RHR: SIBO and Methane—What’s the Connection?

RHR: SIBO and Methane—What’s the Connection?

by Chris Kresser

Published on

revolution health radio

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. 

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.

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.


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 .?

  3. Nobody seems to recommend Caprylic Acid for SIBO. It’s one of the most widely studied herbal antibacterials. So I thought I’d add it in to my rotation. I find it equally as effective as Allicin and Berberine – both in it’s liquid form and as a calcium/magnesium caprylate mixture. I can’t find any expert saying it doesn’t actually work; just nobody saying that it does!

  4. Hi Chris

    Diagnosed with SIBO. My results are contradict the typical results. I have low methane and extremely high hydrogen. Like off the chart hydrogen. Biggest symptom that has lead me this far is chronic constipation and consistent struggles with weight gain. Or maintaining a healthy weight.

    Curious to know your thoughts. As high hydrogen is indicative of diarrhea,malabsorption and weight loss.


    • Kelly – the relationship to weight loss or gain is also related to WHERE in your small intestine the problem is. I assume that you have distal SIBO – ie a late rise in hydrogen?

      • This is me! I have high methane (at baseline and throughout) and hydrogen that starts low and rises very high after 120min in the test. And I have constipation and weight gain that’s very hard to lose!! Can you explain the relationship with this??

  5. Thank you very much for all the information. This has changed my life. I´d had the same problems for several years (cramps most of the time; even after waking up). I used to eat 3 – 4 pieces of fruit every day; in addition, I would have a sweet dessert in the evening. I stopped eating dairy a long time ago because I thought I was lactose intolerant and I rarely eat red meat or carbonated drinks. I no longer eat so much fruit, I don´t eat white sugar, and instead of bread I would have oats (no sugar, with added boiled water and 10 nuts) for breakfast or lunch, and every evening I have a bowl of vegetable soup (with some garlic). I don´t have constipation and cramps anymore and after a long time I feel like a normal person 🙂 Thank you so much for your research! (I did not take any antibiotics or probiotics to cure myself)

  6. Hi Chris,

    Thank you for all your hard work keeping us informed. I suffer with bouts of diverticulitis of the sigmoid and jejurnum all the time. Although I’ve followed for many years a low fodmap and low food chemical higher fiber diet, it never ceases and as of Feb 2016 at the same time as a bout I started experiencing other symptoms which six months later I found out it was SIBO. I have another bout now and am on Flagyl, which after only 3 days has flared the SIBO symptoms again. I have been treating SIBO with herbal antimicrobials diet and have had a round of rifaximin. I seem to have high methane as I’m suffering with constipation. It’s a never ending circle it seems. I have had severe food chemical sensitivities, intolerance to gluten, lactose & FOPMAPS since I was about 16, now 55. I’m at a loss as to how to continue and with what? Thank you.

  7. I have been to the doctor and she told me that I have inflammatory bowel disease and severe leaky gut. I am allergic to corn and milk and wheat also. I have been on the low fodmaps diet and taking probiotics. When I went back the inflammation was better but the leaky gut is worse. I really think that I have sibo and suggested it to her, but she wouldn’t tell me anything about it. She has me taking glycine , b vitamins ,iodine for my thyroid, vitamins for my adrenals, glutathione, magnesium. I only sleep 4 to six hours every night . And I am very under weight. I live in Arkansas. I only eat organic produce and grass fed . All of her test point to sibo and I seriously have all the symptoms of sibo. Please help me.

  8. I would like to know what is best recommended for healing peptic and also duodenal ulcers. And I am not looking for PPIs or anti acids. I’m looking for natural ways of restoring the lining so that proper levels of stomach acid can be introduced.
    I’ve suffered from SIBO and both peptic and duodenal ulcers for years, and have been put on strong doses of PPIs years ago. Even though I’m addressing the SIBO now and have partially healed the peptic and duodenal ulcers, I still cannot get off of the PPIs (now at 20mg a day vs. 60mg 4 years ago). Ideally, I want to get off of the PPI and be able to introduce Betaine HCL/Pepsin to better shield my system from possible recurrence of SIBO. Any help is much appreciated!!! Sending you all good healing vibes 🙂

  9. As I read and research, especially as I am just beginning treatment, I find the advice about diet to be confusing and downright contradictory. In another interview, Dr. Kresser agreed with Dr. Pimental when he advised against the low-fodmap diet while being treated with antibiotics (pharmaceutical or herbal). The theory expressed was that bacteria will simply hide and tough it out when you undergo a restrictive, low fodmap diet. Dr. Pimentel said you want to keep the bacteria “happy” by eating a higher fodmap diet. That way they don’t hide and they are around for the antibiotic to work on. I trust this because he is a gastroenterologist who has a particular interest in SIBO. It also makes sense to me. So there seem to be two contradictory schools of thought. My intuition is telling me that the exclusion of all grain and a large consumption of meat is unhealthy, which is why I am against the Paleo/low fodmap approach.

    • I agree with you Sara, and this is exactly what I am doing right now as I am undergoing the SIBO treatment (as recommended by Dr. Pimentel – rifaximin and neomycin together). I was on FODMAP diet for a prolonged period of time and it didn’t help me in the long run – it acted as a bandaid more or less and every time I added more carbs I had flare ups and unpleasant SIBO symptoms for a day or two. I don’t believe the low FODMAP diet is the way to go in the long run, even though it offers a temporary relief. I would rather turn towards the botanicals (Atrantil) for maintenance after SIBO treatment to prevent recurrence. Of course diet plays a role but as long as it’s a reasonable healthy diet I would not go for low FODMAP.

  10. Hi Chris,

    Appreciate the great info.

    I’ve been diagnosed with SIBO.
    My hydrogen level spikes to 15 after 40 mins and 26 after 140 mins. The methane also jumps to 3 after 140 mins but has a baseline of 0, would you say i am methane positive aswell?

