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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.

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. If you have SIBO/candida and high levels of bacteroides fragilus is it safe to use prescript-assist since it contains bacteroides?

  2. your discussion of pre and pro-biotics made me think of my son. he was born with a hirschsprung’s disease, where a portion (3/4, in his case) of his large intestine did not develop and was eventually removed. he has terrible gas and bloating and we have been told he will be prone to infection but that he will work it out over time.

    as the large intestine is where a lot of the gut flora is located, do you have any thoughts on pre/probiotic regimen you might suggest or dietary guidelines (i have tried to limit dairy but my he loves grains/sugar and my wife has a hard time limiting him in this regard)? we have spent a lot of money on kids probiotics and vitamins and are not sure if he is getting any benefit. we have specialists that we see and they are open to our thoughts on diet but don’t seem to have much to offer in this regard.

    • I’ve also struggled with gas and bloating since having my colon removed a year and a half ago, so I can sympathize! As far as pro/prebiotics, I wish I could help you, but I’m still trying to figure this out myself! But if he still has 1/4 of his large intestine, it seems like it would make sense to follow the general pro/prebiotic recommendations for someone with the entire colon? That is just a guess, but it does seem like the remaining colon would have the same (or similar) needs as the rest of the colon did. As far as I know, the gut flora native to the colon is pretty similar regardless of the exact location in the colon.

      I’d definitely recommend a visit to syontix [dot] com, because that’s the best free online resource I’ve found so far on gut bacteria and gut health in general. Has your son been tested for SIBO? I wish I was more of an expert on the different manifestations of gut dysbiosis, but with the gas and bloating it seems like SIBO might be a possibility, and the breath test is quite easy (though not always very accurate).

      As far as diet, I would suspect most of Chris’ general suggestions would still apply to your son; i.e. make sure he gets enough high-quality nutrients, avoid ‘food toxins’ such as excess omega 6’s from vegetable oils, etc. Have you looked into a Weston A. Price style diet at all? A WAPF diet still includes grains and sugar, but they encourage soaking or fermenting the grains to make them easier to digest. They also are really good about promoting nutrient-dense foods like bone broth, egg yolks, and liver, which I think is especially important for people with gut issues. Also, I know there’s a lot of controversy around dairy, but does your son have noticeable bad reactions to it? There was a really interesting post on the Syontix website recently about how certain components of dairy can strengthen the tight-junctions in the gut, which is a really good thing for those of us with gut issues. Also, milk kefir can be a pretty powerful source of probiotics; Chris has a post on that somewhere. Maybe if you haven’t had success with probiotic pills, food-sources of probiotics might be worth a shot?

      I’ve discovered that for me personally, gluten is very bad news, so if your son isn’t gluten-free already (I couldn’t tell from your comment) I’d get him on that asap. I’ve also discovered that I can’t really handle any fiber, and FODMAPs also cause problems. Food is really a very individual thing, though, so the most important thing is to try different approaches and see what works best for your son.

      I’m sorry I couldn’t be more helpful, and for the excessively long comment! I feel like nutritional and probiotic approaches for people with short bowels is a very under-researched topic, which is frustrating. If you have success with something, I’d love to hear about it (:

  3. Hi, Chris you mention several times when speaking of auto immune conditions/thyroid etc that it is essential to regulate the immune system. How do you regulate the immune system, you mention this is what you would first address with a patient.
    Excellent programme and information
    Cheers Lynne

  4. Chris,

    Would you care to elaborate, as to why cold baths are a bad idea? You say that 74-72 degree water presents also benefits. That would mean that mostly all swimming is subject to a cold thermogenesis benefits. That’s about the public swimming hall water temperature in Finland. Also, I’d argue that most of the swimming in Finland happens in waters colder than 72 degrees. The sea water rarely reaches those temperatures even in the summer. Then we have those thousand lakes that Finland is famous for – many people have cottages or live beside a lake, and swimming in a water that is below 72 degrees is quite common pastime. If that would present the benefits, then I would think us Finnish / Scandinavian would be particularly healthy, when it comes to the areas where cold thermogenesis helps (D2, obesity, immunity).

