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Treating SIBO, Cold Thermogenesis, and When to Take Probiotics


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In this episode, we answer more reader questions on SIBO, probiotics, Hashimoto’s, and Cold Thermogenesis.

Note: The Prescript-Assist supplements discussed in this article are no longer available (please click here to learn more about a substitute, the Daily Synbiotic from Seed), and we’ve launched a new supplement store. Click here for more information. 

In this episode, we cover:

4:12 It’s back – what Chris ate for breakfast
7:50 The most effective treatment for SIBO
18:42 Does Cold Thermogenesis really work?
22:05 What to do when the autoimmune paleo protocol doesn’t work
33:42 Why is my antibody count going up on natural thyroid hormone?
36:40 Proper carb consumption for Hashimoto’s patients
47:10 What does Chris’s daughter eat on a daily basis?
51:48 When to take probiotics

Links We Discuss:

Full Text Transcript:

Steve Wright:  Hey everyone, welcome to another episode of the Revolution Health Radio Show.  This show is brought to you by  I’m your host, Steve Wright, and you can find my work at, but we’re both here for the star of the show, integrative medical practitioner and healthy skeptic Chris Kresser, so welcome to the show, Chris.  How’s it going

Chris Kresser:  I’m doing pretty well, Steve.  How are you?

Steve Wright:  I’m doing well as well.  What’s this big news I hear about The Huffington Post?

Chris Kresser:  Well, I got a gig as a columnist or regular blogger there, which should be pretty interesting, I think.

Steve Wright:  Yeah, no big deal.  That’s a pretty major media outlet.

Chris Kresser:  Well, what I meant by ‘interesting’ is that some of you may know that Dr. Dean Ornish is the health editor at The Huffington Post, and Mark Hyman is a pretty prominent health blogger there too, and they’re both strong advocates of a plant-based diet — and I am too.  It’s just that my plant-based diet includes meat and fat in pretty substantial amounts, whereas their plant-based diet doesn’t.  And a lot of the really active commenters there and just from my — I don’t actually read The Huffington Post very much or any other health or news blog for that matter, but the few health articles I have seen there — and I’ve just scanned through the comments — they’re really heavily oriented towards a kind of vegan/vegetarian perspective.  My first article is going to be on debunking the myth that cholesterol and saturated fat cause heart disease, so I’m really curious to see what the response to that is going to be like and if I end up having the shortest tenure of any health columnist at The Huffington Post!

Steve Wright:  Well, first, Chris, I am totally shocked and just appalled that you’re not a regular reader of my blog, but I understand you’re pretty busy.

Chris Kresser:  Haha!

Steve Wright:  So, what we need to have happen here is we need to have everyone that listens to the show pay very close attention to your Twitter, your Facebook, and when this goes live, we all need to chime in with greens are the greatest delivery vehicle for butter ever.

Chris Kresser:  That’s right, butter carriers.  Yeah, I hope you guys can all come over and make your voices heard and share your experience with a paleo, higher-fat type of diet, because we’re going to be fighting an uphill battle, so to speak.

Steve Wright:  Well, there should prove to be some hilarious comments, anyway.

Chris Kresser:  Yeah.  I’m excited about it.  I mean, I do want to get this message out to a wider audience, and whatever you think about The Huffington Post, whatever your politics are, whatever you think of it as a blog, it certainly has a big audience and a wide readership, so I’m excited about that part of it for sure.

Steve Wright:  Yeah, I think it’s a great honor, and I’m excited for the first post.

Chris Kresser:  All right.  I’m not sure when it’s going to be, but I will definitely post a link to it on Facebook and Twitter and maybe even on my blog as well, at least for the first post.  I still haven’t even gotten the guidelines.  I’m not sure how often I’ll be posting there, but whenever I do, I’ll definitely post a link to it on Facebook or Twitter, so that’s the best way to stay current.  There may even be a way to follow particular bloggers on The Huffington Post — I don’t even know!  But if there is, maybe that’s worth looking into also.

Steve Wright:  And if you’re not following Chris on Facebook, you can go to, and you can also find him at

It’s Back – What Chris Ate for Breakfast

So, Chris, we’ve been receiving some feedback, and people are a little angry that I didn’t ask you a specific question on our last episode.  Listeners, it was totally my fault.  It was my bad.  Chris, what did you have for breakfast today?

Chris Kresser:  Well, I’ll have to call it brunch because I’ve still lately been on my kind of spontaneous intermittent fasting kick.  I’ve been eating around 10:30 or 11 for the first meal of the day and having a couple big meals a day and maybe a snack in between.  Today I had a couple scrambled eggs and a little bit of leftover ground beef from a dish that we made the other night and some collard greens, and here’s how I cooked the collard greens this time, and it came out really well.  I stir-fried them in a little bit of bacon grease, and then I added some chicken broth, but I also added just a little bit of this brine.  My wife and I made some pickled vegetables recently, and so we saved the brine for this kind of thing, and I added just a little bit of brine to the greens and then covered them and kind of cooked them in the broth and the brine for a while and then uncovered them and turned up the heat and kind of cooked off all the extra liquid.  They were really good.  And then I had some sort of almost-ripe plantains cooked in a blend of coconut oil and ghee that I get from Green Pasture, which is really great.  It’s not as sweet as coconut oil alone.  It’s one of my favorite cooking fats.  And then I had some homemade sauerkraut that was actually a blend of cabbage, beets, and carrots and a little bit of ginger that we make that I really like a lot.  And then I had coffee and cream when I woke up, so that was actually the first thing I had not right when I woke up but maybe an hour and a half after I woke up.  So, there it is.

Steve Wright:  That’s a diverse breakfast, er, lunch, brunch.

Chris Kresser:  Yeah, it was a fairly big meal, and I haven’t eaten since then and probably won’t eat until dinner again today.

Steve Wright:  Awesome.  Well, I think today we’re today we’re doing a Q&A episode, correct?

Chris Kresser:  We are.  Let’s do it.

Steve Wright:  OK.  Well, we have a lot of questions here.  Thanks again, everyone, for sending in your questions.  Chris, I’d like to make sure that you have your treadmill set at the right speed and the right height, and while you’re doing that, I am going to go ahead and tell everyone about Beyond Paleo.  If you’re new to the Revolution Health Radio Show, the paleo diet, if you’re coming over from The Huffington Post or you’re just interested in optimizing your health, you’re going to want to go over and check out what over 30,000 other people have already signed up for.  It’s a free 13-part email series that Chris has put together called Beyond Paleo.  Now, in these free 13 emails you’re going to learn about burning fat, boosting energy, and preventing and reversing disease without drugs.  To get this, go over to and look for the big red box.  Go ahead and put your name and email in that box, and Chris will start sending them your way.

So, Chris, you all set?

Chris Kresser:  I’m ready.

The Most Effective Treatment for SIBO

Steve Wright:  OK, so for the first question, it comes from Sheilaa.  She wants to know what is the most effective antimicrobial treatment for SIBO, which is small intestinal bacterial overgrowth, that doesn’t create dysbiosis?

Chris Kresser:  I guess the first thing I would say is if at all possible, it’s a good idea to do this under the supervision of someone who’s experienced with these kind of treatments, because even though what I’m about to describe is relatively benign compared to, let’s say, antibiotic treatment or using prescription drugs, there still are potential issues, and SIBO can be a recalcitrant, relatively difficult condition to treat, so if you do have access to someone that can guide you through this, I do recommend that.  It’s a good idea, in general, for this kind of thing.

Having said that, there are some natural antimicrobials that you can get over the counter that I’ve found to be pretty effective for SIBO and don’t contribute to dysbiosis.  In some cases, the treatment, depending on how long you have to be on it, may moderately or mildly decrease levels of beneficial bacteria in the gut, but we wouldn’t expect that effect to be anywhere near as significant as it would be if you took antibiotics, although the antibiotic that’s typically used for SIBO now, which is rifaximin, is a fairly narrow-spectrum antibiotic that doesn’t completely wipe out the gut flora like some of the broader-spectrum ones that are more systemically absorbed do.  But I always recommend starting with this more natural approach, and as I said, I’ve had really good success with it both in terms of symptom improvement and then confirming the results using follow-up lab testing.

So, one thing that can be helpful that we’ve talked about on a few different shows is Lauricidin or monolaurin.  It’s an extract of lauric acid, which has antimicrobial effects, and it’s pretty well tolerated by most people and, I think, doesn’t really tend to have a negative impact on the gut flora.  It’s pretty safe to take and even safe to take for several weeks at a time.