    The main symptoms of my SIBO are abdominal pain all over including back and shoulder pain. I will have cramps which will only be relieved via stools.

    However the main symptom for me is this chronic and very severe halitosis. It is always there and never goes away despite all my best efforts.

    I have previously taken Rifaximin 3 times previously for 2 weeks (500mg 4x day.) However i have had no relief. What would you advise i do? Would a course of Rifaximin and Neomycin be any good.

    Please can you advise as this halitosis is ruining my life.


    • Salman – your results are not consistent with SIBO. Rises after 120 mins are due to colonic fermentation. A “jump” of 3 in methane is insignificant. Baseline levels are important as well as the various levels before 120 mins. There is a possibility that you have another organism that produces a gas other than hydrogen or methane (such as hydrogen sulfide). Have you had an ENT evaluation/dental xrays for abcesses etc?

      • Hi Sharon,

        Thanks for your response. My mouth situation is perfect and I have no upper Gastroenal issues such as candid or reflux. However around my intestinal area there is a lot of sounds and pain before I go for stools. The halitosis is now extremely bad and have noticed it caries depending on wether I’m going for a stool or not. While always bad it increases when I am ready for a stool and slightly decreases after. The fecal smell is coming out of my nose and is very distressing. Would you say that the gases causing the smell (hydrogen sulfide, skatole etc) are coming from the colon and not small intestine as previous thought? And so most likely causing the halitosis?


  11. Hello.
    5 years ago I was infected with giardia. The infection was not treated for the first 2 years. Then I took multiple antibiotic courses and my stool antibody analyses (taken 2 times) showed that giardia is gone.
    However, my gut dysbiosis is still untreated. I have mild constipation (I use magnesium to relieve it), bloating and my stool is usually green or dark green. I also have an occassional belching and heartburn. Those symptoms are not severe and aren’t bother me much in daily life.
    The main problem that I have is insomnia and depression which progresses since I was infected 5 years ago. For the last year it has become more severe, and I have anhedonia and irritability now. I think its due to neurotransmitter imbalances and possible brain shrinkage that was caused by prolonged malabsorption and stress.
    Last time I visited my gastroenterologist I got diagnosis: IBS with constipation. I took multiple courses of probiotics and prebiotics without success. However, it seems that I sleep better when I take probiotics with lactobacilus.
    My stool test shows that I have very low lactobacilus level. Everything else is in optimal range. Candida is not found in the stool.
    I now suspect that I have SIBO-C. Do you think that it can be the cause of my symptoms? The problem is that only breath test for SIBO that is available in my location is hydrogen breath test with lactulose. There is no methane test. Should I take hydrogen-only test if never had diarrhea?
    I was negatively tested for h.pylori during gastroscopy. I’m planning to take stool test also.
    I will appreciate any help. Thanks.

    • Take rifaximin + neyomicn therapy no need to get tested as these antibiotics doesnt cause any harm when taken acording to the prescription of doctor

  12. I was in a very severe car accident in 2009. I was the passenger, and my boyfriend (at the time) struck a tree while we were traveling 90 MPH. I only had my seatbelt around my waist ( the shoulder strap tucked behind me) From the impact my intestines were SEVERELY perforated, I fractured my L5, and collapsed lung. I was cut open, multiple times to repair the intestines and also, after having hernias appear wrapped from my stomach to my back. Since the accident my digestion has gotten progressively worse. I am 25, and now having so much inflammation and intolerance to almost everything I eat. Its getting so bad, I don’t know what to do. I have been so healthy my entire life, I do not eat processed foods, I am organic and very health wise. Which, I know, is very shocking because my generation isn’t aware of how much food impacts our lives. I guess my question is… Does anyone have any piece of advice? I have restarted the process of elimination in my diet. So, i can find what it is that is triggering this constipation and weakening in moving my bowels. I take probiotics, Omega 3’s, Magnesium, Fiber, Hemp oil, etc… I need a miracle <3

    • I would look into serotonin precursors. You seem to be doing a good job of taking care of your body, but stress depletes neurotransmitters, so I would research both methylation (neurotransmitter synthesis) and adrenal fatigue/stress/depletion. Good luck!

  13. I’ve watched this discussion a few times to see if you actually address the question of using allicin and don’t find that information. It appears that allicin is recommended to treat the methanogens but garlic is specifically proscribed in all the SIBO and CSD. How do you reconcile this apparent conflict of information.

  14. So is there no natural way to combat methane type sibo? I have severe constipation and have followed the diet for years. Tried just about everything. I recently started messing around with kefir (coconut) and trying different probiotics and now I’m in a real mess. It amplified everything horrifyingly.

  15. Hi Chris,
    I thoroughly read the John Hopkins study re: the 2 sets/brands of botanicals they used in their “look back” study. What I cannot find is which patients used what herbal protocol (Metagenics vs Biotics). This is frustrating because I would like to start treatment with one of two but how do you decide without that pertinent information? I have also read through your transcripts of previous SIBO podcasts and some of herbs you mention are in one brand and some in the other. Do you have any idea what might be the better one to start with ideally for a methane producer? I know you cannot recommend treatments here but if there is a link to any relative info on which protocol produced more efficacious results, I would love to see it.
    Many thanks!

  16. Hi everyone, I’m new to this conversation. I have SIBO (methane kind) and have been taking Rifaximin for 4 days. I have Neomycin sitting on my counter but after consideration, I decided not to take it because the potential side effects scare me too much. I skyped with Dr. Siebecker a few weeks ago and she recommended these two meds.

