types of archaea.  And in my mind, this is another reason why botanical treatments can really make a lot of sense.  We talked on a previous show about a study that showed that botanical treatments were as effective, or more effective, than antibiotics for SIBO, and had far fewer side effects.  One of the reasons for this is that botanicals, herbs, plant substances, have a really broad spectrum of activity.  And it’s far less likely that organisms will be able to develop resistance against a botanical, because within each single herb, there are many different active compounds, instead of just one active compound that’s in an antibiotic.  So it’s much harder for the organism to adapt to that.  And typically, herbs or botanicals are used in formulas, where you have many different herbs together.  You’ve got many different herbs, each with multiple compounds, and then they form together to create synergistic compounds.  It starts to become exponentially more diverse, complex, and more difficult for organisms to develop resistance to.  I think given some of the research we have on the efficacy of botanical treatments, given the increasing problem of antibiotic resistance, and possibly these archaea developing resistance to rifaximin and neomycin eventually, given the fact that studies show that about one out of two people who have SIBO and are treated successfully for it will relapse in the future, which is kind of a depressing statistic.

Jordan Reasoner:  Yeah.

Chris Kresser:  I mean, not to get too far off on a tangent, but I bet a lot of people in those studies aren’t doing low-FODMAP, Paleo type of diets or SCD type of diets.  They’re only just taking the drugs, and then they’re going back to eating the same crappy diet that led to the problem in the first place.  In my population, the relapse rates are not that high.  But given all that stuff, it’s possible that people will have to get treated more than once.  That’s what I’m getting at.  And I’m much more comfortable with the idea of someone doing multiple botanical protocols and using probiotics that secrete antimicrobial peptides—which probably may work against methanogens—and food-based treatments, like removing FODMAPs, which are the certain class of carbohydrates that feed the bacteria which produce hydrogen, which feed the archaea.  So if you starve the bacteria, you’re reducing the hydrogen levels.  That, in theory, would reduce the levels of substrate that are available to the archaea for producing the methane.  So the food-based treatments still work there.  I did mention, when we talked about the causal relationship with methane, that some studies show that a bowel lavage, a colonic, or a laxative kind of thing, can lower or even eliminate methane production.  But I would be careful with that, because colonics, while they do wash out some of the bad gut flora, they also wash out a lot of the good gut flora.  They’re also pretty invasive.  I think it’s probably best to try to treat with herbs, diet, and other antimicrobial nutrients than it is to use laxatives or colonics.

Jordan Reasoner:  One of the common objections that I always hear with somebody that follows Dr. Pimentel’s work, they’re very familiar with this type of thing, and they’re going to end up on this combo of neomycin or rifaximin, people freeze.  That’s because we’re all really afraid to use antibiotics now almost in this health community, right?

Chris Kresser:  Mm-hmm.

Jordan Reasoner:  One of the most common things I get asked is, “What can I do before, during, and after this protocol to not totally set me back and destroy all my good gut flora?”

Gut Healthy Treatment Recommendations

Chris Kresser:  That’s a valid question.  The good news is that rifaximin and neomycin are narrower in spectrum than ciprofloxacin or some of the really broad-spectrum antibiotics, and they’re not going to wipe out your gut flora to the extent that some of those other antibiotics will.  They’re also not absorbed systemically, that’s another advantage to those drugs.  I think rifaximin, 99.8 percent stays in your gut and doesn’t get absorbed, so it’s not going to affect flora in other parts of your body as much.  So they are safer than a lot of other antibiotics.