Another thing you want to consider in a SIBO protocol is biofilm disruption because a lot of bacteria can form biofilm, which is an extracellular matrix where they share nutrients and even DNA, and the biofilm protects the bacteria inside it from our innate immune defenses.  It’s much more difficult for us to get rid of biofilm than it is bacteria in other states.  And there are a number of different nutrients that disrupt biofilm formation.  One is lactoferrin, apolactoferrin.  I think we’ve talked about that in the context of iron chelation in the past.  Life Extension Foundation has a lactoferrin supplement.  N-acetyl-cysteine or NAC is another biofilm disruptor, and then there are certain blends out there for biofilm, like Klaire Labs has one called InterFase Plus that I use and Kirkman, which I think is a Costco brand, has Biofilm Defense, and they’re a combination of things that disrupt biofilm.  Lumbrokinase and nattokinase, which are enzymes, also have an effect on biofilm.  So, those are some options for disrupting biofilm, and that’s something that’s often left out of antimicrobial treatments, but it can really make them a lot stronger, and it tends to be one of the things that causes the greatest die-off reaction, so that’s something to be aware of.

There are many different botanicals that are antimicrobial that can be used, including cat’s claw, which also has some other beneficial effects for intestinal health.  It’s a South American medicinal that’s used traditionally for a lot of different gut issues down there.  Wormwood, goldenseal, pau d’arco, olive leaf extract, garlic, barberry, and Oregon grape.  There are many more, but those are some of the more common and readily available ones.  They can be taken individually, or they can be taken in formulas in combination.  Some of those can be fairly strong, and then there are others, like oregano oil extract, that can be so strong that I generally recommend that people only take that under the supervision of a health care practitioner because oregano oil and some of the other wild spice oils are used by the food industry as antimicrobials, and that’s how potent they are.  I mean, they could use anything they want, and they choose to use those because they’re that strong.  I’ve seen actually quite a few people who have gotten on those, you know, they were either self-medicating or prescribed them by a practitioner, and unknowingly continued to take them for an extended period of time and really had an adverse effect on their gut flora.  So, that’s something to be careful about.

Probiotics are actually a mixed bag with SIBO because SIBO often involves an overgrowth of D-lactate-producing probiotic species, and that causes a buildup of D-lactate in the gut, and a lot of the symptoms associated with SIBO are caused by that.  So, you want to avoid in many cases taking any probiotics that have D-lactate-forming species like Lactobacillus acidophilus, which is, of course, one of the most common probiotics that people take.  There’s a D-lactate-free product sold by Custom Probiotics that’s helpful.

I’ve also found soil-based organisms to be helpful when SIBO is present, and the one that I like the most right now is called Prescript-Assist, and I just added it to my store if you go to and you click on the store link in the upper right, I’m now selling it because I’ve actually had a lot of success with it myself and with my patients in my practice.  I recently learned about it.  A few months ago, I started doing some research about it.  There’s one study that was double-blind, placebo-controlled that lasted for quite a long time, especially for probiotics.  A lot of the studies are pretty short in duration.  And essentially the theory behind it is that we evolved in an environment where we were continually exposed to these soil-based organisms.  Our ancestors were not scrubbing their vegetables and fruits before they ate them.  They were taking them out of the ground and maybe wiping them off a little bit and eating them.  They weren’t buying them in the store after they had been scrubbed, and they weren’t scrubbing them themselves.  And the other thing is that the soil diversity and quality has changed a lot since the industrialization of agriculture, and so we’re just not exposed to the same number and types of soil-based organisms to the same extent that we probably were for most of our evolutionary history.  And as we’re going to discuss in a lot more detail in a later question, there’s a lot of evidence that these soil-based organisms have profound immunoregulatory effects.  In other words, we evolved with them over a long period of time, and our immune systems have a symbiotic relationship with them and function much better in their presence.  And so the soil-based organisms are a different approach than the lactic acid-forming types of probiotics, and I’ve found that they’re better tolerated in people with SIBO.  As a fairly unrelated side note, they tend to work better for constipation than a lot of other probiotics.  Oftentimes, probiotics can make constipation worse, so the soil-based organisms and Prescript-Assist, I think, is a really good choice for people with SIBO.

And then another probiotic that can be helpful with SIBO is Saccharomyces boulardii, which is a beneficial strain of yeast, and I’ve had some success with that as well.

So, there’s more to it, but that’s a really good place to start, all of those things that I just mentioned:  Lauricidin, the biofilm disruption, some of the botanicals, soil-based organisms, and Saccharomyces boulardii.

Steve Wright:  Is there anyone that should worry about taking soil-based organisms?  Is there any certain class of patients that you’ve seen that don’t seem to do well with them?

Chris Kresser:  Not yet.  There are certain people who are just very sensitive to probiotics of any type, and I suspect that that has more to do with immune dysregulation than anything else because of the way that I think probiotics are exerting their effect, which we’re going to talk about in a couple questions, but so far, the soil-based organisms are much better tolerated than the lactobacilli in most cases.

Does Cold Thermogenesis Really Work?

Steve Wright:  Interesting.  Cool stuff.  Well, let’s move on to question #2.  This one comes from Andrew.  He wants to know, Chris, what’s your take on cold thermogenesis?

Chris Kresser:  Right, so there was a big brouhaha about this a while back when Jack Kruse was recommending that people get in ice baths and submerge themselves and stay in there for a really long time.  I think that’s a really bad idea, but there is absolutely something to cold thermogenesis, and that’s been known for a long time.  For decades, it’s been something that’s used and talked about in fitness communities, and I’m sure a lot of you have a personal experience with it whether you know it or not.  For me, for example, I’m a surfer.  I grew up surfing, and I’ve been aware for a long time that spending some time in water that’s colder than what the ambient temperature is outside, I’ll feel really good after I do that, after I’ve spent an hour or two in the water.

There was a great follow-up post.  I can’t remember where I read it.  I might have been on Richard Nikoley’s site, but he linked to it and it was a really kind of evenhanded, well-referenced article about thermogenesis, and essentially the gist of it was that you don’t need to go to extreme lengths to get the benefits.  Even water temperature that’s is like 72 or 74 degrees, which most of us would say is pretty warm water, it’s lower enough than our body temperature that it’s going to have a thermogenic effect.  So, even going swimming in Hawaii, for example, could have that effect, or just turning the temperature down a little bit in your house can have that effect, or taking a walk and maybe wearing a little bit lighter clothing than you would normally wear.  So, I think there is something to it, and it is one of many tools that can be useful for weight regulation, but I don’t think you need to be really extreme about it, and I think there are definitely some downsides to being extreme about it.

Steve Wright:  Well, I know that instead of coffee I can definitely use a cold shower in the morning and I will be pretty much ready to go after that.

Chris Kresser:  Um-hum, yeah.

Steve Wright:  There’s something to the — what is it, the endorphin release?

Chris Kresser:  Is that the way it feels for you?

Steve Wright:  That’s what it feels like to me.

Chris Kresser:  Yeah, there are a lot of different physiological effects of it, and so it’s a little hard to answer the question.  It depends somewhat on why you’re asking.  I mean, a lot of times when people ask about it, they’re talking about weight regulation.

Steve Wright:  Right, right, and I was just commenting on cold showers.

Chris Kresser:  Haha, right.

Steve Wright:  And we’ll leave it at that, Chris.

Chris Kresser:  No comment.

What to Do When the Autoimmune Paleo Protocol Doesn’t Work

Steve Wright:  We’ll leave it at that.  We’re going to move on to question #3 from Bobbi:  “What to do next when after six months of autoimmune paleo eating doesn’t work for chronic fatigue and fibromyalgia?”

Chris Kresser:  Yeah, that’s a good question.  Diet is always a great starting place, of course, but as I’ve said many times, it’s not necessarily magic.  I mean, it can’t solve all problems.  With autoimmune disease, it’s just a really fascinating topic, and it’s a really active area of research, and believe it or not, there’s really no consensus on what causes autoimmune disease, and identifying the underlying cause of a problem is always the most important step in figuring out how to treat it.  My take on autoimmunity is that it’s multifactorial and there’s more than one cause, as is the case with most diseases.  But I think infection is probably one of the main causes of autoimmunity, and it could be an infection that comes and goes and it’s sufficient to dysregulate the immune system and throw it out of balance and create an autoimmune condition, or it could be an ongoing infection that has been misdiagnosed as an autoimmune disease.  There is plenty of evidence behind both of those theories and a lot of attention there.  We had Dr. Fasano on the show a while back, and he has written and spoken about a theory of autoimmune disease which holds that you have to have leaky gut to develop autoimmune disease, that it’s a precondition to developing autoimmune disease.  You need a genetic predisposition, but you also need intestinal permeability, and the inflammatory cytokines that get produced in that intestinal permeability and the immune attack against substances that make their way through the intestinal barrier is part of what initiates the whole process of autoimmune disease, so focusing on gut health is another key thing to do when you have autoimmune disease.