    After reading all your advice and experiences, I’m sold on taking allicin (Allimed brand) starting ASAP — and I want to take the liquid version (can’t swallow pills) — so my question is, please: how do I know how much liquid to taker per dose? Someone wrote above that Dr. S. told them that the protocol is 2 caps/3x day … so how would I know how much liquid med to take? I can’t even wrap my head around it. I’m going to call the company tomorrow (it’s Sunday now) as well as maybe call my pharmacy, too, but if anyone knows the answer to this, I would be VERY thankful!

  17. Chris,

    I just took a Genova SIBO test that came back negative for SIBO. My baseline methane level was 5 ppm and on the last sample it went up to 12 ppm. Does the high methane baseline mean I have an issue that needs to be treated?

  18. Chris: Im wondering how many of the anmicrobial botanicals I have to take and how often? How long do I take these botanicals for? When do I use the prescript- assist?

  19. My son is taking 550 mg Rifaximin 3x day and 500 mg Neomycin 2x day for methane SIBO. He is experiencing liquid diarrhea. What should he do? I saw in one of the comments Allicin was substituted for the Neomycin. Might the diarrhea pass? Could it be die off? Would something like Imodium help?
    Or Saccharomyces?

  20. Hi All,

    I’m currently working on a school research paper focused on methanogens and their growth in the gut. I’ve found that one of the key positive feedback cycles with methanogens is that the production of methane as well as the small changes in biochemistry of the gut. The positive feedback cycle is propagated by the methane produced by methanogens, which makes meals move through your gut more slowly, which helps methanogens grow more and produce more methane, both of which allow other bacteria to grow more…which helps methanogens produce more methane and also causes more irritation of the gut etc.
    One of the key ways that you can increase the speed that meals move through your gut, other than laxatives, is to exercise more. This will decrease the time the slow-growing methanogens have to grow which should help stop that positive feed back cycle.

    Summary: Try exercising more – esp. walking and other full body movement. Hope that helps!

  21. I have SIBO with constipation. I have read that methanogens, specifically methanobrevibacter smithii, is commonly found in infected teeth (read in this articlehttp://www.nature.com/ajgsup/journal/v1/n1/full/ajgsup20126a.html) and I strongly feel that my gut issues began a few months ago when I had a severely infected tooth treated with two rounds of antibiotics followed by a root canal. I still feel like the tooth isn’t right, despite the dentist telling me it’s fine. I’m wondering if I should have the tooth extracted (even though I’ve spent a few grand on my nice crown and the root canal) in case the tooth is still the source of the methanogens and causing my SIBO? I’m currently using herbal antimicrobials and following a low FODMAP diet. I was doing great for a few weeks but then symptoms reoccurred. I will be starting the antibiotic treatment soon (prescribed by a GI doc) but still wonder if I should have the suspicious tooth removed?

    • CJ please research dental cavitation. You can also learn about it on Dr. Stuart Nunnally’s website. He is in Marble Falls TX and did my surgery in Jan, 2017. I travelled there from CO.

  22. Rifaximin and Neomycin warning: i’ve been actively fighting methane SIBO (high measure was 115) for almost a year now. I’m doing well and tested at high 50 about 5 months in and so I’m getting results. My protocol is botanical abx, low FODMAP, autoimmune paleo diet and finally tried the Rifax/neomycin protocol to knock out last bit. I have since developed oxalate overload. Not sure, but I believe that the strong prescription ABX wiped out the anaerobe, oxalobacter formigenes which eats oxalates. Now I have a whole new issue (kidney stone risk) and even more food elimination. To do this again, I would not have taken the pharmaceuticals. I have read about this same reaction in 2 other SIBO sufferers.

    • Hi Michellev, thanks for sharing your warning about the Rifaximin/neomycin protocol. I’m newly diagnosed with both hydrogen and methane SIBO. I desperately want to avoid prescription drugs. Would you mind sharing which herbal antibiotics have helped you?

      Thank you so much! Hope this suffering will end soon, for all of us.

  23. 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 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?

    • 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.

  24. 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

  25. 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.


  26. 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.

  27. 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!

  28. 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.

  29. 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.

  30. 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.

  31. 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?


  32. 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

  33. 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.

  34. 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.

  35. 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.

  36. 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?


      • 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.

  37. 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.

  38. 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?!

  39. 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.

  40. 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.

  41. 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?

  42. 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…

  43. “They were originally classified as bacteria, but they’re now classified as prokaryotes, which again are a completely different class.”
    Hmm slightly off, I think. Yes, they were originally lumped in with bacteria, but now they’re classified as archaea. So “prokarya” have now been broken down into “bacteria/monera” and “archaea”, not “bacteria” and “prokarya” (which bacteria would belong to).

  44. Thanks again Chris for your podcast and responses, and also all others who have posted comments/questions. This info has been a revelation for me. Just looked at the high FODMAP food lists for the first time…WOW! Over the past few years I’ve had bad GI reactions to a short list of foods, but didn’t know until now that they are all high FODMAPs!!! Most notably: butternut squash, beets, cherries, and dried fruits, especially in large servings. Now I have something concrete to work with!

    I’d also like to learn more about the antimicrobials that Chris mentioned. Perhaps the combinations and doses need to be customized to each patient, so a generic recommendation from Chris may not be feasible?

  45. With autoimmune disease, I find that treating my SIBO with antimicrobials can easily cause serious flares of my immune system. How can I prevent this from happening? I haven’t tried the antibiotics yet, just some of the recommended antimicrobials.

    Typically I have a positive response at first, but after a few doses or a few days, my immune system flares up and I regress. Since we believe SIBO is one of the main causes of my autoimmune disease, how can I treat it safely without these nasty side effects?

    Many practitioners, even the holistic or functional ones are unfamiliar with the specifics of autoimmune disease, and can offer little help.