My strategy is to start with the botanical protocols, and use antimicrobial botanicals like olive leaf extract, uva ursi, cat’s claw, yerba mansa, coptis, artemesia, sida, et cetera.  Then use soil-based organisms that secrete antimicrobial peptides—Prescript-Assist, which I sell in my store.  It’s available in my store, because I’ve just had such great success with it in just about everybody, which is rare with probiotics.  You know, a lot of people don’t respond to probiotics very well.  Then we have nutrients like Lauricidin or lauric acid, which are antimicrobial, which may be helpful in this kind of situation.  So I like to start a protocol with a whole bunch of natural things like that, and see how they do.  I only really recommend the rifaximin and neomycin combo if a couple of rounds of this initial protocol aren’t successful.  Then I would definitely suggest patients take things like Saccharomyces boulardii or other probiotics while they’re doing the protocol and after the protocol.  Then ironically, prebiotics often are a big part of the healing process.  This is where it gets tricky, because prebiotics are the fiber that feed the bacteria, which then produce hydrogen, which feed the archaea.  You have to make sure you reduce the levels of those bacteria and archaea first, and then come in with the prebiotics to rebuild a healthy gut flora that will make it less likely that you’ll develop this problem again in the future.  So it’s a pretty involved process, there’s a lot to it, and it has to be timed right.  But it’s definitely possible, and it works.  It just takes more time, in some cases, than people expect.  Generally, with SIBO, and especially if it’s a recalcitrant case and the levels of methane are really high, I tend to tell patients that this is going to be a 6- to 12-month process to fully deal with it, and that’s what we’re seeing in the clinic.

Jordan Reasoner:  Well, Chris, I think we answered Simas’s question pretty in-depth today.

Chris Kresser:  All right.  Great question.  Keep them coming, everyone.  It’s really fun to hear your questions.  Of course, we don’t have the chance to answer them all.  We try to choose ones that we think will be of greatest interest to the greatest number of people, and kind of spread out the topics.  Keep them coming and we’ll see you next week.

Jordan Reasoner:  If you want to get more info about what Chris is researching in-between all these show recordings and all the studies that he’s sharing, head over to Facebook.com/ChrisKresserLAc and Twitter.com/ChrisKresser.  Thanks, everyone.

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!

184 Comments

Join the conversation

  1. Hello!

    Unfortunately, Mr. Kresser makes the mistake which many practitioners make in treating SIBO. The overgrowth of bacteria/aracea is not the problem, it’s the END RESULT of the problem. The actual problem in SIBO is the damage to the migrating motor complex, which moves food out of the stomach and into the gut and then through the small gut into the colon, where peristalsis takes over. Its damage to the MCC, via damage to the nerves/interstitial cells of cajal and the muscle fibers/vincudin, which is the disease. The end result of the disease is colonic backwash of bacteria into the small intestine which then proliferates, damages the lining of the small gut, causing an inability to produce disaccharidases and causing leaky gut. Using antibiotics as the main focus of SIBO is not the way to go. Yes, you need to kill the bacteria, but then you need to 1) eat a diet void of disaccharidases; 2) heal the lining of the gut; 3) heal the nerve tissue and 4) initiate prokinetic movements in the small gut or a recurrence of bacteria overflow from the colon is highly likely. All of those are required to properly treat a patient with SIBO. Dr. Mona Morstein

    • Excellent post. Good to have different perspectives.

      what does a diet devoid of disaccharidases mean. Any examples.

      • I don’t know if she’ll reply, but I’m just guessing here:
        disaccharidases — they “ases” at the end of the word implies that this is the enzyme capable of breaking down disaccharides? This makes me think that she later meant to write “…a diet void of disaccharides” (i.e., ides, not axes), which would be included in FODMAPs. Anyway, this is how I interpreted her comments.

      • I think that’s a typo. I think she just meant disacharides: lactose, sucrose, maltose. You know, sugar.

    • I also am looking for ways to actually heal my gut– not just kill the bacteria. I’m following SCD/low fodmap diet already, and doing the herbal abx, but am unsure what to use as a pro kinetic agent, and how to heal the MMC. Any ideas?

    • Dr Morstein, could you please explain how the nerve tissues would be treated to get healed. thank you

    • Thank you for that comment. From my reading, I’d concluded that a healthy migrating motor complex (MMC) is crucial to overcoming SIBO. It is the digestive system’s way of cleaning out pathogens.

      Some papers point to problems with the MMC as a cause of SIBO.

      While the MMC can be slowed by many things — sedentariness and aging among them — it seems to me that stimulating gut motility is important, before, during, and after any antibiotic activity, herbal or otherwise, or the dysbiosis is likely to recur.

      Our old friend ginger root is a prokinetic (for others, see the ingredients in Iberogast). There’s also exercise, as another commenter noted.