    Then there is polar dipping – the name is misleading as it is not really “dipping” it is swimming in the 35-39 degrees water in the icy lake/sea. There has been some studies that state the benefits of “polar dipping”. Polar dipping is done mostly by a bit older folks and often a daily practice for those that do it. There has been really no reports of adverse events or harm to one’s health related to swimming in the icy water in Finland.

    I would like to know, why taking a cold bath (or swimming) in a cold water would be a bad idea.

    And I disagree that swimming in a quite warm water like 72-74 has really anything to do with cold thermogenesis.

  5. Chris,

    Would Prescript Assist be a helpful probiotic for someone with histamine intolerance?


  6. This was a particularly informative episode to me. Thanks! I have a couple of questions, though.

    You wrote: ‘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.’ What are these signs and how do you look for such signs? Is it possible to do it on your own? Do you need to take lab tests?

    You wrote: ‘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.’ The Scribner edition of Perfect Health Diet discusses the optimal amount of fiber on pages 163–167 and suggests that supplemental fiber might actually be a bad thing. What do you think of this statement on page 164?

    ‘If the immune system is targeting a certain level of gut bacteria, too much fiber will not lead to more gut bacteria; it will lead to more bacterial “births” as they feed on the fiber, but also more “deaths” as the immune system works to keep the bacterial population down. This means that with high fiber intake, the gut will be exposed to more bacterial endotoxins and also to inflammation generated by immune activity.’

  7. Hi alyssa, thanks. It’s definitely not ‘die-off’ unfortunately. The bad bacteria that cause d-lactate build don’t necessarily have anything to do with the lactobacillus strains, which I do need but can’t take because of the SIBO.
    Those diets are indeed for a broad spectrum of things, it’s just hard to know what to do if you are one of those people with d-lactate issues, as ferments are the backbone of them. I have a bottle of prescript-assist, I’m just waiting to do a stool test with my doc first before starting it. I’m really, really hoping it’ll help.

    • Yes, I think bifidus strains and E. coli both produce lactate as well, so it’s definitely not just lactobacillus.

      From what I understand, the backbone of the SCD is the idea that eating no complex carbohydrates will ‘starve’ the bad bacteria, although they definitely push yogurt and probiotics as ways to repopulate the gut with the good guys. But like I said, I’m really not sure how effective that strategy is, because many of the bacteria that live in the GI tract can subsist on a wide variety of food components, including simple sugars and proteins; not just starch. Bifidus and E. coli can both ferment glucose into lactate, and glucose is certainly allowed in both diets. Also, even if the theory did hold, I don’t think the SCD would be a very effective strategy for SIBO. From what I understand, the idea is that only consuming simple sugars will allow your body to absorb those nutrients before the bacteria can get to them. With SIBO, depending on where the overgrowth is, your small intestine won’t absorb those nutrients before the bacteria can access them. I know less about GAPS, although I’m a fan of its emphasis on bone broths, egg yolks, etc.

      If I were you, I’d definitely try something to actually kill the overgrowth, rather than just trying to ‘starve’ it. And I’m also intrigued by the prescript-assist…might have to try that myself!

      Also, I’m curious – how did you find out you have issues with d-lactate build up? I’m pretty sure I’m dealing with some kind of overgrowth, but I’m not sure how to tell what kind of overgrowth I’m dealing with.

      • Hi Alyssa,
        I mainly figured it out from symptoms, esp when I took lactobacillus probiotics/any sauerkraut etc. Like headaches, speech, and crazy stiffness in my body. I know klebasiella is a common bacteria that causes trouble with that, so I’ll see if it’s on my next stool test.
        Yeah I don’t agree with the sugar (fruit/honey) really in GAPS, but that’s mainly in my case, since it feeds the upper GI bacteria/yeast. I’ll be trying the prescript-assist in a few days, hopefully it’ll flush some bad stuff out. I might try the biofilm stuff too if the PA doesn’t do much.
        If you do an organic acids test it’s a good indicator of SIBO, but it won’t tell you exactly what bugs you have, if that’s what you want to know. I’ve done that a previous stool test so I knew I had it and some of the bad bugs that were in there, but they are pricey tests. There is a blood test for d-lactate, but if you have all the symptoms, then as chris said in another podcast, if it’s not gona change the treatment, then there’s no point spending tons of money on them.