I think those two things would be where I would put my attention.  If you came to see me in the clinic, I would be looking for any evidence of infection, like a chronic viral infection — viral infections seem to be particularly associated with autoimmune disease — or bacterial infections, particularly intracellular bacterial infections like Chlamydia pneumoniae, and then I would be paying a lot of attention to gut, so are there any gut pathogens like parasites or fungal infections or opportunistic or pathogenic bacteria?  Is SIBO present, which we were just talking about?  Is the gut permeable?  In that case, I might even do a test for gut permeability.  So, doing all of those things, trying to figure out if there is some underlying cause that hasn’t been identified, that’s definitely step one.

But let’s say you that and nothing is there.  Your gut is perfectly fine, and you can’t find any evidence of infection.  With fibromyalgia in particular, I’ve read some pretty interesting research recently on the use of low-dose naltrexone in fibromyalgia, which we’ve talked about before, and the theory is really interesting.  Endorphins, which you just mentioned, Steve, in your cold shower story, they play a significant role in pain perception, and studies have shown that beta-endorphin levels are lower in patients with fibromyalgia, and then other studies have shown that met-enkephalin and dynorphin, which are two other endorphins, are elevated, which suggests that there’s some kind of abnormality in the endogenous opioid system.  And this could actually lead to a desensitization of opioid receptors, in other words, opioid resistance.  So just like in insulin resistance and even cortisol resistance, which we talked about before, there is plenty or hormone — or in this case, opioids — but the receptors are not being stimulated by them.  They’re not listening, so to speak, and so what you get then are symptoms of opioid deficiency and a decreased inhibition of substance P, which is an important neuropeptide or neurotransmitter in pain perception, so if you have increased substance P levels, you’ll have increased perception of pain.  And so, what low-dose naltrexone does is it temporarily blockades the opioid receptors, and that causes an increase in production of opioids, and it also causes an increase in the expression of opioid receptors.  So, the net effect of all of that is an increase in opiate activity, and that then, in theory, because of the changes that have been observed in opioid levels in fibromyalgia patients, that’s why low-dose naltrexone can be helpful in those situations.

So far, there haven’t been any big studies.  There have been some smaller pilot trials.  One trial, I remember, was 10 patients and there was a 30% reduction in symptoms.  And then there are a few case reports where the results were even more dramatic, like total remission after a month of taking low-dose naltrexone.  So, more research definitely needs to be done there, but LDN, which is the acronym we use for that, is a very safe medication because it’s such a low dose, it’s really well tolerated, it’s cheap, it’s off patent, and you know, my philosophy in terms of treatment is whatever works and causes the least harm.  Usually that’s not a drug, but there are times where a drug does fit that criteria or a drug is the best choice according to that guideline, and I don’t know that that’s the case for LDN in fibromyalgia yet, but it’s something that I would consider if all of these other things have been ruled out, like gut dysfunction, chronic infection.  Of course, addressing diet comes first, which the questioner has already done here.  Adrenal function is something else you’d want to pay a lot of attention to because low cortisol levels or dysregulated cortisol levels can cause muscle fatigue and a lot of symptoms that are reminiscent of fibromyalgia.  I’d want to make sure that micronutrient status was adequate and there weren’t any significant deficiencies, so there’s a lot of work to be done before I would even get to the point of considering low-dose naltrexone, but I think it is worth consideration if all that work has been done.

And then there are some other things to consider that are kind of out there too and are maybe a few years away in terms of their availability, but one would be fecal bacteriotherapy, because if there is a strong connection between the gut microbiome and immune system, which the research certainly suggests, then fecal bacteriotherapy could be a really powerful way of modulating the immune response, and I think there is almost certainly some kind of immune dysregulation going on in both chronic fatigue syndrome and fibromyalgia.  I think in the next 10 years we’re going to start seeing fecal bacteriotherapy becoming available for conditions other than C. difficile, which is what it’s primarily used for right now.  Already some doctors are more progressive in how they use it.  They’re starting to use it more for inflammatory bowel disease and even IBS, but I haven’t yet seen it used for autoimmune conditions other than inflammatory bowel disease, but I think it will be at some point.

And another promising treatment along those same lines is helminthic therapy, and I won’t say too much about this now because we’re going to talk about it in detail on one of the next questions, but this will sound totally bizarre to some of you who haven’t heard of this yet, but this is actually introducing worms, either whipworms or hookworms, into the gut in order to get an immune-regulating benefit from these organisms.  And if you’re scratching your head and wondering how that works, we’re going to talk about it in a lot more detail, but this therapy is available in Europe. There have been a lot of interesting studies done on it.  It has been used for ulcerative colitis and Crohn’s disease.  They actually give patients pig whipworm, Trichuris suis, and it’s remarkably effective in some cases.  I think the remission rate in one of the studies for Crohn’s disease was about 70%.  I may be wrong.  I’m just going from memory there, but pretty incredibly effective.  So I think that’s a therapy that we’re going to see a lot more of in the future, and in fact, it’s not preposterous to imagine that at some point people might go to the doctor and get inoculated with hookworm or a similar organism in the same way that people get vaccination now.

Steve Wright:  We’ll obviously hear more about that in a little bit, but I wanted to circle back to a few ideas that you hit on in that answer.  One would be that — just throwing in my two cents here — but something that they could do on the cheap and easy right now would be to definitely do a 24-hour cortisol panel and definitely check what’s going on with the hormones and the adrenal system because they might be able to get to some short-term relief there on the energy front.  And then the other thing is that actually I have a PR Newswire article here from January 8, 2013, where TNI BioTech has exclusively picked up the rights to LDN, so hopefully as we go forward, they don’t try to take over the market and jack prices up on us.

Chris Kresser:  Yeah.  Can you send that to me?  I don’t even understand how that’s possible.  I mean, it’s a low dose of a medication called naltrexone, so how could they — That sounds strange to me.  Definitely send that to me, Steve.  I’d love to see it.

Steve Wright:  Yeah, I’ll send that over, so just a couple newsworthy pieces there.

Chris Kresser:  Yeah.  Let’s see.  What’s next here?

Why Is My Antibody Count Going up on Natural Thyroid Hormone?

Steve Wright:  All right, this next question comes from Alicia.  She asks:  “I have Hashimoto’s.  Why is my immune system now attacking itself even more despite being on natural thyroid and following a gluten-free, soy-free, dairy-free diet?  My antibodies were 272 at diagnosis, and it’s three months later, and I’m trying two NTH replacements and they went up to approximately 1300.”

Chris Kresser:  NTH being natural thyroid hormone, for anyone who got lost in the acronym soup.  So here’s one possibility:  There are different arms of the immune system.  There’s the Th1 side and the Th2 side, and the Th2 side is the one that’s responsible for antibody production.  Some autoimmune diseases can be Th1 dominant, and others are Th2 dominant.  If an autoimmune disease is Th1 dominant and the Th2 side of the immune system is suppressed, it’s conceivable that antibody production would be reduced, and if the immune system improves and things kind of balance out and the Th2 suppression decreases, then it’s possible that antibody production would actually increase in those circumstances, and that wouldn’t necessarily reflect a problem.  It would actually reflect an improvement that was happening in the immune system.

So, I guess I would ask what the other symptoms are.  If she’s feeling better and doing better in every other way and the only thing that’s happening is the antibodies are going up, I wouldn’t worry too much about that necessarily, and it’s possible that they’ll go back down as time progresses.  But if the whole picture is getting worse, you know, like the antibodies are going up and your symptoms are getting worse, then I would actually think that the autoimmune condition is getting worse, so it really depends on that distinction there.  And if the whole condition is worsening, then I would suspect there’s something else going on that’s aggravating things that’s not related to diet, and some of the same things we talked about in the last question would apply here.

Steve Wright:  So how long do you think she should wait before getting those retested?

Chris Kresser:  If she’s feeling better in general and the symptoms are getting more and more under control, maybe wait another three months or something.  If she’s getting worse, then I think the testing should be more focused on what’s causing further immune dysregulation in spite of a healthy diet.

Proper Carb Consumption for Hashimoto’s Patients

Steve Wright:  Gotcha.  OK.  Well, this next one is sort of a follow-up question to this first question, and it comes from Jill.  She asks:  “Also on Hashimoto’s, can one ever get off thyroid meds?  There are differing opinions on carb consumption and Hashimoto’s (some like moderate, some like low, some like high).  What’s your opinion?”