      If you want to go the drug route, low-dose naltrexone (LDN) is an option.

      Although few practitioners seem to address mobilizing the MMC as step one in fighting SIBO, for my own marginal methane-dominant SIBO, I plan to try herbal prokinetics or LDN with herbal antimicrobials (and biofilm disruptors such as coconut oil or lactoferrin) before considering antibiotic drugs.

  2. Hi Chris and folks,

    Has anyone had the joy of having SIBO while pregnant? If so what have you done to manage the discomfort?
    I already follow an even stricter FODMAPS diet: bone broth, stewed meats, low FODMAP veggies and rarely fruits. Sometimes eggs are tolerated but I have on going morning sickness which just makes all of this even harder.

    I believe treatment will not be an option for awhile so what can I do now to alleviate the extra GIANT swollen belly, and SIBO/pregnancy symptoms? As if pregnancy wasn’t hard enough?
    I have had SIBO on-and-off (never truly eradicated) for two years. The docs are at a loss b/c I am loosing weight and having a hard time managing the extra bloated belly. The concerns are I am B vitamin and fat soluble deficient thus will this effect the baby’s development? Do you have any suggestions to help me get through oh the next 5 months please? Multiple vitamins don’t stay down but I am taking Green Pastures cod oil…
    Other suggestions are welcomed please?

    • Hi Annie,

      It doesn’t look like anyone has acknowledged your comment but I am in the same boat as you! I even got pregnant during the two weeks we weren’t trying while I was on a round of antibiotics to help treat the SIBO. What are the odds? I’m coming up on 8 weeks and nausea has reared it’s ugly head… nothing but indulging in my (usually not diet friendly) cravings makes me happy. Just wondering if you’ve come up with anything regarding sibo and pregnancy.. This is the first mention I have found on the two.

      • So it seems I am also in the same boat. Apparently pregnancy increases SIBO symptoms by 2000%! I really have to watch out my diet, it is super strict AIP /Low FODMAP now, otherwise I get terrible terrible constipation. I really hope there would be some approach to treat SIBO during pregnancy

        • Hi ladies, I’m wondering how your pregnancy went, and how your baby is doing? I am pregnant with SIBO and face so many anxieties about the nutritional health of the baby and potential effects of SIBO, and there is so little information! I have read that gut inflammation can be damaging as can certain toxins from the overgrowth of bacteria. I would love to hear about your experiences and any advice you have for someone just 2 months in…

    • Annie, I wasn’t definitively diagnosed with SIBO until 2 years ago but recognize that my IBS was just a variant of SIBO and it became almost unbearable while I was pregnant 34 years ago. I made it through with a normal delivery eventually.

      Knowing what I know now, symptomatic treatment of the symptoms brought on by the slower motility might be helpful; such as ginger acting as a prokinetic agent.
      Good luck,
      Patricia Duarte, MD

  3. Please let me know where can I buy Allimed brand Allicin to fight Nathaniel bacteria. I look in amazon and see only Allimax allicin 30 capsule for $19.79.

    Thanks!

  4. I did the treatment with the rifaximin back in October and am following the FODMAP diet. I feel a lot better but still have the constipation issue. Can I do neomycin or do I have to combine it with the rifaximin again.

  5. Hi Chris
    I have all the symtom of sibo: bloating,constipation,burp,gas pain and uncontrollable weight lost (only 79 lbs now). For the last 9 months I went to see 4 different GI doctor with numerous test and endoscopy and was told that I have gastritis and acid reflux. I take 9 months of PPI with no improvement. Last week I saw a new doctor. She said I have SIBO and schedule the breath test for me the end of this month. Can I try scd diet and l glutamine now or should I wait until I finish the antibiotic treatment. I ask my doctor but she is not familiar with that. I do not know much about sdc diet, glutamine or sibo. Please give me some advices. Thank you!

  6. I believe the root cause of digestion issues are Allergens, that nobody seem to talk about!

    Does anybody know of good Naturopaths or clinics in Europe that treat and do test for digestion issues including thyroid, hydrochloric acid and pathogens like Dr Siebecker?
    Much appreciated.