        • Thanks Denise. I’ve never gotten any negative symptoms from probiotics, so I guess that doesn’t help me much. I might just need to bite the bullet and get another stool test. Good luck with the prescript-assist! I hope it helps you.

    • Hi. I have used the organix acid test and it stated I have c.diff overgrowth in small intestine, and numbers were very high for a specific toxin B. it was 3-4, d,hydro else of some sort, but still i am not better and don’t know where to start. Probiotics and saccromyces boilardii make me worse and that the recommended supplement?? I think I have d-lactate buildup though after reading about this recently. Makes sense but I can’t find sources stating c.diff bacteria produce this? I ordered custom probiotics, to give it a shot. But symptoms are: colitis, awful skin issues that I never had before getting sick, fatigue, and awful confusion and memory issues that for 31 yrs old I should not have. What to do or take for this, any help??? SIBO has ruined and consumed my life for over 5 years! How can there not be a cure? I don’t understand?

      • Saccharomyces boulardii isn’t the same as probiotics,, just take Saccharomyces boulardii without probiotics.

  8. I know the GAPS and SCD diets are both designed partly for SIBO, and GAPS in particular uses a lot of d-lactate probiotic sources, like sauerkarut, bio-kult and yogurt. If these are bad for SIBO how come they’re so recommended? I’d been taking them and feeling terrible though so I’m glad I came across this! I’ll be trying prescript-assist, and most likely the custom probiotics. But with regards getting some probiotics from food, what can you do if d-lactate is a problem? or are all fermented foods out of the question? or at least until the SIBO is more under control?

    • Hey Denise! This won’t fully answer your question, but I think those protocols still recommend those probiotics because not all SIBO cases involve an overgrowth of d-lactate bacteria. Also, SCD and GAPS are supposed to help many other digestive issues as well as SIBO, and many of those (UC, Crohns, etc) can involve levels of lactic acid bacteria that are too low. In those cases, fermented foods and probiotics such as acidophilus can be very helpful! Because of that, I think probiotic recommendations need to be very individual.

      Also, you’re probably familiar with this, but another note is that when people first start taking probiotics, they often feel worse for a couple days, even if the probiotics are beneficial for them. The idea is that the probiotics can cause ‘die-off’ of the less beneficial bacteria, which can create worsened GI symptoms or flu-like symptoms for a couple days. I haven’t done a ton of research on ‘die-off,’ but it seems to be generally accepted as legitimate, and I’ve certainly experienced it. But if you’re still feeling terrible after taking probiotics at the same dose for more than a few days, I’d guess they probably aren’t good for you!

      And I know you didn’t ask about this, and this is totally based on my own experience, but I don’t think the theory behind the SCD (that it will starve the ‘bad bacteria’) always pans out. I would highly recommend looking into some of the anti-bacterial supplements that Chris recommends, or raw garlic, as an adjunct therapy to the diet and probiotics.

  9. Would it be OK to eat coconut oil instead of Lauricidin? If so, how much would I have to eat every day? Unfortunately, I can’t find Lauricidin in my country.

    What do you think about the herb oregano itself? Can I eat it as spice as much as I want or should restrict my intake?

    Thank you.

  10. Excellent info Re: “Old Friends” hypothesis for autoimmunity. Great stuff. My parents were definitely too sanitary with all the hand sanitizer and crap like that. Not to mention large frequent doses of antibiotics for chronic ear infections. The result: seasonal allergies, which I am still battling, although they seem to be getting better over the last couple years. Looks like my next step may be to try soil based organisms. Although I don’t wash most organic vegetables…don’t tell my wife 

  11. The big difference between NDT and thyroxine, as I understand it, is that the hormone in NDT is wrapped up in thyroglobulin – a large molecules that makes up the structure of the thyroid gland. Not all patients with Hashimotos have thyroglobulin antibodies, but I’m wondering if the ones that do see an increase when they take NDT?