Chris Kresser:  My opinion is that it’s completely dependent on the individual.  I mean, I think we’ve talked and I’ve written about the potential issues with a very low-carbohydrate diet and thyroid conditions because some insulin is required to convert T4 into T3, which is the active form of thyroid hormone.  If you’re on a really low-carbohydrate diet, then your insulin levels will be chronically low, which is not necessarily a bad thing in the context of blood sugar regulation and things like that, but insulin actually has plenty of beneficial effects.  It has kind of been labeled as a bad hormone in a similar way that cholesterol has been labeled as bad, but the truth is that insulin plays a lot of important roles in the body, and of course, all you have to do is look at type 1 diabetes to see what kind of problems can happen when you don’t have enough insulin.  There are a lot of studies that show that people who are fasting or people who are on very low-carbohydrate diets have lower levels of T3, and there’s some controversy about the significance of that, but in my practice I would say in general, people with thyroid issues do better on a moderate-carbohydrate diet than a low-carb diet.  However, there are always exceptions to these kinds of rules, and I do have some patients that do just fine on a low-carb diet and don’t seem to experience any decline in thyroid function.  And then I have patients on the other end of the spectrum who need actually quite a high-carbohydrate diet to feel like they function well with thyroid issues.

Steve Wright:  Chris, just because I hate low-carb and high-carb because they’re really totally contextual, what are you saying?  Is low-carb to you anything under 150 g roughly a day?  What are kind of your markers?

Chris Kresser:  I would call low-carb under 100 g, and I would call very low-carb under 50 g.  And when I speak about carbohydrates, I’m only talking about carbohydrates from starch and fruit.  I kind of agree with Paul Jaminet on that.  I just don’t think that carbohydrates from non-starchy vegetables really contribute much to carbohydrate load because you have to expend some glucose to digest them, and so the net intake of glucose is probably very low with something like broccoli.  So yeah, when I say very low-carb, it’s below 50 g, and when we’re talking about the effects of very low-carb diets on thyroid, that’s primarily what I’m talking about.  There are studies, though, that show that increasing carbs above 100 g or even 200 g continues to increase the production of T3 and reduce the production of reverse T3, which is the kind of dead-end, decoy form of T3 that blocks the thyroid receptors and doesn’t perform all of the beneficial functions of T3.

So I guess I could sum this up by saying the only way to really find out is to experiment.  You have to try different macronutrient ratios, try a period of time where you’re eating a higher-carbohydrate diet, try a period of time where you’re eating a lower-carbohydrate diet.  Be aware, though, that low carb might work for a period of time, but then after a while and after the effects become prolonged, then you can start to experience some symptoms, and that’s often what happens with people.  It’s pretty common for me to see someone who comes to my practice and they have some variation of this story.  They say:  I switched to paleo.  It was amazing.  I lost all this weight.  I had more energy than I’ve had in a long time, just felt so much better.  And then I say:  OK, so when you say “paleo,” tell me more about how much carbohydrate you’re eating.  Then they go into detail and it becomes clear that they’ve been doing a very low-carb paleo.  You know, the full extent of their carbohydrate intake is maybe a quarter cup of blueberries a day or something, so that I would consider to be a really very low-carb diet.  And then after a while, their energy starts to drop, they start to develop insomnia, their hair starts to fall out, they get cold hands and feet, they start to develop a number of symptoms, and then they call me.  That’s a very typical kind of presentation that I see a lot.  So, I do think it’s an issue, but I think that it’s very individual, and the only way to really find out is to experiment.

Steve Wright:  OK, Chris, let’s not gloss over the first question there.  Have you ever seen any of your patients or do you know of people who actually get off their thyroid meds while they have Hashimoto’s?

Chris Kresser:  It depends, again.  I know people are probably tired of hearing me say that, but that is really how it is.  Some people might not know what actually happens with Hashimoto’s, so let me explain that because it’s relevant to this question.  Hashimoto’s is an autoimmune disease where the body attacks the thyroid gland and destroys tissue progressively over time if it’s not treated.  And this is actually one of the problems with conventional treatment of hypothyroidism.  If someone goes in to the doctor and their TSH is high and their T4 or T3 is low, usually the doctor is just going to put them on thyroid hormone replacement medication without doing any testing to determine if they have Hashimoto’s.  And the fact that they get put on thyroid replacement medication isn’t necessarily the problem, because sometimes that is necessary, but the issue is that the underlying cause is not being addressed, which in this case is the immune system attacking the thyroid.  So, the person will likely need to take a higher and higher dose of thyroid hormone and even switch to different kinds of thyroid hormone as they progress because the immune attack is just going without being addressed and more and more thyroid tissue is being destroyed, and thyroid tissue is where thyroid hormone is produced.

This is also a common story, and I’m sure many of you listening to this might be able to relate, where first you start out with a certain dose of Synthroid, and then you have to take more Synthroid, and then Synthroid stops working altogether, and so you switch over to Armour and you feel a little bit better on Armour at first, but then you have to take more Armour, and then the dose of Armour that you have to take to maintain your thyroid function starts causing other side effects like insomnia and anxiety.  The problem there in many cases is that the immune dysfunction has never been even identified, much less addressed.

If you catch Hashimoto’s early before much tissue has been destroyed and you’re able to intervene and stop or mitigate the tissue destruction by regulating the immune system, then I do think it’s possible to not take thyroid hormone.  But if you catch Hashimoto’s after it’s been going for several years and after a significant amount of tissue has been destroyed, then the capacity to produce thyroid hormone in that situation might be permanently impaired.  And even if you, at that point, regulate the immune system and bring things back into balance, you just might have not enough tissue or capacity to produce the amount of thyroid hormone that you need to function well.  So, in those cases, I think thyroid hormone probably is necessary and that the goal should just to be to continue to regulate the immune system and minimize the dose that you need.  I often will have patients come to me, and they’ll be on a particular dose of thyroid medication, and when we start regulating their immune system, I’ll always warn them and say:  Look, you might start to feel hyperthyroid.  As we adjust your immune system, the dose that you’ve needed up until now will be too much, and you’ll have to talk to your doctor about decreasing the dose.  So, in those cases, just minimizing the dose of medication that’s required is the goal, not necessarily getting off of it.

Steve Wright:  OK, great.

Chris Kresser:  One more thing about that.  I mentioned before whatever works and causes the least harm.  In this case, when you’ve lost the capacity to produce thyroid hormone, thyroid hormone is so important, you know, every single cell in the body basically is affected by thyroid hormone, so it’s really, really crucial, and going without enough thyroid hormone, I would argue, is more problematic and dangerous than any potential side effects of thyroid hormone replacement over the long term.

What Does Chris’s Daughter Eat on a Daily Basis?

Steve Wright:  That’s great news to know.  This next question comes from Davidrei:  “In the spirit of The Healthy Baby Code, what is your daughter’s day of eating like?”

Chris Kresser:  Well, it varies quite a bit, but she basically eats what we eat, what we have around.  One thing that really just makes me scratch my head is this concept of “baby food.”

Steve Wright:  How old is Sylvie?

Chris Kresser:  Sylvie is 19 months now, so yeah, obviously it does depend on what stage they’re at, but pretty much from the beginning she has eaten what we’ve eaten.  And early on, we had to maybe chew up some of the stuff before we fed it to her because she just wasn’t able to process it in the same way.  Let me think about today.  So, today we woke up, went on a walk together, which we often do, and came back, and she was hungry so I gave her some of the same ground beef that I had from my lunch that was left over.  It has some broth and some carrots and a little bit of tomato in it and some chopped-up liver in there.  And with that, she had some sauerkraut, which she absolutely loves, and some blueberries, so that was her breakfast.  Then when I ate, she was hungry again.  She’s eating a lot right now, so she had basically a little bit of everything that I had.  So, she had some eggs, which she loves, and she eats greens if there’s enough fat on them.

Steve Wright:  Haha.

Chris Kresser:  She had some of the greens, and she likes plantains now.  She didn’t at first.  In fact, she really didn’t like any starch or much carbohydrate other than berries, but now she’s enjoying some starches more.  Plantain is one that she likes.  And I’m not sure what else she’s had because I haven’t seen her since 10:30 or 11 and it’s like 2:30 right now.  But she has probably eaten again, and then she’ll have dinner probably around 5:30 this evening, and we’ll just give her either something that we’re cooking for ourselves tonight, or another common meal that we feed her is salmon.  She loves salmon.  We’ll either give her salmon that we’ve cooked recently and left over, or we give her Vital Choice canned salmon, which is really yummy and one of my favorites.  And maybe some broccoli with butter on it and some bone broth with some vegetables in it, or if she’s not having salmon, we might give her some bone broth with chicken or something like that.  So it’s mostly meat, fish, fruit, vegetables, some starch, although she’s just really not that crazy about it yet.  Like for example, she’ll eat some potatoes if they’re in broth.  And she likes taro chips when we make taro chips.  Sometimes she’ll eat a little bit of yuca, but not really crazy about starch right now.