    • Hi dport. Not sure if you got an answer… but actually its the digestive issues that cause the allergies. Generally speaking food is not the problem – rather food is “feeding” or aggravating the problem. This is particularly true of SIBO.

  7. I have a Commonwealth SIBO kit, have stopped taking probiotics and natural antibiotics…but I’m also supposed to stop taking digestive supplements like Betaine HCl, enzymes and bitters. I upped the enzymes when I was having severe sternum-area pain after eating–nutritionist interpreted this as pancreas-related but pancreas tests came back normal. AND I reintroduced animal proteins into my then vegan diet at the same time as I introduced Betaine HCl. (This after doing the simple morning baking soda test which revealed I have very low stomach acid.) So I take 1300+ Betaine and 2-4 enzymes for a meal.

    SO…I’m actually scared to do the 5 day prep and then the 12 hour only meat and a bit of rice before actually doing the SIBO test, which I think could be quite helpful. I anticipate it will show high methane as constipation is my problem for 6+ months.

    Alongside this, I keep skirting around connective tissue autoimmune symptoms (seem related to scleroderma and relapsing polychondritis)…so that’s a concern, too….

    Anyone had/have a parallel experience or can point me in the direction of some clarity?!

    Thank you and peace.

  8. Are there herbs to treat SIBO that shouldn’t be taken during pregnancy? I’ve had chronic constipation for over 10 years with a history of antibiotic over-use (acne as a teenager) and 2 rounds of Acutane. My naturopath doesn’t believe a SIBO test is necessary, so I’m not sure how to treat/where to start. Anyone with advice, please help!

    • Hi! I’m wondering if you found anything? I’m also wondering how your pregnancy went, and how your baby is doing? I am pregnant with SIBO and face so many anxieties about the nutritional health of the baby and potential effects of SIBO on the child’s health, and there is so little information! I would love to hear about your experiences.

  9. How important is taking a biofilm disruptor along with an antimicrobial treatment?

    I am exclusively a methane producer. Right now I am leaning towards following what Nadira posted above: allicin + berberine + neem. I have noticed that Dr. Siebecker has recommend that protocol on several occasions.

    Is that enough or will I need to add Interfase Pus (I am wary of the egg white listed on the ingredients) or lactoferrin or even NAC?

    Thanks!

  10. Hi,
    I would love if someone could answer my question. And sorry for the graphic details.

    I am self-treating my sibo (IBS-C) – I’ve only just begun, but already experienced a change in bowel movements. Before I would have a bowel movement every 2-3 days, but now I’m having a bowel movement a day.

    I assume that what caused my sibo was a salmonella infection some years ago – so I don’t have any reason to believe that I have underlying cronic motility problems.

    I’ve heard that Siebecker advises people to use pro kinetics. Does anyone know if everybody should be using pro kinetics, or just the people with underlying motility problems? – would I have to take pro kinetics?

    • Actually it’s the opposite than you said. Infection leads to autoimmune damage to the gut, which leads to compromised motility. It is pretty well established process. It’s actually very very likely that you have decreased motility. I think you should either follow SCD-low FODMAP, as prevention after treatment, or prokinetic, or both. That’s how I look at it. Iberogast is the herbal prokinetic option that has been studied, but not specifically for SIBO, Siebecker is now trying it in clinical practice. Pharmaceutical option that is most commonly used

  11. Many years ago I experienced bloating and indigesting. When I was starting to experiment with CLA (Conjugated Linoleic Acid), those symptoms disappeared within days.

    Bloating is one of the symptoms of SIBO.

    I notice Dr Oz sites had antibloating regimen

    Two of the things mentioned were (the other was a smoothie)

    Tonalin CLA Supplements
    L-Glutamine Supplements

    I don’t know how relevant this information is to each of you but there it is.

  12. Anyone try to treat SIBO when you also have methylation issues that dictate a low protein (to avoid ammonia buildup) and sulfur foods? Take FORMATS out of the mix and there is not much left to eat. I am self medicating with the 2 candibacins and interlaced and feel some better but I can’t not eat protein and safe starches… any advice or experience would be appreciated.