    • I had no abnormal anti-TG readings, but high anti-TPO. My antibodies have decreased a lot on NDT. I’ve also supplemented with selenium and iodine and stopped all gluten. (I started supplementing selenium way ahead of the iodine.) I adhere to Dr. Brownsteins theories regarding usage of iodine, but remain skeptical to the doses he recommends. I had a slight and transient increase in TSH upon starting iodine, but no “low thyroid”-symptoms. I believe that the increased TSH reflected an increased bodily uptake of iodine, more than a decreased thyroid function that time

  12. Wouldn’t testing for MTHFR be indicated in someone with Fibromyalgia who isn’t responding to AIP?

  13. Awesome podcast! Loved the stuff about SIBO and probiotics. What do you think about raw garlic as a natural SIBO treatment? I know Ray from Syontix had great success with it, and that’s what I’m currently trying, although the die-off has been (surprisingly) almost nonexistent.

  14. Chris,

    Thank you for the podcast, that was a fascinating episode. About the probiotics- is it equally a good idea for people with intestinal permeability issues to take them, or should more caution be exercised? Thanks so much.


  15. My husband has severe psoriasis (just diagnosed last week with guttate, plaque and inverse types) and for several years it seemed we were able to control it through a paleo diet. He is 39 and a personal trainer – no other diagnosed health issues ever. But about last year (8/1) we started the auto-immune protocol (eliminated eggs, nuts, nightshades, all dairy, etc.) and he started to go downhill. His diet looked like the GAPS diet – lots of fermented foods and homemade bone broth. Absolutely no cheating – he takes this very seriously! We have been told our only hope is Humira due to the severity. I have been in contact with a Dermatologist at UCLA who uses an alternative approach and has a 90% clearance rate after 4 months (using Keflex – antibiotic, Diflucan, Curcumin Cream and changes with clothing along with a dairy free diet – we of course already do that). She believes that psoriasis is caused by several things including strep and staph infections and LPS (which may explain why my husband has flared with all the fermented foods and leftover broth each day). We are hoping either our naturopath or integrative MD will be on board with this latter approach though we have to wait 1-2 weeks for appoints.

    Our other concern is a stool test (Doctors Data) we just got back – his Secretory IgG was sky high (551 -reference range is 51-204), his elastase was super low (42 – range is >200) and his lactoferrin is super high (106 – range is <7.3).

    We now been to 4 integrative MDs or holistic practitioners here in Atlanta and everyone seems stumped except the 5 person (Dermatologist) who is pushing the Humira. If anyone has any insight it woudl be greatly appreciated.


    • Your husband could be sensitive to histamine/amines, as fermented foods are high in them. Usually people sensitive to amines are also sensitive to salicylates as well. You could look at the Feingold diet.

      Have you checked his copper, zinc and histamine levels? He might have high histamine, low copper, and would benefit from supplementing activated folate (5MTHF), methylcobalamin, B6, methionine, copper, etc. There are blood tests for these that can guide therapy…

      • Tim,
        Do you know what the name of the test is for the histamine levels? What other tests would you suggest?
        I think I am sensitive to salicylates simply because of my reaction to aspirin. It’s not an unpleasant reaction (tiredness and relaxation and I can seem to taste the aspirin taste for hours after) but it’s always been there…

        • Both Quest and LabCorp have tests for whole blood histamine. Life Extension doesn’t list it as a standard product, but if you call LEF they will usually let you order anything LabCorp offers.