Steve Wright:  All right.  It sounds like she eats pretty well.

Chris Kresser:  I think so, and she loves the food she eats.  It’s kind of crazy when her friends come over and they have all kinds of crackers and cookies and things like that.  And I imagine Sylvie will show interest in those things at some point, and I’m not too worried about it because she eats so well.  I just don’t think it’s going to be an issue for her.  But really she loves the food she eats and is satisfied, and she’s at the 80th to 90th percentile for height for her age, and I think the 75th percentile for weight.  She’s super healthy.  When you provide the right raw material, the body does the rest.

Steve Wright:  That’s pretty powerful right there.  Do we have time for one more?

Chris Kresser:  Yeah, is this the probiotics question?

Steve Wright:  It is.

Chris Kresser:  Yeah, this will be a longer answer, so we might go a little over than normal time, but we have to answer this because I referred to it about four times in an earlier question.

Steve Wright:  Foreshadowing.  Dang it.

Chris Kresser:  Let’s do it.

When to Take Probiotics

Steve Wright:  All right.  This comes in from Jessica.  She wants to know more on probiotics, Chris.  “When are they a good idea?  Do they facilitate healthy endemic microbiota populations or compete?  How effective are they for dysbiosis or recolonization after loss of microbes?”

Chris Kresser:  All right.  Well, this is a fascinating question.  In fact, to some extent, this will be the topic of my presentation at the Ancestral Health Symposium this year.  I’m going to answer this in a way that’s maybe not obviously or directly related to the initial question to start with, but you’ll see how it all ties together.  I think at this point that probiotic bacteria should really be mostly considered as old friends.  And I’ll say more about that.  We coevolved with certain organisms like worms, which I mentioned previously, cowshed microbes like saprophytes and soil-based organisms and microbes that you would tend to encounter amongst animals on the farm more recently, and then lactobacilli and fecal bacteria.  And they helped shape our immune system and the development of our immune system, and we have a symbiotic relationship with all of these microorganisms.

There’s a great quote from a book called An Epidemic of Absence, which I highly recommend if you’re interested in this subject, and the quote is that:  “It is now widely appreciated that humans did not evolve as a single species, but rather that humans and the microbiomes associated with us have co-evolved as a ‘super-organism,’ and that our evolution as a species and the evolution of our associated microbiomes have always been intertwined,” and that’s from the beginning of one of the chapters in the book.  It’s from a physician or researcher named William Parker from Duke University.  So, what this means is that our immune system probably evolved in part as an adaptation to the microorganisms that we were hosting for millions of years and more importantly that our immune system may not be able to function optimally without the presence of these microorganisms.  That’s the weirdest thing to get your head around because in the modern kind of sanitary conditions we’ve done everything we possibly can to eradicate these organisms from our systems, and now we’re learning that eradicating these organisms might have profound impacts that we didn’t really foresee.

The old friends hypothesis is the idea that the increase in inflammatory disorders and autoimmune disease that we’ve witnessed over the past several decades is caused by a lack of exposure to these microorganisms that we evolved with.  And when the normal background levels of immunoregulation that these organisms provide is taken away, our immune system goes haywire and starts to attack itself.  One analogy or way of understanding this would be if you’re standing and facing someone, let’s say, standing up, two people facing each other, and you put your hands up and you press against each other’s hands and you lean into each other, if you’re using the same amount of pressure, you’re going to both be kind of standing in a balanced way.  But what happens if the person you’re doing this with all of a sudden steps away?  You’re going to fall down on your face.  It’s kind of a crude analogy, but these microorganisms provide a background level of immunoregulation or something that our immune system is kind of continually in a state of dynamic tension with.  Our immune system has been tuned for millions of years to work in that dynamic tension against those organisms, and if you take them away, then that energy that the immune system uses to fight those organisms will be directed at self-tissue in some cases if there’s a genetic predisposition to that. So, this is actually one of the most exciting and popular and well-supported theories on what causes autoimmune disease at this point, and it explains a lot of the apparently contradictory observations that have been made epidemiologically with autoimmune disease.  For example, we’ve known for a long time that people in developing countries have far lower rates of autoimmune disease than people in developed countries.  Early on, one theory was that that was more related to latitude and vitamin D and since more developed countries are in northern latitudes with lower exposure to vitamin D, but then they found some groups of people — For example, there’s a group of, I think, Finnish people.  There’s a town or an area where on one side is a highly developed industrialized culture, modern culture with really sanitary conditions in Finland, and on the other side of the border, just a few miles away, is a group of people in Russia, and it’s far less developed and far less sanitary so that they have the same genes but the incidence of asthma and allergies is way, way less on the Russian side that’s poorly developed and has the less sanitary conditions, and the kids there are more likely to have hookworm or whipworm and other parasites, and they’re also more likely to be exposed to saprophytes and other mycobacteria.  So, that kind of threw out the latitude theory because there was a difference even at the same latitude in people with the same genetics.  But when you see a country developing better sanitation, then you see the rates of autoimmune disease start to go up.

In fact, even in the US up until about 100 or 150 years ago, most people still had hookworm and were carrying some of these other organisms, and incidentally, H. pylori is one that might have some of these beneficial immunoregulatory effects, and that’s one of the reasons that I’ve mentioned before that it’s not so black or white with H. pylori as we learn more about the old friends hypothesis and the beneficial impact that some of these microbes can have.  It becomes a little bit more of a gray area in terms of knowing what to do when these organisms are present.  And this theory also explains why asthma rates, I think, are lower in kids who live on farms, for example, and why kids who drink raw milk have lower rates of asthma and allergies than kids who drink pasteurized milk because some of the microorganisms in raw milk can have this immunoregulatory effect.

So, I think that there is probably more than one mechanism for how probiotics work, but I think that perhaps the main way that they work is through this kind of “old friends” effect, by stimulating immunoregulatory mechanisms and activating these ancient pathways that have been part of our physiology long before we were human, that probably originated with the emergence of mammals, which was a really long time ago.  The idea that taking probiotics is simply about replenishing gut flora and just kind of adding bacteria to the tank, so to speak, is probably overly simplistic.  There may be some truth to that, I think there is some truth to that, but it may be a smaller contribution than the immune-tuning effects that the bacteria have.

I hope that answered the question to some degree.  In terms of recolonization, I think prebiotics actually may be more effective because they’re selectively stimulating the growth of the flora that are present, and particularly growth of flora in the large intestine, which is where most of the flora is.  So, prebiotics and soluble fibers and fermentable fibers may be more effective at actually increasing the number of beneficial bacteria in the gut, whereas probiotics may have a more potent immunoregulatory effect.  And I’ve also seen some studies that suggest that probiotics, because of their immunoregulatory effect, they cause changes that predispose us to having a better balance of bacteria in the gut, so kind of indirectly they do lead to recolonization.

Steve Wright:  Do you consider probiotics just coming out of pills, or do you consider them coming from all fermented foods?

Chris Kresser:  Yeah, anything that has bacteria in it would have this effect.

Steve Wright:  OK.  So, then when she asked when would it be a good idea, would you be arguing that every day for everyone getting some of this in your life is probably generally a good rule at this point in time in the research?

Chris Kresser:  Yeah, I think that’s probably wise, and I think that we were exposed to that for most of our evolutionary history.  Refrigeration is ubiquitous now.  Most of us, at least, have the capacity to store foods in the refrigerator, but that’s a relatively recent development, and most of our ancestors didn’t have that opportunity, so they would probably ferment foods to store them, and they probably ate foods even sometimes that were spoiled.  So yeah, I think our exposure to these “old friends” is much less than it used to be, and I think increasing our exposure to them is probably a really good thing we can do for health.  And just like I was talking about with probiotics, the reason that fermented foods are beneficial may be more related to this than just the kind of mechanical replacement of bacteria.

Steve Wright:  It’s fascinating.  I’m going to have to check out that book that you mentioned.  Great question.  I’m looking forward to seeing that presentation at PaleoFX.

Chris Kresser:  I’m looking forward to doing it.  It’ll be a lot of fun to put together.

Steve Wright:  All right.  Well, that wraps up this episode, Chris.

Chris Kresser:  Yeah, it was a lot of fun.  I enjoyed it.