      • Izzy, I thought Chris said to add S Boulardii AFTER the microbes/archaea were gone, because otherwise it will feed them. The only one that I’ve seen has MOS added to it which is a pre-digestive, a no-no while ridding the bad bugs. Do I have this wrong?

    • Shelley, I’m compound heterozygous for MTHFR mutations and also have methane SIBO. I’ve been following an ancestral type diet for ~ 6 mos while doing testing and learning about my conditions. I haven’t modified my ancestral diet for the MTHFR, only added NAC (glutathione precursor) and a methylated B/folate formula (Thorne and Seeking Health have good ones). I haven’t read that protein is bad, just to avoid excessive protein which most people should anyway. Daily I eat 3 eggs and a variation of ~ 4-6 oz of red or white meat, poultry, liver, wild salmon and other seafood, all meat being pastured/grass-fed/organic. That doesn’t seem excessive to me, so I haven’t changed it.
      Like you I’d boosted my sulphur containing foods, eating alliums and mushrooms daily. Having just learned about my SIBO, I’ve been restricting my diet with FODMAPs for a few weeks. Like you, I’ve got multiple conditions that seem to dictate opposing treatments, and so far with FODMAPs, I’d say I feel worse, not better, so I’m not convinced FODMAPs is right for me. Have you tried it yet? I guess another option is SCD, but with low wbc and low total cholesterol, I’m not convinced that going low carb is a good idea for me, and even Chris’s low carb post and chart last week would support my concern.
      No doubt, this is complicated and frustrating. But I’m learning that stressing about the food is worse than eating whatever. Unless Chris has any specific ideas, it seems like it’s trial and error with these diets since each of us is unique.

  13. Hi Chris.

    Please tell me. What are the other available tests to detect SIBO besides breath tests?
    My country does not offer sibo breath tests they do offer endoscope with culture. Any others that are accurate?
    My face is swollen 90% of the time nomatter what i eat. which made me chronically depressed I have done stools test which show dysbiosis.

    Thank u.

    • I heard Dr Siebecker say that the glucose only test kit can be ordered online, but I think that will only detect hydrogen, not methane. But that’s better than nothing, Also, I wonder if you could obtain a test kit from one of the labs that offer lactulose testing if your doctor orders it for you. Would those be options?

      • No, my country does not offer home kits for hydrogen breath tests, however they do offer hydrogen breath tests for fructose, lactose, sucrose intolerances but when i mention SIBO, they dont know what im talking about. i wonder if i can go for the test and interpret the results for SIBO myself since it is the same thing anyway(hydrogen breath test for bacterial fermentation), its just that over here(south africa), they dont use it for SIBO.

          • Wow. Thanks susan. Very helpful. I will try to get the breath test done internationally. However. I really think i am going to take xifaxan and another antibiotic for 10 days meant for methane producing sibo because i have all the symtoms. Gaps.scd.gluten free diet etc had no effect. My face is swollen 95% of the time and sometimes antihistamines take it away. So i believe sibo is producing too much histamine aswell although thats a guess. All i know is. Im constipated with alot of food intolerances and if i empty my bowel(enema) or get diarea, my facial swelling goes down. I have been through so much. Stool test shows dysbiosis in colon. I have nothing to lose. I am going to take xifaxan just based on my symtoms without a diagnosis of sibo. I have nothing to lose.

            • That sounds terrible. Dr Siebecker says carb malabsorption with SIBO can partially result from enzyme deficiency (genetic and/or acquired) because SIBO decreases our brush border enzymes. So I wonder if your histamine intolerance hits its overflow point due to enzyme deficiency? (If you think so, have you tried a product like HistDAO by Xymogen taken before eating histamines?) She says Betaine HCL and digestive enzymes can help with malabsorption. These address symptom management and potential prevention, not root cause; but sounds like you have plans to address that with Rifaximin + another. Note: she says avoid Rifaximin sourced from India.