      • Hi! We eliminated high histamine foods (including the fermented foods) about 4 weeks ago (also bought Histame type supplement and he started taking Quercetin) but his skin has gotten progressively worse. I don’t think it hurt to take those foods out but we haven’t yet noticed a difference. We are going to our naturopath next week and I think it’s worth doing further bloodwork. My guess is that he is zinc (not sure about copper) deficient from what I have read. We started supplementing zinc/copper about a week ago. We just got his standard bloodwork back today and everything was in line except his D was 125 and his Triglycerides were quite a bit higher (139 vs. 60) than last year (same diet). I feel uneasy about supplementing without getting a baseline back first – he’s obviously oversupplemented himself with Vit D….not a good thing!

        • Hi Maija,

          I was prescribed Humira for fistulizing Crohn’s accompanied by moderate + arthritis (and occ psoriasis) a little over a year ago. I refused it to seek out what i hoped would be a more natural / less aggressive approach and over the last 14 months or so have undertaken a massive effort to educate myself. It has been richly rewarding in many ways, I now feel at home in some pretty advanced technical literature, and as far as diet goes I can see through the hype to the science pretty quickly.

          However, I started on Humira 3 days ago and I’m not looking back. I had been trying to suppress TNF production through a low-ish carb SCD, combined with four ‘potent’ natural TNF blockers. It wasn’t working at all — I was too far gone into the vicious cycle and probably have been for many years. Once I realized I was basically trying to mimic the action of Humira by ingesting massive amounts of extracts from Asian and South American plants, it wasn’t too huge of a stretch to just stop worrying and love the bomb, so to speak. The injections have been surreal but the effects have been almost instantaneous — I definitely am getting my life back, and life is short enough as it is.

          Anyway, this is pretty long, but I thought it might help to have a committed Paleo (which I essentially still am) voice speak out in favor of the nasty drugs. It is not going to suppress the whole immune system (lunacy), and I believe that if one maintains a non-inflammatory Paleo-esque diet then one should be able to leave the drugs behind at some point — but you have to get ahead of the screwed-up immune reaction that causing so much damage, and I wasn’t able to until now.

          Good luck!

          • Thanks Grayson for sharing. We are going to try the psoriasis protocol prescribed by the dermatologist at UCLA that I mentioned and see where we are at in 30 days. We are not ruling out the Humira. Like you, we’ve tried everything natural for years and will continue eating paleo for the rest of our lives – we believe strongly in it. A few months back, I couldn’t have imagined considering a drug like Humira, but when your life is so greatly impacted you sometimes have to reconsider options. And when you make a decision you need to come to peace with it like you’ve done. I really appreciate you sharing your experience – we have been feeling a bit alone lately, as most folks in the paleo world talk about coming off medications but not the reverse….

            • The protocol sounds like a really smart one, from what I understand of psoriasis. It seems like it will come down to whether the antibiotic and anti fungal can gain a foothold amidst all the inflammation. I sure hope so!

              Best wishes and I’m going to remain curious — I’ll plan to check back here in a few weeks and see if there’s any update….

            • Hi Maija,
              I’ve had psoriasis for 23 years now and have been medication free for 7 years now. It’s been a struggle. I’ve been focusing on getting my stomach in order since that seems to be the key to my skin. I’ve recently begun a bone broth regime, but my stomach is currently not dealing it with it well. I was a little discouraged to hear your husband wasn’t clearing on diet alone. Anyway, I just wanted to know if your husband has had success with this new protocol.

              • Hi Barbara,

                My husband has done Dr. Madalene Heng’s protocol for almost 4 months and is about 90% clear (still has psoriasis on his elbows/knees and a few guttate patches on his back). I think the sun has helped greatly but his stress level is also alot less so it’s hard to tell ultimately what is helping the most. He has also been on the paleo autoimmune protocol – we are slowly introducing foods (ghee, nuts, etc – staying away from eggs and nightshades for now). We find that bone broths and fermented foods aggravate his psoriasis – he can do a little of both but not too much. We believe this is due to the high histamine content of both. Our focus now is to add more vegetables (8-10 servings a day) and some lower sugar fruits. I believe his diet is too protein-heavy. We just keep playing around to see what works best.