Steve Wright:  We got a lot of questions from the listeners.  Thanks again for sending those in.  Please keep sending us your questions at using the podcast submission link, and if you enjoyed the show, please head over to iTunes and you can leave us a review there.  I think that’s all for now.  Right, Chris?

Chris Kresser:  I think that’s it.  Just a heads-up, I may be away and unable to record the next show.  I’m not sure yet.  I’m still working that out.  So, if we miss a week, that’s what’s happening, and we’ll be back with the regularly scheduled programming the next week.

Steve Wright:  All right, thanks.  Thanks everyone for listening.


Join the conversation

  1. Just wondering which starches i can eat while treating sibo?? I know gaps is listed to follow but beans arent paleo and that seems to be the only starch allowed….I cant go low starch or I start having thyroid problems.TIA

    • In my experience, and based on the work of Dr. Norman Robillard (the Fast Tract Diet), jasmine rice is the safest starch to start with because it’s absorbed very quickly and therefore is unlikely to feed your SIBO. Start with small amounts (¼ serving) in each meal and gauge your reaction, gradually moving to larger servings and other low-FODMAP starches as you tolerate them. Resistant starches may also be helpful, but again, start small (½ tsp. unmodified potato starch) and back off if it causes a worsening of symptoms.

  2. Just to clarify: when treating sibo, if the types of bacteria in the probiotic supplement are different than the types of bacteria that have overgrown in the small intestine, will that probiotic supplement have antimicrobial action against the sibo? And second, if the probiotic does have antimicrobial activity, will it kill off the current bacteria and then recolonize the small intestine itself? Does this last part hinge on there being any causal factor to the sibo, like motility disorder, autoimmunity, etc?

    • It’s worth mentioning that certain commensal bacteria are transients. L. Plantarum, for instance, is known to kick some butt, and it’s a fantastic commensal. But, it tends to only hang around for a few days and then departs. So, I would imagine that it helps de-colonize the SI over time. It’s hard to ever go wrong with L. Plantarum and the foods that it tends to be found in (if tolerated). Check it out.

  3. hi..let me tell u my symptoms first :
    diarrhea, acid reflux, skin problem, anal fissure, pain at pelvic area on and off, flank area on and off, pain at the left n right abdomen (on and off) , mucus in stool, indigestion.gas, bad breath.
    i’ ve met specialist, he diagnosed I have Ibs, he only did colonoscopy, we didn’t analysis stool, breath, urine, blood and etc… I consumed all the medicine he gave, but after 3 days consumed those medicine, my symptoms get worsen..vomits, very frequent diarhhea, gas, headache, fatigue, lack of water.. after that I stop took those medicine.. and about the my pelvic pain, urine test showed its clean.also my blood means my kidney healthy right? I’m really mad to the doc.. he wasted my money, all those medicine is quite expensive, im only a student! ever since, i never believe to doc.. I did research by my own, i really think I have SIBO.. I consumed supplements; peppermint-ginger plus shaklee, energizing soy product esp shaklee, my symptoms improved.. but till now, i still having skin problem, diarhhea had stopped, but sometimes constipate ( on and off ), sometimes I got anal fissure. I was about to take natural remedies to cure it like apple cider is ok? please still studying.. I’m dying everyday.. I suspected my SIBO because of food poisoning untreated well 4 month ago.. and i never have ellergy before, i can tolerate all kind of food..i also have g6pd deficiency..what shoud I do ? sorry for bad grammar

  4. Hello, does anyone (especially Chris Kresser!) have any thoughts on the safety of EDTA in Interfase Plus and how long one can safely be on Interfase Plus?
    Thank you for your thoughts!

  5. “like Klaire Labs has one called InterFase Plus that I use and Kirkman, which I think is a Costco brand,”

    Um NO!!!

    Kirkman is not Kirkland

    You’ve been seeing Amazon Typos. I do like your articles though… seem to be doing things very right as you are all over Google on a lot of Health Topics I research. Someday I’ll know half as much as you… and that will have to do 🙂

    Found this one by searching Kirkman Defense vs Klaire Interfase in Google.


    • Hi Tyler – I saw your update & question and wanted to respond. My husband was doing well last summer but he was then in 2 car accidents in August and Sept (he’s okay – a deer totaled our car and a driver hit us from behind) and he flared with the stress. Beginning in January, we tried 2 new things. While he continued on the AIP diet, we also took out FODMAPS and saw HUGE results. His psoriasis has almost completely cleared over the past 2 months and his bowel issues (which he had 90% of the time) disappeared (except once on my son’s birthday when he ate a GF muffin that had sugar/grains in it). He is going to slowly try FODMAPS one at a time – we think coconut is a big culprit (he was drinking tons of coconut milk each day). We also added in a glutathione/SOC product at the same time called Oxicell. He’s been doing that along with Pure Encapsulations Caprylic Acid and their Nutrient 950 with K. Also taking Prescript Assist, l-glutamine and digestive enzymes by NOW. And he’s in ketosis most of the time just due to the nature of his diet (meat/fish, green veges and lard/ghee/olive oil).

      So it’s hard to say what is making the biggest impact but we think it’s the removal of fodmaps based on the dramatic improvement with his digestion.

      He was covered on 95% of his body and since he’s doing so well (maybe 5%? His plaques on knees haven’t totally healed but are 75% better) we don’t want to change anything, but if he does flare again, we are going to look at doing Interface Plus (biofilm) and Lauricidin. There is definitely a yeast/fungal connection in my husband’s case. And testing at our chiropractor showed that his liver is very congested (doesn’t detox well – that’s why we added in the Oxicell – I’d look into that product. It’s formulated by an MD who specializes in AI diseases and has been recommended by alot of professionals includuing Nora Gedgaudus – I originally found info on her site).

      I wish you all the best – I know this is a long, tough journey!

      • wow, where to begin. thanks for all the good stuff in your email; it was chalked full of resources and ideas. here’s my deal, so you know a little of my back story: i’m a 42 year-old male, 168 lbs, fairly lean, so weight isn’t the issue. i first started having swollen hands and feet in my late 20’s after a period of much stress. over most of my life i ate poorly, a lot of processed foods, sugary snacks, etc. but on and off over the years made attempts at eating better, but always fell back into my poor habits. after officially being diagnosed with psoriatic arthritis around 2001, and other NSAIDs and methotrxate not doing the trick, my rheumatologist gave me enbrel in 2002; that seemed to be a miracle drug, i went from barely functioning to playing tennis and mountain biking a few months later. so over the years i functioned pretty decently, with slight ups and downs. my psoriasis was always minor; a few patches on my knees and legs, etc. but it seemed to start creeping a little the past couple years, so my dr. recommended trying humira in 2011/2012, and by summer of 2012 i noticed that for the first time in 10 years my skin was completely clear. but then came june of 2013 and getting lymes disease (to this day i do not know where the tick came from; i hadn’t been in the woods or anything for weeks before i found a bulls-eye rash in my armpit. the scary thing is i never saw it so i worry that it could be in the house somewhere. i live in the city suburbs in upstate NY, so not a woodsy area, for sure.) i took doxycyclene for 3 weeks so i nipped it in the budd, hopefully. but in august i began getting roving muscle and tendon pain (knee, shoulder, and especially jaw pain, along with fatigue. my doc said it’s prob just recovering from lymes and that it’ll take some time. by october the pain and inflammation in my hands and feet and elsewhere got so bad i asked for something stronger, my rheumy gave me prednisone, it worked wonders but when i finished i started to feel bad again. so i did one more round of the 6 day taper, and it seemed to keep the pain at bay, sometimes better, sometimes a little worse, but bearable. but one thing i noticed, and my dermatologist confirmed when i saw him 2 days ago, was that prednisone causes a rebound affect with psoriasis after finishing it. so on top of my arthritis, my psoriasis has gotten a lot worse: upper arms, back front a little, and esp legs(thank god not on the head or face, at least so far.) but one thing i noticed is it gets worse with certain foods or drinks such as beer or fermented foods like kimchi.
        and that leads me to your husband’s situation. how did you suspect there is a fungal connection, and how did you find out that he doesn’t tolerate fermented foods (is this where the histamine intolerance comes in?) i came across a show called know the cause with doug kauffmann, and his whole shtick is fungus, everything is caused by it; and they had an episode about fungus being the root cause of psoriasis. so that’s when i started searching my favorite blogs, like chis kresser, for this connection, and that’s when i found your posts. for years i suspected candida because of the amount of sugar and baked goods i used to consume (don’t judge) and that it was playing a role with my ill health. but since going through this flareup, or whatever it is, last summer/fall, i notice how horrible i feel when having anything like beer with yeast in it (tired, headaches, feeling in my gut like i’ve been mildly poisoned). i’ve started to realize how messed up my gut is and that i better heal it, so i’ve been gluten-free since novemeber, and for a while i felt better but have been backsliding for the past few weeks. i’ve been taking prescript assist probiotics that chris kresser recommended, but to be honest it seems to make me feel a little yucky (tight in the stomach, horrible smelling gas [sorry, TMI] and i swear my fingers feel more puffy). so i went from 2 a day to one and same symptoms but more tolerable. i’ve been trying to consume a lot of fermented foods because i know they’re very good for you, but i swear it makes my fingers more puffy and worsen the gas. fodmaps might play a role as well, i notice certain fruits cause a lot of bowel issues.
        i’m starting to ramble and cannot believe i’ve gone on like this to a complete stranger for all to see in the forum, but basically i’m curious about a few things that you mentioned about your husband’s situation: how does zinc play a role, and does he take supplements? how come bone broth aggravates his symptoms (since starting a quasi-paleo diet last fall i haven’t gotten around to trying the bone broth yet, but i’ve heard it’s supposed to be excellent for the gut)? has your husband followed dr. heng’s protocol to the T? because i don’t think i’d be quite prepared to try such an extreme protocol unless my psoriasis got a lot worse. how did he fare with the diflucan? i got my dermatologist to write me a script for a 100mg pill/daily for 2 weeks; i was really surprised he went with my fungus connection because he’s very conventional. but i haven’t taken the diflucan for fear that it’ll make me feel very sick, but i want to see if it helps my skin then i’ll know there’s some connection. i realize it’s a nasty chemical and i’d prefer natural remedies, but i figure i could give it a try to get jump-started. any feedback on his experiences with diflucan would be appreciated. and lastly, how can you tell he is sensitive to histamines? just by the reactions to certain foods, or is there a test i can order? well, i hope i haven’t overwhelmed you with this tome of a post, but any feedback would be very helpful in making some decisions moving forward.