              • thanks, i will research what Dr Siebecker says.
                i did also read some time ago to get quality sourced rifaximin.
                Yes Susan, i did try betaine hcl and digestive enzymes and it did work for a few days then the swelling returned and all my other sibo symtoms i am still taking them but believe me, i feel no different however i know sibo,leaky gut is causing a deficiency in those so ill continue it for 3-6 months after rifaximin if it cures me.
                many people are reporting that probiotics puts sibo in relapse after antibiotics have worked, which makes sense. I wonder if its better to do a probiotic enema rather then letting probiotics enter your small intestine via oral route after taking the antibiotic to prevent sibo relapse and replenish the lower colon where bacteria is supposed to be.
                Thats my plan after Rifaximin and neomycin to do probiotic enemas and digestive enzymes and betaine acid with SCD diet for 3-6 months then stop everything and live a normal life, if it works, i ask GOD.

  14. Chris, I wonder what’s the actual mechanism behind probiotics causing constipation? I see tons of people reporting that on the internet, including mysf. I know people with SIBO should avoid lactate forming bacteria, because it can make them worse, but I wonder if that is also true for fermented foods like sauerkraut? It seems that my constipation got worse after introducing sauerkraut, could this be the reason why?

    • Chris, I wanted to ask a really important question that I forgot to. How do you actually look at SIBO fundamentally? As I understand the main cause of SIBO is food poisoning, which means that you have damaged gut nerves (slowed motility), and assuming that it is the problem, it follows that one has to either:
      1) limit fermentable fibers, basically limit carb intake, low FODMAP+SCD combo, OR
      2) use some kind of prokinetic, either herbal or pharceutical.

      It seems to me that better strategy would be to use a prokinetic if it’s necessary, because having the knowledge about the importance of microbiome, makes me think that low car, low fermentation diet, is not the best idea.

      What do you think? How do you approach this in clinical practice? Do you use prokinetics? Pharmaceutical or herbal? (I’ve heard that Iberogast might be as effective as low dose antibiotics) Do you advise your patients to stay on a low FODMAP or SCD diet for life?

      Cheers!

      • Yesterday I listened to a few Allison Siebecker podcasts about SIBO; she recommends pro kinetics as the final step in treatment AFTER ridding the bugs with either herbal antimicrobials or antibiotics, but mainly as a way to help avoid recurrence of the condition. I’d like to know what Chris thinks of this. (Simas, the podcasts were with Marcie Peters (may have expired today) but the one at SCDLifestyle is still there.)

        • Susan, I have listened to that podcast also. I totally understand the idea behind prokinetics, but the actual fact is that if you have SIBO, you have slow motility(except few other causes). That means that you need to either help gut motility by using prokinetics, and eating whatever you like, or do a SIBO diet, or both depending on circumstances. That’s how I think about it.

  15. Wow, so many of you are very knowledgeable about all of these issues. Have any of you found FODMAPs lists that include more unusual foods, spices, i.e. for foodies? Turmeric is one example.

    Also, why do some lists say no to butter and coconut products, yet others have them on the consume list? I don’t consume huge quantities of either, but they are staples and main oils and solids for me. (I do understand it’s the other additives in commercial coconut milk that can be problematic, but I don’t use coconut milk.)

    And if butter IS ok, then why isn’t pure whipping cream ok since butter IS whipping cream (at least that’s how I used to make butter as a child: shaking or whipping cream until it is solid)? And along these same lines, why is ice cream listed as AVOID, but gelato is listed as OK? My understanding is that gelato has less cream and more carb. I get that lactose is the issue with milk products, but high fat should be low lactose, right? I’m assuming that Ghee is totally safe, since no milk solids, but I don’t see it on any of the food lists to consume or avoid.

    Other examples of foods I’m not seeing anywhere: escarole; chicory greens (not chicory root): celery root (not celery); various cucumber varieties; kabocha, delicate, blue, acorn, and other squashes (I just find pumpkin, butternut and zucchini, and the rest are all lumped into the term “squash”).

    I also wonder, following a similar concept of the fermented problem foods being tolerable in low doses for some of us, whether sprouted nuts (and possibly sprouted lentils) might be less problematic too.

    If anyone has input/answers to any of these, I’d be much obliged!

    I can’t believe how incredibly complicated it is to treat SIBO, and I sympathize with all of you who have tried so many things and still not overcome this. It makes me feel very cautious about treatment protocols, other than the simple things like dietary mods.