  46. I had a consult with Dr. Whitney Hayes, ND, a colleague of Dr. Siebeckers. She told me that she and Dr. Siebecker compared the results of their hydrogen/methane breath tests from Commonwealth and from other laboratories using Quintron machines and find that Commonwealth’s tests tend to under-report methane. This means that if you have a Commonwealth breath test, your methane results could be higher than what the test actually shows. It was frustrating to learn this as Dr. Siebecker still lists Commonwealth on her list of labs to use for breath testing, so I paid for a test with results that may be inaccurate. I’m posting this here so that others will know and will NOT use Commonwealth for their SIBO testing.

    • Nadira,

      So interesting to hear this about Commonwealth. It definitely fits with my experience. I was tested in February (via Commonwealth) and showed high hydrogen but NO methane (which did not make sense because I have IBS-C). I have been working with Dr. Keller and experienced quite a lot or relief from my treatment. I was convinced that I had gotten rid of the bugs! I just retook the test a couple of weeks ago (this time through NCNM Lab) and while my hydrogen had gone down, methane now appeared (not super high, but still a high enough level to indicate it was a problem).

      • Hey Riley!
        I have the same case as you (IBS-C), and super curious to read that your treatment gave a lot of relief. What did you do? 🙂

        You probably always had methane producers and it just didn’t get picked up in the Commonwealth lab? From what I’ve been told it’s the methane producers that cause constipation. But sounds like you already knew that since you were also confused by the lab results. That is strange!

        • Hi Marianne,

          It is hard to know what helped the most between my first and second tests because I did several treatments and was reluctant to retest. I work with Dr. Keller at the NCNM SIBO Center. I have done 2 rounds of Rifaxamin, high dose neem for over a month after that, then started a prokinetic (I have used resolor and low dose erythromycin- separately) then allimed and neem combo (this is supposed to be the most helpful when you have IBS-C and/or methane- Dr. Keller recommended it based on my symptoms). I also get nutrient IVs every couple of weeks. During all of this I have followed a pretty strict low FODMAP, no fruit, Autoimmune Paleo diet. The diet I was following was too low carb though and made me exhausted. I started adding more carbs in (white rice, sweet potatoes, winter squash) which made my brain work sooo much better, but I may have overdone it because my SIBO seems to be creeping back a little bit since my last breath test.

          • Hi Riley,

            Thanks so much for your answer, I really appreciate it. That’s really interesting, I didn’t try Rifaximin, but I did try all the other things (except the prokinetics) and they surprisingly didn’t work for me either. I’ve never heard of resolor so I’ll have to read about it. I’m always looking for something to help with regularity, seems like nothing ever really works or only works for a short while.
            Funny, I had the same problem with going too low carb! I was super strict for about a year and a half but lately I started adding more fruit (low FODMAP) and oatmeal, although I think I also am overdoing it :S I can tell.
            My doc recommended two antimicrobial products that were shown in a study to be as effective as the antibiotics, which are actually different than the many herbal protocols I tried before, they’re called Biotics FC Cidal and Dysbiocide. They need to be taken in conjunction with EDTA (as a chelator) or an enzyme to improve their efficacy. I haven’t been able to try it yet bc I moved to Germany in July and everything gets confiscated that is shipped here 🙁 I’m trying to work something out..
            But once I try it, if it works I’ll let you know! It’s been already such a long long process, I just can’t accept that we can’t beat this! Best of luck,


            • Marianne- The prokinetic has been a lifesaver in terms of keeping me regular. I don’t want to be on it indefinitely though, which is why I am trying to figure out and treat my root cause as well. In the meantime, the prokinetic keeps me sane and detoxified. Best of luck!

  47. Chris said “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.”

    what specific brands of these treatments do you use? All too many of us have to self treat because our doctors have no idea about SIBO.

    • FYI
      one interesting thing about uva utis is that one needs to take 500 mg twice a day with 8 oz of water that has 1 tsp of baking soda in order to release the active component. It requires an alkaline solution. One should not use it longer than 7 days.

  48. I would love to hear doses and more specifics on the herbal/botanical treatments for methane producers as well. Thanks!

    • I had a consult with a colleague of Dr. Siebeckers. Here is what she recommended:

      1) Neem Plus by Ayush Herbs: 1 cap, 3x/day

      2) Berberine Complex by Integrative Therapeutics: 2 caps, 3x/day

      3) Allimed brand allicin: 2 caps, 3x/day. (Note: I found that the capsules of Allimed contain a SIBO-unfriendly filler, but the liquid does not). You’d just have to do a little conversion of the caps to liquid to obtain liquid dosing).

      4) (opt). Monolaurin- I specifically asked about this supplement because it is proven effective against certain viruses, yeasts and parasites in addition to bacteria. The ND recommended:

      a) Ecological Formulas: 1-2caps, 2x/day

      But I chose:

      b) Lauricidin because it’s not in capsules, so no fillers, and I can individualize the dosing per my tolerance. Equivalent dosing would be approximately: 1/4tsp, 2-3x/day. It’s very powerful so if you’re sensitive or have autoimmune issues I’d start out much lower.

      • Wow this is phenomenal. Just to clarify, is this protocol for methane SIBO or Hydrogen? Or Perhaps it doesn’t matter?

        Would you be following this regimen for 30 days and then retest?

        • Yes, this is the protocol for both hydrogen and methane. The Allimed is for the methane.

          Yes, it’s for 30 days, then re-test. Presumably if symptoms are not 80-90% improved! continue treating until symptom improvement and a positive test.

          Another option is to combine Abx treatment with the Allimed to treat methane (instead of taking 2 antibiotics):

          1) Rifaximin, 550mg, 3x/day
          2) Allimed brand allicin: 2 caps, 3x/day (or liquid equivalent).

          Here the Allimed stands in for Neomycin.