        • Tyler, your story is very similar to mine. let me know if you want to swap notes. I believe SIBO is the cause and am about to start on antimicrobial treatments.

          You can also reach me on the Talk Psoriasis forums under the same name.

        • The borrelia bacteria behind Lyme disease can exist in the body for long periods (very likely most if not all of us harbor some strain or another) and like so many other illnesses, the disease symptoms can emerge when an imbalance (i.e. another stressor) become present in the body. Many Lyme sufferers who achieve a remission in symptoms later see another bull’s eye rash without a tick bite when another health situation stresses/suppresses the immune system. Mounting evidence is clearly demonstrating that these borrelia can be transmitted sexually and from mother to child. Lastly, any steroid (predisone) suppresses the immune system by design. If one has an underlying stealth infection, steroids a green light to the offending pathogen. You may get symptom relief (all the majority of pharma drugs are designed to produce), but the infection (imbalance) is magnified.

  6. I found this yesterday – so interesting:

    Inconsistencies in testing, no standardization, and lack of a laboratory “gold standard” have long made the subject of testing for small intestinal bacterial overgrowth (SIBO) controversial. However, promising new research shows a simple antibody test could diagnose SIBO. In SIBO, the small intestinal bacteria create an autoimmune reaction against a gut neuropeptide, due, it’s believed, to molecular mimicry. Studies showed positive antibody results correlate strongly with the presence of SIBO. Hopefully this will lead to the development of more uniform SIBO testing in the future.

  7. Since HCL is only produced to digest protein, and not really needed for other foods, then it doesn’t make sense that taking HCL would help with bloating due to grains or various vegetables. True?

    • Hi Kris,

      I am not a doctor nor a herbalist and have no idea why this worked for me except from what I already said. Therefore none of what I said is in anyway a recommendation to others its only my testimony.

      I am doing my own research as to why this happened but the opinions are so mixed its not even funny. I am seriously contemplating studying to become a Gastroenterologist…….

      My question to a doctor or anyone here would be: I want to know on what minerals does the intestinal flora or any bacteria that grows in the intestines and colon good or bad feed on to survive?

      Kris – check out this site:

      • Hi Corne,
        Your question re our intestinal flora, and what they feed on. Check out Chris’s Radio interview podcast ( 20th Nov 2013) with Jeff Leach – Feeding Your microbiome – fascinating. Will answer your question. Anyone in the world can join the Human Food Project. Have their feces analysed (see what makes up your own personal microbiome and add to data they are collecting.
        Should be fascinating for you who is thinking of a career in gastroenterology.

      • I tried the trained doctor route and from $400 was told to spend another $3000 plus to rule out cancer–even though I have none of the symptoms for it. And he instructed me to start taking MiraLax every day for the rest of my life. The fellow spent maybe 10 minutes with me and when I requested to discuss options, he said “All I can give you is the protocol”, which I, by the way, already new thanks to the internet.

        The peppermint and oregano I used came from a forum post and it helped a lot–no doctor offered such advise. But like you, when I stop, symptoms lurk back in. My diet is quite healthy–I haven’t eaten a typical American diet in almost 30 years.

        Enzymes help a lot, but I have to keep taking them. I’m almost 50 and realize we produce less as we age, but I feel far too young to need supplement support.

        My goal is to get re-train my digestion and enzyme production. And frankly, I’ve had more useful and healing ideas from the internet (go figure) than from the medical community. In the end, I’m looking to heal, not mask.

        Finally, as for food for micro-organisms, think pre-biotics. If you google it you’ll get a ton of info and foods that have it. Lots of educational info out there.

  8. My victory over IBS/SIBO

    I was diagnosed with IBS in 2010 with my symptoms being bloating, abdominal pain and diarree. This diagnoses was made after an full physical, endoscopy, blood tests and samples from stomach that all came back clean and healthy. And when that happens you are diagnosed with IBS. The doctor told me there is nothing they could do for me and prescribed me a PPI that almost immediately stopped the bloating and abdominal pain – although a light diarree persisted.

    As a 30-year-old male did not accept my fate taking very dangerous chronic medication and so since then made a promise to myself that I will find and cure the issue causing my IBS.

    It took me a total of 3 years of research and a lot of prayers to find and cure my IBS. I have tried and tested so much diets, pills, herbal pills, types of fasting that that in it –self will make up a book, therefore I’ll only share what healed me and how it works according to the professionals.

    What healed me?

    If someone told me this in the beginning I would not have believed him or her and not even tried it and I think that’s why it took me over three years.

    1. Near the end I actually discovered I have SIBO.
    2. When taking antibiotics, peppermint oil or garlic the symptoms almost disappear, only to worsen when the course was done.
    3. This was because I had dangerously low stomach acid that did not kill the bacteria. (The opposite of what I was told by doctors)
    4. Vicious cycle – SIBO leads to mal absorption of Vitamin B12 and that leads to stress that leads to your stomach not producing enough acid to breakdown protein and get vitamin B12 from it.

    So what I started to do (actually by accident) was take a strong Vitamin B12 supplement with folic acid. On the second day my symptoms were already much better and on the third day completely gone.

    Then to get my stomach to produce a lot of acid again I supplemented with Betaine HCL with pepsin until my stomach produced enough of its own acid to get the minerals my body needs again. Please see page below I used to understand supplementing with hcl:

    • Many thanks for posting this. I’m still taking peppermint and oregano along with enzymes. I’ll consider your ideas if when I stop the peppermint next week trouble re-occurs. Right now I think the enzymes are doing the most good.

  9. Hello, I have been diagnosed with SIBO. Also have several autoimmune illnesses,and amdealing with high then reg levels of thyroid, testing pos for autoimmune antibodies of thyroid.
    whew, so, I am interested in learning more on how to treat my SIBO naturally, as taking Alinia off and on is not getting rid of my condition. My auto immune illnesses are very well controlled, and at this time my thyroid keeps lowering on its own ,after going high on occasion. Help , lol . Thanks so much.

  10. “studies that show reverse t3 drops even more with carbs over 200 grams”
    I’d love to get links to these studies!!!


  11. After 10 years of looking for the cause of my constant muscle pain, and having a rheumatologist, allergist, general practitioner, chiropractor, and hormone specialist all tell me my tests were negative, I finally read a book about candida, and seemed to have most of the symptoms. Of course, “they” all said systemic candida didn’t exist, even though books had been written on the topic. That’s because “they” think they know everything, and get pissed when it’s a mystery to them. Now that it has a cute little name, SIBO, some are slowly starting to accept it’s existence.