  16. I would be interested in how to make the broth that is SIBO safe? You said there was a way to make chicken broth but without the whole chicken. So it sounds like you were saying using bones to make broth can cause problems?

    • What is the problem with bone/bone marrow broths? That almost sounds like a histamine issue, or is there more to it than that? I haven’t seen mention of such restrictions on any FODMAPs lists and I make and consume stock/broths regularly. Someone please explain. Thanks!

      • The problem with bone broths for SIBO is not a histamine issue (although, as histamines are inflammatory, and with SIBO one is already inflamed, there may be some potential benefits in lowering histamine for some people).

        The problem with bone broth is the joint and cartilage tissue that is still attached to the bone. This is the case with beef bones used for stock and of course chicken and poultry, etc. carcasses. These tissues are mucopolysaccharides, which encourage bacterial growth/re-growth.
        See Dr. Siebecker here: http://www.townsendletter.com/FebMarch2013/ibs0213_3.html (page 1 re mucilaginous herbs not appropriate for SIBO), and in her handout titled SIBO Supplement Checklist, in which mucopolysaccharides are listed as things to avoid.

        Dr. Siebecker specifically talks about appropriate broth in 2 places:

        The 1st was on a podcast, but I cannot remember which one. I’m guessing it was the Underground Wellness podcast (# 107). It was in regards to using broth as an alternative to amino acid powder in the elemental diet (at the time, Dr. Siebecker hadn’t yet found one, now she has, you’ll see it in her homemade elemental diet recipe). She says in order to NOT feed the bacteria, you can use only meat broth, no skin, no bones due to the joint tissue. And she recommends not cooking it very long (ie NOT the GAPS/WAPF method).

        The second is her website on the handout page: http://www.siboinfo.com/handouts.html

        In the SIBO Specific Diet: Food Guide- pg. 4, under the Protein/Meats section she states, “Broth: homemade meat or marrow bones (no cartilage).”

        It is possible to still make bone broth this way but it is quite tedious. I do it, but I don’t like it. :-). I can’t wait until I can just toss a chx carcass in a pot of water again, easy as pie. I may try to post instructions on SIBO meat and bone broths here if I have time later today. Let me know if this would be helpful.

        • Wow, Nadira, so interesting; I obviously have a lot of reading and catching up on this to do on all of this; it seems endless! I wish I could just plug into your brain and do a download to save me some time 🙂 Thanks for sharing this info and links!

        • i have been making broth by boiling a whole chicken with some ACV, and skimming off the fat. Is this an ok way to do it or am I totally wrong?!

        • Nadira, that link to the townsend letter was excellent, all 4 pages. I learned many new things, most notably, that this could be one of the causes of what I now know to be severe Restless Leg Syndrome!!! I’m having the worst sleep ever, which is terrible for my immune system. It started in the last few months and rapidly developed into apparent abnormal leg veins/capillaries, along with the ongoing discomfort, the worst being in bed at night. Never would I have associated this with SIBO! (BTW, I’m seeing a vascular surgeon next week about this.)

          Also, I’ve been a cyclical headache sufferer for decades, but since beginning menopause they are more rare, but still do happen, usually in conjunction with mild-moderate constipation.

          I also have some of the commensal flora that she describes.

          And of course, rosacea.

          Until one year ago, the only symptoms were C or C-D, and headaches. Then, over the past year all of the other symptoms have begun, one by one, possibly prompted by addition strain due to beginning menopause.

          Oh, and my TSH keeps creeping up too (3.5 in Jan, and up to 4.4 in July), so add hypothyroidism to the list.

          The article’s also making me wonder whether I should be doing a stricter GAPS or SCD diet for awhile. I’m also thinking intermittent fasting (16-8) with full 4 hours breaks between food and spacing out my vitamins and supplements (vs daily) would be beneficial because my understanding is that they can feed bacteria too. (I was taking S Boulardii twice a day too, and I’m assuming MOS is bad with SIBO present, so I’ve stopped that.)

          This is like peeling a seemingly endless beach ball sized onion, although with SIBO, that’s probably a poor choice for analogy 🙂

        • Hello Nadira,

          I would love to have your instructions on SIBO meat and chicken broths. I have a better understanding of how to do meat broths correctly – but chicken broths – I don’t quite get it! Do you actually cut the joint off of each little bone?!