                • I’m glad to hear your husband is doing so much better. Stress tears down the GI tract, so leaky gut, more food intolerance and inflammation occurs. It sounds like he has yeast, that is why only low sugar fruits are ok for him. An anti-yeast diet is when you avoid fermented foods, foods with vinegar, mold, yeast, etc.

                  Ask your Integrative MD for something to treat the yeast – prescription or supplement. If he’s not better, come see me.


                • hi maija, how is your husband doing lately? i have similar psoriasis issues as he did as well as psoriatic arthritis. i’ve been taking enbrel for over 10 years and successfully kept it at bay. however, last june i had lyme disease and supposedly cleared it with a prompt course of antibiotics, i have not been doing so hot with arthritis and psoriasis flareups for the past 5 months. i coincidentally switced from enbrel to humira a year or so ago because i didnt think it was working as well as it used to. i’ve been taking humira now every 2 weeks since august and my rhuemy suggested i try it every week; i have been taking it every week for the past month but dont seem to be getting any better. i somehow feel that their is a fungal connection to this all and wonder how your husband has done with his condition. any suggestions or links would be greatly appreciated. thanks.

        • Some other things you could try.

          (1) sunlight around solar noon. Sunlight is tremendously healing, as long as you don’t burn. It produces vitamin D, sulfates Vitamin D and cholesterol, releases nitric oxide, and kills bacteria, virus and fungus. Obviously don’t wear sunscreen, and don’t bathe/shower for 20+ hours after sunbathing.

          There was a study done with mice genetically modified to get MS. The control group all got MS. The group fed Vitamin D supplements mostly got MS. The group exposed to sunshine did not get MS.

          For TB, they used to start people with 5 minutes each side, and over the course of a couple of weeks build up to 5-7 hours per day, with 100% cure rates for cases where the lesions hadn’t opened yet, and 80+% for the more severe cases.

          (2) HCl to can help restore good digestion

          (3) Digestive and systemic enzymes. Very powerful, Karen DeFelice has some good books.

          (4) Garlic, see the Syontix web site for more info. This provides both nutrition and is anti-bacterial, anti-viral, anti-fungal

          • Definitely second the HCl. I think it’s difficult to either cure or prevent recurrences of SIBO if you don’t have enough stomach acid, because the acidic environment in the upper part of the small intestine deters the growth of excessive amounts of bacteria (and other microorganisms). Ideally, you’ll have minimal bacteria growth in the upper part of your small intestine, and increasing growth as you move towards the ileum and colon. This is partially because the acidity of the food/digestive juices decreases as it moves through your digestive system.

    • As a psoriasis sufferer and fellow traveler on the journey to health recovery I recommend you look into the work of Kerri Rivera at Her work on autism recovery likely applies to many GI/neurological/mental health disorders. Her newly published book is Healing the Symptoms known as Autism. Chris I recommend you add this information to your store of knowledge. Kerri’s work is in part based on the work of Andreas Kalcker whose new book titled Parasites: the Silent Enemy examines the high rate of undetected parasitic infection in the developed world as a unrecognized cause of many chronic modern day illnesses such as autism, fibromyalgia, chronic fatigue, arthritis and mental dis ease. Both Kerri and Andreas work is built upon Jim Humble’s work with chlorine dioxide. I have not been following Kerri’s protocol long enough yet to be sure if it is helping my psoriasis, but I have been able to eliminate my prescription psoriasis medication. The GAPS diet did not help my psoriasis either.

  16. What a coincidence you speak on hookworms.
    My first batch of hookworm larvae will be arriving some time this week.

    I’ll be infecting myself with 35 larvae.

    • I am curious if your health has improved or worsened as a result of infecting yourself with hookworms? For a different perspective I recommend you look into the work of Kerri Rivera at Her work on autism recovery likely applies to many GI/neurological/mental health disorders. Her newly published book is Healing the Symptoms known as Autism. Chris I recommend you add this information to your store of knowledge. Kerri’s work is in part based on the work of Andreas Kalcker whose new book titled Parasites: the Silent Enemy examines the high rate of undetected parasitic infection in the developed world as a unrecognized cause of many chronic modern day illnesses such as autism, fibromyalgia, chronic fatigue, arthritis and mental dis ease. Both Kerri and Andreas work is built upon Jim Humble’s work with chlorine dioxide.