          • So the hydrogen protocol would just be

            1) Neem Plus by Ayush Herbs: 1 cap, 3x/day

            2) Berberine Complex by Integrative Therapeutics: 2 caps, 3x/day

            and optionally the Lauricidin.

            • No, there are no other herbal alternatives that are as powerful as the ALLIMED allicin garlic extract. This is according to Dr. Siebecker and her SIBO colleagues.

              I bought mine at optimalhealthusa.com for $80 for a 1oz liquid bottle. Each oz contains 600 drops which is about 12 days on the protocol. So you’ll probably need 3oz at least. If you buy a larger bottle the price per oz decreases. The 4 oz bottle is $55/oz. The bottles must be stored in fridge or freezer.

              I chose liquid over capsules to avoid then maltodextrin in the capsules but caps nay be more convenient if you’re not worried about the maltodextrin.

              • Monopoly by the company that makes “allimed”. Ridiculous. I’d rather take one crushed whole clove of garlic for my allicin, and simply reduce fodmaps elsewhere in my diet to make up for the small amount in that one clove of garlic, than pay $80 to some arrogant “patented” company.

                One clove of garlic can’t have as much fodmaps as the multiple servings of wheat that people indulge in – look at the small size, and much of that small volume is fiber, sulfur, and water.

                If ANYONE cared about human health they would finally test fodmaps levels in reasonable serving sizes of foods, instead of lumping one clove of garlic into lists of “high” fodmaps foods. No lab has ever done this that I’ve ever found.

          • Nadira,

            I am considering using Rifaximin with Allicin together as you mentioned above but I had never heard of anyone using that combination before, so I am worried about its safety etc (just because it is the first time I had seen them suggested together). Could you tell me where you heard that this combination can be used? Thanks 🙂

            • This was suggested to me by a colleague of Dr. Siebeckers who treats SIBO patients. The alternative is taking neomycin with Rifaximin but she wasn’t sure I’d be able to handle the intensity of the dual antibiotic therapy. For others they may handle it better.

              • Nadira, can you tell us how your antibiotic therapies went? I have methane SIBO and am considering Rifaxan (200mg 3x/day) + Allicin. Can Allicin be used alone for methane SIBO?

      • Hi Nadira,

        Do you mean you take all the supplements together in a day or rotate them every few days?

        I might have SIBO but I dont have any breath test available in my country and no Naturopaths or natural functional doctors. If the CommonWealth breath test is unreliable what kind of breath test is best used?

        I know about Dr Siebecker but couldnt find an email address to ask her some questions,as I am in Europe and dont know if she can work with me. I contacted NCNM but no reply as well

        Thanks a lot for your help

  49. Hi Chris.

    This may be a silly question but it pops into my mind every time I read anywhere that Rifaximin is not absorbed beyond the gut. How is that possible? And more importantly, what if you have a leaky gut, would it then get through the gut wall and what effect would that have on your system?

    Thank you,


  50. Chris – one of the criticisms I hear in regards to the soil based organisms such as Prescript Assist is that there is not enough evidence yet for their efficacy and safety. What is your response to that?


    • There’s a one year RCT supporting Prescript Assist, which is more than many probiotics have behind them. I can tell you from clinical experience that it’s the single most effective and best tolerated probiotic I have ever worked with.

  51. I see that this is a VERY complex issue and I also realize that I may have some of the symptoms you describe, Chris. And it probably very difficult to self-treat, isn’t it? Chris, do you have a directory of physicians and other professionals qualified to treat patients with SIBO, etc.? I live in the Washington DC area.
    Thank you very much.

    • Unfortunately, I don’t know of such a directory. You’d want to look for functional medicine practitioners, and then ask if they have experience with SIBO.

      • Is this in reference to treating SIBO while pregnant? I am looking for help myself and am in this boat. I have been doing Paleo and not nuts, eggs nightshades and so on for years… I have not had FODMAPS for about 1plus year and now pregnant and with SIBO at is worst. Any suggestions or is this a 9 month waiting process?

        • Hi! 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 would love to hear about your experiences and any advice you have for someone just 2 months in…

    • I live in DC area and have some practicioners open to treatments and even have heard of Chris! JHU was useless, and tried treating the very off the charts methane positive with rifaxamin only. Three positive tests and systemic involvement. Now understanding that the actual number of methane level should be looked at to see if the peak methane levels are lower. Please contact me privately to share resources.

      • Green Smoothie –
        Please send me your information on doctors in the Washington DC area who can treat SIBO and related conditions. This listserve hides email addresses. Contact me at
        Grace AT TakomaVillage
        DOT org (Use the proper symbols and leave out the spaces). Thanks

  52. Hi Chris,

    In your professional experience, do methane producing archaea and constipation predominant IBS have any relation to the fecal SCFA levels or n-butyrate levels you see on stool tests?

    After listening to your show I did a quick Google search for archaea and butyrate and came across a study titled “Methanogenic archaea in adult human faecal samples are inversely related to butyrate concentration” Authors: Guy C.J. Abell, Michael A. Conlon, Alexandra L. Mcorist.

    Would increasing butyrate be a way to manage IBS-C or reduce methane producing SIBO, or is it more likely that butyrate levels are only low in these high-methane people coincidentally because of altered diet or some other cause?

    I ask this because I did a GDX GI Effects test in August before a rifaximin-only course and to my surprise I had no microbial imbalances. With the severity of my abdominal cramping and IBS-C symptoms I really didn’t expect that. The only red flags in my results report were low SCFA, very low n-butyrate and low butyrate %. Now I’m wondering whether or not I should try to increase butyrate levels or try some other natural antimicrobial. Not surprisingly, the rifaximin-only course didn’t help to reduce symptoms.

    I was under the impression that RS should be generally avoided along with other fermentable fibers even in methane producing SIBO cases with IBS-C.