  17. I’m curious about dose timing – that is, how does one optimally distribute multiple doses of probiotics, anti-microbials, bio-film disrupters, along with meals throughout the day? It seems like it might be easy to counter the effects of one thing with another, if taken at a non-optimal time.

    • They say the best time to take Probiotics when your stomach is quiet so sometime before bed.

      Biofilm removers like bromelain are best taken with the antimicrobial. It would make sense to take it away from meals and stomach more empty.

      For people who are on Antibiotic protocols, they take the probiotic 3 or 4 hours after they take the antibiotic.

  18. this is a redundant post from diverticulitis … if there is any other unique probiotic out there that has something unique about it, please post

    I have been researching probiotics and I have come up with a list of products that represent a diverse representation of whats out there. Whatever you buy or have, compare it to the ones below. The sheer number of probiotics can get overwhelming.

    1) Jarro-dophilus (enteric coated)
    a quality brand that uses enteris coating that is very popular

    2) Enzymatic Therapy Pearls IC (Beads)
    This uses Beadlet technology The IC brand has the most number of unique microbes of their all their specific products although only 6 or 8 unique microbes.

    They do have brands with less. This can be important if one is allergic to a microbe species. If one is having problems in tolerating probiotics, it may make sense to try some with fewer microbes to see what you can tolerate.

    “This [Beadlet Technology] process was developed in Japan and involves enclosing live probiotic bacteria in a small, pearl-shaped beadlet, where the walls of the beadlet are formulated to survive stomach acid and release their contents only when they reach the more neutral environment of the intestines.”

    3) Renew Life Florasmart 24 Billion Probiotic Caplets
    (Biotract) 30 count

    Interesting thing about this is the high microbe count vs other brands that uses Bio-Tract technology.

    “Controlled-Release Technology. Controlled-release formulas are specially coated to protect the probiotics from gastric acid and ultimately deliver a high percentage of live probiotic bacteria to the intestines. One of my favorite such technologies that both protects the majority of a supplement’s probiotics from stomach acid and also provides optimal release of live organisms throughout the entire digestive tract is called BIO-tract.”

    4) RAW Probiotics Ultimate Care-100 Billion Garden of Life
    30 VCaps GMO free

    ConsumerLabs rated Garden of Life the top brand based on their survey. A unique thing about this is the sheer number of unique microbes listed on it.

    5) Master Supplements Theralac, 30-Count

    This uses a unique patented method to protect against lactic acid and different method to fertilize microbes (lactostim etc) when they get there.

    6) PRO-15 by Hyperbiotics
    This uses beadlet technology also. It seems the most economic price and has a lot of positive reviews on amazon

    7) PrescriptAssist

    Soil based probiotic

    Somethine Chris Kresser has had lots of success with this in his practice.

    Not something to take when your gut flora us wiped out. You should understand why you really need to take it.

    Garden Of Life brand has a lot of soil based probiotics.

    I think this is a good sample of the interesting things that are out there as far as probiotic products. If someone is on the search for a probiotic, this list may be a short cut to figuring out what they want especially when your sick.

    • Why not the Prescript Assist in those instances? And how would one know that they were a person who ought not to use it?

  19. 9 months ago, I tested high for hydrogen but no methane. I did antibiotics and followed a low FODMAP/SCD/Paleo diet (99% strict). I never got relief. I recently was tested again and showed no signs of hydrogen or methane, yet I still have horrible daily bloating that gradually gets worse through the evening and night, only to be releived by a regular BM the next morning. Is this normal? To show no signs of SIBO anymore, following the diet, but STILL having problems? I have been on resalor for 2 weeks, which doesn’t seem to help. I have also been off Prescript Assist for 3 months due to the advice of Pimantel, et al. Why am I still having daily issues? Could it be hydrogen sulfide?

  20. I would just like to say how _hugely_ I appreciate these amazing podcast transcriptions! It’s so rare to find podcasts that are so full of useful information, and it’s rarer still to get to _read_ the content, rather than listen – works much better in my busy, noisy, kid-filled house…