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SIBO and Methane – What’s the Connection?


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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.

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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.

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Join the conversation

  1. “other than the fact that you don’t get methane production until three years of age”.

    I just wanted to say that I got my 2.5 year old son’s results back yesterday from ‘SIBO test’ and he tested positive for Methane dominate SIBO. I’m instincts tell me he has had it for at least 6 months.

  2. So i got hiatal hernia and had symptoms like heartburn and problems with breathing and have been misdiagnosed with GERD and doc prescribed me PPI pills (even though it was a mechanical problem and I just had to readjust the hernia)
    I took the pills for 2 weeks and felt really bad but didnt listen to my body and also because I felt bad I also eat a lot of chocolate . Later I found out it was all because of the hernia and got it fixed by myself and had no more GERD symptoms like heartburn etc. The problem is that because I used this pills I got an overgrowth of the bacteria and I can not eat simple sugars or I get bloated and gas and stomac pain,I can literary hear the fermentation only few minutes after I ate somehting “sweet” .
    How should I aproach this problem ?
    Is this plan any good .
    1)stick to sibo based diet (lower fermentable food)
    2)start with herbal protocols and soil based probiotics and other useful herbs.

    I dont know if I have methan based or hydrogen based SIBO ,I dont have diarea at all ,but sometimes I got constipated but not so freaquent .?