    Do you think attempting to increase butyrate levels in people who are methane-positive and have IBS-C is a good or bad idea?

    Thank you.

    • That is very interesting! I hope Dr. Kresser answers your question about increasing butyrate levels.

      I’d like to also write to Dr. Kresser, because I’ve been dealing with SIBO for a couple years.

      I’ve done the elemental diet, all the herbal antimicrobials a couple times for 2 months minimum each, and then taken allimed for 3 months all while over these 2 years on a strict paleo/SCD diet w/o any fruit, carbs or sugars. I still am at the same place I started and I can’t understand why. Still very distended stomach, very constipated. I feel lost and helpless, and all the NDs and FM doctors I’ve been to don’t know what else to do either. I only have turned down the Rifaximin/neomycin combo because I’ve read that many people have a relapse anyway and it costs a ridiculous amount of money for those antibiotics.

      Any help, leads, tips, words for hope would be greatly appreciated!!

      Love your work, thank you for all that you do.



      • @ Marianne,

        I can think of a couple things here…did you take the anti-microbial WITH the Allimed or did you take them during 2 different times? You would need to take Allimed PLUS 2-3 other herbal antimicrobials.

        Did you have a SIBO breath test done? Were the results positive? For both methane and hydrogen, I presume?

        After treatment with the e-diet, the herbals, and the Allimed. Did your symptoms improve but just come back, or did they never improve?

        Another thing to consider is SIYO AND SIVO. (Yeast, Viral). In theory, the herbals used to treat bacterial overgrowth also have antifungal and antiviral properties, so may take care of this. However, personally I find that I need to add in some specific anti- yeast and Lauricidin to make my treatment effective. I mix Caprylic acid, Thorne SF5722, and the Lauricidin. I can tell a big difference with the addition of these supplements.

        Okay, so if your symptoms went away but came back, then you need to find your root cause. Dr. Siebecker has a great list of 7 causes of SIBO and ideas to prevent its recurrence. The #1 reason is lack of small bowel motility. You could try ginger, Iberogast, MotilPro, or LDN, but Dr. Siebecker says usually these aren’t strong enough and low-dose erythromycin may be needed.

        If your symptoms never went away, and assuming you do have SIBO, maybe you weren’t treating intensely enough. With the elemental diet, you may to stay on it 21 days if you’re not much improved by 15. The e-diet can worsen yeast overgrowth, so you may need to do e-diet plus some anti-fungals at the same time. Again, adding in the supps I mentioned above could be helpful as well as increasing dosages of the herbals you were taking, or switching to others that may be more effective for you.

        In addition, you are on a very low-carb SCD, have you also eliminated FODMAPS? This is huge, if you don’t, you will keep feeding the small bowel bacteria. Eliminate them ASAP. Also, if you drink broth or homemade soups, make sure that you do not use any joint material, tissue, collagen, etc. This means only pure meat broth/meat soups. (Ie from stew meat, ground meat, not a whole chx, for example, or from beef bones). However, you can still make these foods- chx broth and bone broth, it’s just a lot more labor intensive. If you’re interested, I can explain how I do it.

        Also, I’m sure you’ve done this, but make sure you’re not accidentally eating any of the starches, gums, fillers, etc, that upset SIBO. Again, the http://www.siboinfo.org has a great listing if these things in the resources section.

        Lastly, if your symptoms have subsided,for a time, but came back, you may need to trial supplements like: zinc, resveratrol, glutamine, colostrum, betaine hcl brush birder enzymes, pancreatic enzymes, and probiotics.

        Hope this helps!

        • Wow Nadine, I can’t thank you enough for taking the time to write so much helpful information!

          I did have a breath test that showed low hydrogen and very high methane. I remember my methane was so high it surprised my doctor (and that was with Commonwealth Labs)

          I unfortunately never saw any improvement with the antimicrobials. I remember I did do both the allimed and berberines together, plus something else and biofilm disruptors an hour just before the antimicrobials religiously. Then in a later round I did oregano, neem and the Allimed (1 cap 4x/day), while at the same time taking NAC and candex. I have also been aware of low FODMAP on all these rounds, and following it.

          In between I did make bone broth, but found out what you mentioned about the mucopolysaccharides so stopped 🙁 I have taken just about everything you listed…

          The one thing I did see improvement with was the elemental diet. My stomach actually looked normal like it has almost all my life! That ended teh day I started to eat food again. I had already read every word on Dr. Siebecker’s website as well when I started all this 🙂 I used her homemade elemental diet because it was healthier but it made me nauseous so I can’t imagine doing it again and for longer than what I did (14 days). Also that diet set me back, the honey caused my candida to come back so I was very upset after all that effort to be even worse overall. I would like to try a version of that diet again but without the sugar.. I just don’ t know how to do it. I heard it’s possible to try a water fast for 14 days with supervision, but that is quite intense. I like it though because it won’t cost me anymore money haha!

          I think you had a great point about going back to the causes. I am quite confident my cause is low small bowel motility. I have had constipation issues for years. I even went to a visceral manipulation therapist who said my small intestine is crawling at a snail’s pace. I don’t know how to improve this though. If I don’t get things moving faster, I can kill things off as much as I want but it will just grow back.

          I have tried so hard at this that the past 2 months I stopped all antimicrobial herbs and started Prescript Assist SBO, with taking home made kefir and yogurt (made with VSL3) because my latest stool test still showed NG for the main bacteria. Good news was I totally kicked the fungal infections. However bloating and distended stomach always still the same, plus of course the constipation.

          I’m mostly trying to not restrict myself so much anymore on food (I have been eating some FODMAPs..) and work on the probiotics, with good doses of HCl at every meal and small amount of digestive enzymes. I am about 10% better than I was a year ago in bloating, but I really don’t feel like I’m making any progress still.