  17. Regarding the antibodies – it is vital that she uses the same laboratory for the tests. There are two different test types for Anti TPO. One will typically have a low normal range and excact antibody numbers, the other will have a slightly larger normal range and ofte give results like “> 1300” – which should be interpreted more as a boolean answer than a gradual one, like the first. Both will be called an ati-TPO test on paper.

    Read the chapter about antibodies in this document: LABORATORYMEDICINE PRACTICE GUIDELINES – LaboratorySupport for the Diagnosis and Monitoringof Thyroid Disease

    “The estimate of TPOAb prevalence depends on the sensitivity and specificity of the method employed. The recent NHANES III United States survey of ~17,000 subjects without apparent thyroid disease, reported detectable TPOAb levels in 12 % of subjects using a competitive immunoassay method (18). Whether low levels of TPOAb detected in healthy individual sand/or patients with non-thyroid autoimmune diseases reflect normal physiology, the prodrome of AITD, or an assay specificity problem, remains unclear.
    Normal reference values for TPOAb assays are highly variable and often arbitrarily established, so that a large majority of patients with AITD test positive, and most subjects without clinical evidence of AITD test negative.
    The lower normal limit appears to relate to technical factors. Specifically, assays citing a low detection limit (10kIU/L)typically cite a TPOAb “ normal reference range”. Since such methods appear to have no enhanced sensitivity for detecting AITD, these “normal range” values may represent non-specific assay “noise” and may not be pathologically meaningful.”

    I had an analysis done on two different labs done on blood from the same drawing. Here is my results:

    My local Lab: > 1300 (0-100)
    A hormone lab in Oslo: 209 (<35)

    After this drawings my doctor uses the Oslo lab in order to follow variations, not only to get a "have antibodies"/Have not" type of answer.

  18. I think many of us have been taking Klaire Ther-Biotic Complete, but it contains Lactobacillus acidophilus, so it looks like we need to throw it away and get Custom Probiotics and Prescript-Assist instead.

    • Only if you have SIBO. Even then, SIBO doesn’t always involve overgrowth of lactic acid forming bacteria.

      • Is there a good way to tell what type of overgrowth you’re dealing with? Would it have anything to do with whether results from a breath test indicate more hydrogen or more methane production?

      • Can you please address the controversy about soil based organism probiotics that went into high gear around Rubin’s popular brand? Despite their being able to help many ( like Rubin’s cure of Crohns) other experts say they are spore-forming and some found it became pathogenic in time.

        Natasha Trenev and Ray Sahelian MD etc, say some pretty scary things about the problems with soil organism probiotics.

        I’d love to see a logical counter to those type of arguments.

        I’ve tried endless things for my mystery disease including some you mention ( which may or may not be SIBO but is in that area) with top MD’s ( every test in the book) and alternative healers on 3 continents ( including top Chinese Medicine doctors in Beijing,Penang,Barcelona, California) various umpteen tweaks to Paleo/WAPF/GAPS/SCD/PHD/Aajonus Vonderplanitz versions for several years including every top probiotic and making my own kefir from raw goats milk and fermented foods and even a try at a soil based one.

        Nothing has cured it yet, but I am hesitant to try another soil based one without more info about the concerns raised about long term affects. ( BTW NAC and Chinese genseng has helped more than anything along with diet and at least has me functioning again and thankfully I have never had diarrhea or constipation but eating ANYTHING, even bone broth causes pain…which is a heck of a teacher).

        Since my problem began with an antibiotic in 2009 ( Flagyl or Metronidazole) I would never take them to cure this ( and had tried to avoid them my entire life).