    I nearly got fired from my job for being plain miserable because I constantly had flu-like achiness that grew increasingly worse when I ate the wrong food. Sure, I had gas and bloating when I ate broccoli, so just added digestive enzymes, and that took care of the problem. Yeast products, all forms of sugar except xylitol in my mints and gum, ALL fruits except avocado, white grapefruit, jicama and cranberries make me feel achy. I had to learn to never eat bread again. I got used to it. When I do eat it, and the other things, my mouth and gums develop sores and my teeth are sensitive. Blueberries, grapes, cherries, nope. Can’t do it. My mouth tells me which foods are feeding my candida (or SIBO). And of course, the body aches get worse. How do I know my problem is primarily candida and not another SIBO bacteria? EVERY food listed in the candida book by Jeanne Martin matches what I can and cannot eat by giving me muscle pain and a sore mouth. I looked at a FODMAP diet, and some of those things recommended as safe to eat would kill me! I never get the thrush people say they have with candida, but boy, I get nasty breath if I cheat and eat lunchmeat or bread, or an unapproved fruit. When I say “cheat”, I mean I’ll have 2 grapes. One bite of bread in 2 weeks. A small sliver of pumpkin pie on Thanksgiving. Just that tiny amount, and I can feel the achiness. It’s so deep inside my intestinal walls, I don’t know if I’ll ever be able to truly kill it.

    I did the anti-candida supplements, as well as most of the diet recommendations, and felt better, but either I didn’t do them long enough, or I cheated just enough to keep the buggers alive for the past 10 years. Yes, there is more info available now from people like Chris Kresser, but there’s still a lot of different opinions as to which anti-fungals to use and an exact protocol. I’ve lost ALL faith in doctors under this current inaccurate form of “health” care. These same people told me candida was in my head, so I’d just prefer to do it my own way. Again.

    I’ve ordered just about all the stuff mentioned here, and by Chris, but I’m just not sure how many to take each day, how long to take each one. How do I know when to start probiotics again? I’ll keep searching the net, but if anyone has some sort of protocol that actually killed these bastards, I’d worship you forever. Right now, the only anti-fungal I had in my cabinet is Caprylic Acid, and I’ve been taking 3 a day (1800 mg total) for the past 3 days, and feel an immediate difference. I’ve used Oil of Oregano for a long time, not knowing how much damage it’s probably caused, so of course, I don’t take it now. I’m sure the bugs are immune to it. I always felt better when I took it, but again it doesn’t last that long.

    So I’m asking if anyone had the body aches form of SIBO, and what protocol you could possibly recommend? I cook all my own food, already have a strict diet, but will make it even more strict, and am female, 115 lbs., age 46. Thanks for any response.

  12. Chris

    My daughter (who is 5) has these symptoms as has had them for a while: frequent gas and stomach bloating (but seems to be a little better since she stopped drinking milk), a skin rash – possibly eczema, migraine headaches every few weeks and bad breath (smells almost sweet after she eats). I was wondering if she has SIBO – and wondering what sort of treatment you would recommend for such a small girl. I am a little worried about her longterm health. She is a bit of a fussy eater too.


  13. I had a long standing issue with SIBO but enteric coated peppermint capsules finally cured it. For good measure I included oil of oregano and pau d’arco, but what really made the difference was the peppermint. I tried many, many natural supplements(herbs, probiotics, prebiotics)/diets(FODMAP, SCD)/antibiotics with limited success. I also had a whole host of non digestive related ailments that turned out to be various vitamin and mineral deficiencies. Although I was putting all this organic, whole, home cooked food into my body, nothing was being absorbed. Notably iron and B12 were critical. They helped with my exhaustion, myoclonic jerks, orthostatic hypotension, “light” sleep which I would not even call sleep, brain fog, poor memory, muscle twitching and buzzing nerves. Initially I didn’t supplement with iron because the doctor said my ferritin was fine and my RBCs looked “essentially normal”, but apparently inflammation can cause a high ferritin reading which doesn’t accurately reflect your iron stores and a simultaneous iron and b12 deficiency can result in your RBCs looking normal (iron deficiency makes your RBCs small and B12 deficiency makes them large so you end up with normal sized cells). After checking into it, it turns out I was very iron deficient. Vitamins and minerals that might be low if you’ve lived with SIBO for a long time: the fat soluble vitamins A,D,E and K, B12, iron, calcium/magnesium, copper and zinc. I noticed improvements with all these additions (I tend to stick with whole food vitamins or “food” supplements such as fermented CLO). After taming the infection I was tempted to try soil based probiotics, but instead I just ate raw, organic vegetables and fruits from my garden and local farms. It seems to have worked out since my digestion is quiet and efficient these days. I sincerely wish everyone good health!

    • Your post gives me hope, Kate. Did you have a breath test to confirm the SIBO was gone after the peppermint or are you going by lack of symptoms? How did you figure out about the iron deficiency- you said checking into it- I also had/have a B12 issue so I want to check on the iron too. I am going to buy some peppermint capsules today. Do you recommend a particular brand or dosage? how often do you take it?

      • Hi Tara, I haven’t had a breath test to confirm that the SIBO is gone, but I no longer have noisy digestion, bloating, gas or early satiety. If I get the test redone I’ll report back. Tests for inflammation (to investigate whether your ferritin is elevated) would include those such as C-reactive protein or liver function. Although it’s not possible to know precisely how much the inflammation is elevating your iron, I said ‘very iron deficient’ because once I started supplementing there was a remarkable difference (notably in regards to my short term memory, attention and body temperature). I used Floradix iron with which there isn’t a risk of excessive iron storage. For the peppermint, I used Natural Factors Peppermint and Oregano Oil Complex and I would highly recommend it (I know you can buy it on iherb). I took two capsules 30 minutes before meals and anytime my stomach/intestines were noisy or cramping (although I would avoid taking it after large meals because it will open in your stomach and the peppermint may repeat). On another note, a lack of stomach acid seems to be common in people suffering from SIBO and for me this was true. I had a lot of burping after meals and adding HCL stopped that.

        This is where I first read about the peppermint:

        I really hope the peppermint complex works well for you!

        • Thanks for taking the time to respond to me Kate. I really appreciate it. May I ask, was your body temperature high or low and did you have cold or heat intolerance. I just checked my ferritin from the last test and it was 20 and the range is 10-200 so sounds like low to me. I usually have low grade inflammation – my crp last time was <.5 and my sed rate was 22 which is 2 points over "normal" but then again, I have had ZERO and felt amazing so I know that 22 makes a difference. I just looked up the Floradix and it contains gluten 🙁 I'll have to look for a gluten free alternative.

          • Actually I just did another search and found a version of the Floradix that is gluten free. Hurrah!

            • Hi Tara,

              I had very cold hands and feet and was generally cold intolerant. I’ve tried the gluten free version of Floradix and it works just as well as the regular!

      • Hi Tara, although I feel the peppermint was the essential factor in improving my digestive health/reducing the SIBO, I do think the pau d’arco helped a great deal. I had some success with the berberine containing herbs (Goldenseal, oregon grape root etc) in regards to calming my digestion but pau d’arco seemed to do more. A few herbalists have told me it’s a good idea to combine herbs.

        • Any recommendation on brand of pau d’arco? I’m making a list and I am going to go to the store later.

          • I used Nature’s Way and a housemade tincture from a local holistic pharmacy. I was doubtful at first, but the Nature’s Way brand was effective. NOW Foods also has a pau d’arco that gets good reviews.

            I took 1000mg three times per day. Sometimes I took it 30 minutes before meals and sometimes just at the beginning of a meal. It never bothered my stomach, although for the first two days I felt quite tired.

            • My peppermint/oregano oil and Floradix arrive today. I think I will do my SIBO test I have first and then start them. The Pau D’arco won’t be here until August 5 anyway. I’ll report back and let you know how I make out.

              • Doing so well on the Floradix!!!! I definitely notice a huge difference. I am going to start the peppermint/oregano tomorrow.

                • Tara,

                  Can you give a follow-up on how your doing? I’m desperately trying to help my SIBO and nothing works!!!

    • I should add that after getting the SIBO under control (which I judged by the lack of noise coming from my intestines after eating) I then added Bio-Kult probiotics, homemade kefir, kombucha and acacia fibre to improve the microbial environment of my digestive system. I found no negative side effects from these products.

      • Kate,

        I would love to hear more about your healing and the food you eat. The info you’ve already provided here is terrific. Do you have a website, FB page, or would you be willing to email?

        Many thanks,
        Kris K

  14. Are the SIBO treatments/supplements introduced all at once or separately, and with or after the SCD/GAPS intro stage? Thanks

  15. Hi Chris,
    great topics lately.

    RE: SIBO treatment – are these supplements safe for nursing mothers? And, have you ever had an infant test positive for SIBO? i’m considering testing my son at the same time as myself.

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