          Do you think it would be worth trying another round of antimicrobials? I really feel like I’d be beating a dead horse. If you have any thoughts on a fungal´-safe elemental diet though, I would be very eager to try!

          I also will look into your suggestions for low motility. I did try LDN and it helped only a tiny bit and then wore off. Probably if LDN didn’t work the others won’t (I did try ginger tablets and nothing). I didn’t want to take erythromicin because I try my best to avoid antibiotics.

          Thanks again so much for your post. Means a lot!



          • Marianne, yes, there are several things you could do to avoid a yeast flare up on the e-diet.

            *Make sure you follow the low-sugar version of the homemade diet listed on Dr Siebeckers website, not the high sugar, low-fat one (the Vivonex ratios). Start there.

            *Also don’t use honey it’s way too sweet. Order organic dextrose online -it’s cheap and not very sweet. And just use less sugar and make up your calories in fat if you can. If you can feel it that you really need the sugar for energy, then just add in an antifungal.

            *Make sure that you rest and relax as much as possible – no stress. If you work you may want or need to take off some days or the whole time, depending on how much energy you consume at work. Or try to work from home, part-time. Ideally you need to stay home, sleep as much as possible, read books, nap, take baths, watch tv, etc.

            *Use coconut oil as your sole fat source on the diet. This alone may stop the yeast problem. Take it with your dextrose.

            *Add in an antifungal- Monolaurin, neem, olive leaf, etc., there are many. Start with a small dose bc you don’t want too much die-off. If you still are feeling yeasty then increase the dose SLOWLY, or as you feel comfortable. Take it with your dextrose.

          • Hi, I’m interested to know how you’re doing. You sound like me in terms of symptoms and everything you listed, just about, is what I’d follow, too. But it sounds like it didn’t help you as much as you’d hoped. That is disheartening!

            Curious how you’re doing now. This is overwhelming! But your posts and answers from everyone is very enlightening. Thanks for sharing your journey!

    • Hey Nathan,

      Thought I’d share my experience with GDX – mine showed no obvious dysbiosis at all even though I had severe overgrowths that other testing picked up here in Australia. I think it often comes down to what specific bacteria are being reported on, these tests really only touch the surface of the numbers of bacterial species in the gut. When I revisited my GDX results, I did see that there were other markers of putrefactive dysbiosis, but the test didn’t show me which bacteria specifically were a problem – the Bioscreen test in Australia was much more useful in that regard.

      None of these tests are infallible unfortunately.

    • I think it’s worth a try. RS is hit or miss with SIBO; some respond well, others don’t. Trial and error is a valid approach.

  53. Chris, are you saying that a breath test reading high methane only (no hydrogen) still considered SIBO?

    I’d been told no by my doctors, yet everything that I’ve read seems ambiguous. But your podcast seems to say that it IS SIBO, which makes sense to me, because otherwise, why test for methane. Other than sudden onset rosacea, I’m told that I don’t have the classic SIBO symptoms (excessive bloating, gas, nor very bad breath). Serum and stool tests negative for h pylori, no parasites or bad bacteria, other than a few commensal e coli. Also, are you saying avoiding FODMAPs could help with the high methane? I haven’t tried that yet. FYI, my hydrogens, including baseline, were 0 (except for a 4 ppm at 20 mins), but methane was 80 at baseline and 56-74 at all other test times.

    Thanks in advance for clarifying this point about SIBO vs not SIBO for me. This would help me try to figure out what to do next.

    • Yes. According to Dr. Piementel, a baseline level of methane over 3 ppm is considered a positive result, regardless of baseline hydrogen or increase of hydrogen or methane after challenge. Whether this qualified as “SIBO” according to the strict definition is debatable, but from a practical perspective it doesn’t matter what you call it. The question is whether to treat, and I’d say yes if symptoms are present.

      • One more thing. Commonwealth, the lab I now use for SIBO testing, also marks methane over 3 ppm at baseline as a positive result. They recently made this change because of what the scientific literature suggests.

        • THANK YOU very much Chris!

          Dr. Jolley (the GE at Baycro in Mill Valley) wrote “Methane Positive” on the report. Since I couldn’t find the answer online, I asked my FM doctor who ordered the tests if that meant I have SIBO; she told me no, that I was just constipated and needed to increase my fiber and exercise (which is silly because both were already very high, and fiber possibly too high).

          Would rosacea (sudden onset 1 year ago), without other typical extreme symptoms, still qualify as “symptoms are present”? For example, bloating isn’t common (never severe) and only mild at that; rare bouts of constipation — generally regular (once a day); chronic bad breath was an issue years ago — not as bad lately, though it could be better.

  54. hey Chris, this podcast is so appreciated , thanks.

    i have been wondering though, if a stool test (doctor’s data) shows little to no beneficial bacteria in the colon (eg. bifido and lactobacillus), is it still possible to have an overgrowth in the small intestines? I have all the symptoms of methane version of SIBO.

    • Seconded. (Same situation: “No Growth” readings for beneficial bacteria and methane SIBO symptoms; additionally, ambiguous breath test results.)

        • Hi Chris,

          Along those same lines, would a stool test indicating “heavy growth” of non-pathogenic bacteria (both gram negative and positive) be in any way indicative of SIBO (especially if the patient is symptomatic)? I realize the stool tests are only reflective of bacteria in the large intestine, but couldn’t this still mean something?

          Thanks for the fantastic post!

  55. Great article, I am a methane producer, and I have been battling sibo for about 3 years. I believe I am antibiotic resistant now. So my next step is trying to starve out the bacteria by doing an elemental formula (vixonex ten) via NJ tube along with herbal antibiotics (candibactin AR and BR). In this discussion elemental formula was not covered. What are the success rates for getting rid of methane dominant sibo with this protocol? Any reply would be greatly appreciated! I’m desperate and down to my last options, I continually lose weight and fear for my life and health.