        • As a fellow traveler on the journey to health recovery I recommend you look into the work of Kerri Rivera at Her work on autism recovery likely applies to many GI/neurological/mental health disorders. Her newly published book is Healing the Symptoms known as Autism. Chris I recommend you add this information to your store of knowledge. Kerri’s work is in part based on the work of Andreas Kalcker whose new book titled Parasites: the Silent Enemy examines the high rate of undetected parasitic infection in the developed world as a unrecognized cause of many chronic modern day illnesses such as autism, fibromyalgia, chronic fatigue, arthritis and mental dis ease. Both Kerri and Andreas work is built upon Jim Humble’s work with chlorine dioxide.

      • Chris, I have sibo and overgrowth of c.diff toxin b as confirmed by organix acid test in small intestine. It showed a specific toxin, but 5 years later I’m still sick, underweight, and nothing works. And I just read what u stated about d-lactate and I definitely have buildup, just can’t find sources stating c.diff bacteria produce this lactate? But what should I be doing to eradicate this? I know the bacteria, I know this location, and the specific toxin per organix test? Why can no one help me? Please any info or could you direct me to someone? I live in philadelphia. Thank you.

        • Anthony, I think I may have something to help you. I’m currently using a Doug Coil Machine to heal my intestinal candida overgrowth. This form of SIBO, which everyone told me for 10 years didn’t “exist”, suddenly now is being recognized. It has caused me body aches every time I eat a food that typically feeds candida: Sugar, yeast, most fruits, & most starch. I’ve stopped eating all the offending foods, and took anti-fungals for a long time, but they eventually gave me painful diarrhea.

          I got my machine from a man in Scranton, PA, and it has literally changed my life.

          The machine has four parts to it:

          1. Frequency generator. This is the kind of device one might find in an intro physics class at a university. I’m not sure what it is used for outside that setting. For me, it serves as a way to generate alternating magnetic fields at specific frequencies that kill microbes.

          2. Capacitor box. This piece was custom made and has several capacitors that can be turned on and off so that the frequency generator can transform the 60 Hz coming out of the wall socket to the frequency I want.

          3. Amplifier. This is what is normally found hooked up to an electric guitar to make it louder. In this case, it amplifies the electric frequencies so that what comes out of the coil is of a high enough amplitude to penetrate 6 to 8 inches into flesh.

          4. Coil. This is a pretty heavy box. It looks like a doughnut made of about 40 feet of insulated copper wire attached by a 14-foot long heavy duty wire to the side of the capacitor.

          This machine vibrates offending bacteria, based on a specific frequency that they are adapted to, and it causes them to vibrate out of control to the point where they explode. It uses only Hz frequencies that are safe within a range of 200-2000 Hz.

          I can literally feel my body aches disappear when I use this machine. I’ve been using it since early January, and have weaned down to 1/2 a dose of my pain meds. I’m close to cutting that down even more. I don’t think I will ever be able to eat yeast or sugar again like a normal person, but I feel so incredibly good and pain free thanks to this machine.

          I checked the manual of frequency settings from the website and they DO have a frequency for c.diff that is in a range that is safe to use. Start researching online about the Doug Coil Machine. The man who originally made them is not currently making any more due to adrenal exhaustion from doing the work non stop for 5 years. He most likely won’t respond to your email unless you click a High Priority button on it. He trained 5 people in the US on how to make the machines, but he has a page of schematics for you to make it yourself if you are a tech geek. I don’t want to put my email address on this public site, but maybe we can exchange info thru Steve Wright or something so I can give you the name of the technician that makes the capacitor box in Scranton. The other parts you have to buy yourself. It’s so close to where you live. I’ve been searching for relief from my intestinal candida for 10 years, and NO ONE could help, or their protocols weren’t enough. THIS has helped. More than helped, this machine is a miracle for me. Maybe it can help you too.

          • Hi Cheryl,

            Thank you for the response. I have been reading about coil machines, and have seen all positive outcomes for many things. Please email : [email protected]. I would like to know about side effects and your personal use and how it’s been alittle more in depth before I purchase one. Look forward to hearing from you. Thank you so much!


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