  56. Now I am totally confused. I was told I was negative for SIBO because my methane concentration barely increased from its baseline reading of 3ppm to just 4ppm after 120 minutes.

    Is the takeaway from the podcast that I am merely a “methane producer” but nevertheless one without SIBO? Or should I rethink my diagnosis and seek treatment?

    The part that has me the most confused is that in the study Chris mentioned, it sounds as if the people were treated based on their baseline levels alone. That can’t be true…can it?

    • If I remeber correctly, Dr. Siebecker says that even a baseline methane increase is considered positive. Especially if the symptoms are present, I believe.

        • I too have seen several statements that a high methane baseline level can be considered positive for SIBO even WITHOUT an increase in the subsequent breath samples. It seems logical that a high baseline reading for methane means you are a methane producer, but how is this then associated with the SI? According to the logic of breath testing (time stamps matching up to a specific part of the digestive system as the sample transits through) the SI is indicated by a certain time frame. I have not been able to find an explanation as to why the high methane seen at baseline is produced in the SI rather than the LI.

          • If I remember correctly, doesn’t high baseline mean that the archaea are high up (at the beginning of) the SI? Can’t remember if I heard that from Chris ore elsewhere.

            • The high baseline value for methane is produced by food that is ingested prior to the fasting period (a minimum of 12 hours before the breath test). Surely this food has long since passed through the SI when the baseline breath sample is taken? (Remember the baseline is taken before swallowing the glucose or lactulose sample). I’m sure there is a good reason to associate a high baseline of methane with SIBO, but that reason is certainly not clear in any of the ‘interpreting HBT results’ articles I have read.

              • Well you’re light years ahead of me in understanding the science, so this will probably be a stupid comment/question: since it’s the archaea’s consumption of food that produces the methane (and not actually the food itself), then maybe the existence of the archaea at the beginning of the SI might indicate that they continue to produce methane for a period of time even after the food has passed thru the tract? As a methane SIBO sufferer I’d really like to understand it better myself.

  57. Great article Chris,

    One question, is your treatment protocol outlined in more detail in your book?

    I have 68ppm methane baseline and have been feeling better with 2 months of low fodmap but feel awful with even a small amount of dark chocolate as a test. I’d really like to add in some of the supplements you recommend but would like more detail on dosage and timing.

    Thank you.

  58. I’m sorry if this is a stupid question, but I’ve been unable to find a direct answer to this anywhere:
    If you take the breath test and hydrogen is ~ zero, but the methane is high, does this definitively rule out SIBO? (And I guess the other question is, but does it rule in IBS?)

    My doctors say high methane and no hydrogen means no SIBO, but based on Chris’ explanation, it seems that it could actually mean that I am in fact producing hydrogen, but it’s all being consumed by the archaea, so it’s not showing up on the test.

    In my case hydrogen is 0 at baseline and all other times (except for 4 ppm at 20 min). But methane is 80 ppm at baseline and 53-74 at all other test times.

    Other than sudden onset rosacea, doctors say that I don’t fit the typical SIBO profile, ie, not bloated enough, don’t pass enough gas or have horrible breath (although I feel at times that I do). My h pylori tests (serum and stool) are negative.

    Any clarifications/insights you can provide would be very helpful.
    And thanks for this excellent podcast.

    • I would say this is definitely SIBO based on what I’ve learned from Siebecker class and SIBO symposium! I wonder what doctors are you seeing? Do you have constipation?

      • Simas thanks! It’s a functional MD who’s been thru all of the IFM courses. Constipation is not typical (I’m once a day regular) and actually more regular than I’ve ever been in my life before now. I do get occasional bouts though, often alternating with loose stools. I’ve concluded that when this happens, it’s due to consuming too much insoluble fiber at one meal, and not enough water. Maybe I’m wrong though now — maybe it’s the SIBO or maybe it’s FODMAPs which I’ve never paid attention to before. I did a long drawn out elimination diet several months ago and never found a specific food that causes allergic or distress or any other bad reactions (other than things that cause my face to heat up due to rosacea, like hot peppers or alcohol, or anything thermally warm). Does Siebacker say to avoid FODMAPs?

        • Rosacea + alternating diarrhea with constipation are very typical signs of SIBO. My guess is that your doctor is not very familiar with it.
          FODMAPs is not a condition btw, they are certain compounds in food that can be fermented by bacteria. So you may benefit symptomatically by avoiding them, but I doubt it would solve the problem. I’m not a doctor, but based on extensive reading and conferences I saw, you have most definitely have SIBO.
          Wikipedia has a nice article on SIBO, and it’s link with rosacea. Have a look http://en.wikipedia.org/wiki/Small_intestinal_bacterial_overgrowth#Proposed_link_with_Rosacea

          • Thanks Simas, that’s a great article too. See my post later in this string — I’ve actually had reactions to high FODMAPs foods as it turns out; I just never knew that FODMAPs were the common link between them before now. Yes, I knew about the strong link b/w rosacea and SIBO which is why I insisted that my doctor prescribe the test; the problem was with my doctor’s interpretation of the results.

            Interesting about metronidazole, because all the dermatologists push MetroGel or Lotion at rosacea, which I’ve found completely ineffective. The main oral that they push is Doxy in the low-dose form of Oracea, which I’ve refused to take. I don’t relish the idea, I’m not at all opposed to taking an antibiotic if I know it’s going to help with the root cause, not just the symptoms.

  59. Great podcast! Thanks for answering my question! I have also submitted another question about the various causes of SIBO that I hope could be answered someday. It’s really really interesting, because as far as I know, there’s only one established cause, which is called “post infectious IBS”. But I guess it’s not the only one, and there are other reasons for slowed motility.
    Thanks again!

Leave a Reply