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Episode 4 – Hashimoto’s, Leaky Gut & Autoimmune Disease


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Here we go with another episode of the podcast! I finally got myself a decent mic so I don’t sound like I’m talking in a tin can. Also, we’ve decided to group questions together into 1-2 distinct themes for each show, instead of doing a random grab bag of questions. This will allow me to go into more depth on topics, and it will allow you to quickly see whether the subject of the podcast is of interest to you.

We’ve received some great feedback on the show. If you have a moment, we’d be grateful if you could head over to iTunes and leave us a review. It seems the so-called “skeptics” from the sciencebasedmedicine.org cabal have showed up to proclaim in their typical myopic and ignorant fashion that anything challenging the dominant paradigm is not factual, accusing me of sharing “anecdotal” evidence and making “unsubstantiated” claims. Obviously they’ve neither listened to the show nor read my blog – but that doesn’t stop them from feeling qualified to write a review! A few people have already responded to their nonsense, including a physician who listens to the podcast, and I’d be grateful if you’d do the same.

This week’s show is focused on hypothyroidism/Hashimoto’s, leaky gut and autoimmunity. Specific topics covered include:

  • Do plant goitrogens influence the thyroid?
  • Why do I continually need higher doses of my thyroid medication?
  • Kelp’s effect on the thyroid
  • Synthroid vs. Armour, what is the best thyroid medication?
  • Can antibiotics cause autoimmune disease?
  • What is the best diet to heal the gut?

And remember, keep those questions coming in!

Full Text Transcript

Danny Roddy: Hello everyone, and welcome to The Healthy Skeptic podcast. My name is Danny Roddy and with me is Chris Kresser, health detective and creator of TheHealthySkeptic.org, a blog challenging mainstream myths about nutrition and health.

Chris, how are you doing, man?

Chris Kresser: I’m doing pretty good! I’m a little stressed out. We’re moving. I hate moving, but with the baby coming, we need a little more space, so we’re playing that game now. Looking for a place, and it’s stressful for me. I don’t like it.

Danny Roddy: Moving is not fun, that’s why I got rid of most of my possessions in my early age and sleep on a mat on the floor.

Chris Kresser: Yeah, maybe I should try that. I don’t know if my wife would be really into that, though.

Danny Roddy: My girlfriend at the time was not happy with it.

Chris Kresser: Yeah. I’ve been there. Been there, done that, and at this point a house sounds better.

How’s it going for you? What’s up?

Danny Roddy: Nothing much. Busy with school, work, blog. I just had an interview with Jimmy Moore which went really well. I finally had―I told myself I wasn’t going to listen to it because I thought it was so bad, but I finally did and I thought it was okay.

Chris Kresser: Yeah, I never listen to my interviews or podcasts for that same reason.

But let’s get to it!

Danny Roddy: So, we’re going to do some questions about specifically Hashimoto’s disease, leaky gut and autoimmunity. Kind of specialize this podcast.

Chris Kresser: Sounds good.

Danny Roddy: So let’s get to it.

Do Plant Goitrogens Influence the Thyroid?

Danny Roddy: Okay, the first question is from Bonnie Snyde, and her question starts with:

I was diagnosed with Hashimoto’s disease a few years ago. I currently take a natural thyroid supplement that is formulated at a compounding pharmacy. I recently started living the paleo lifestyle. I have been eating a lot of leafy greens, but making sure to cook them. I was told that raw cruciferous and raw spinach were not good for me, but cooked was okay. Now I am reading that I should totally avoid cruciferous and spinach. Is this true? If so, what vegetables am I supposed to eat? I love leafy greens! Help.

Chris Kresser: That’s a good question and one that comes up a lot. I haven’t seen any evidence that cruciferous vegetables, raw or cooked, really play a significant role in thyroid disease. The studies I’ve seen suggest that there is no relationship at all between thyroid cancer and cruciferous vegetables, and if anything, the compounds in cruciferous veggies may actually protect against thyroid cancer.

And then I’ve never really seen any convincing studies showing any association between cruciferous veggie intake and thyroid disease. There are some animal studies that suggest that cruciferous veggies suppress TPO, which is an enzyme in the thyroid, and other aspects of thyroid function, but those are in really high doses that humans aren’t able to obtain from food. You’d have to eat a lot of raw broccoli for that to happen. And I think most people are going to have a pretty loaded stomach before they get to the point where they can depress their thyroid function with raw broccoli. So I say go on eating the cruciferous vegetables. If you want to be extra cautious, it’s probably a good idea to cook them.

Danny Roddy: I think it was on your blog―somebody was―or maybe it was Dr. Kharrazian that said you throw away the goitrogen list and you add in the gluten list, because all the foods with gluten are much more deleterious to the thyroid than any goitrogen would ever be.

Chris Kresser: That’s exactly right. I wrote that, and I probably heard it from him, originally. I went home after that seminar, I think, where he talked about that, and I did a lot of research on PubMed about cruciferous veggies and thyroid. And I just didn’t find anything that convinced me that there was a connection at the level that most people are eating them. I completely agree that if you want to talk about dietary concerns about thyroid, that gluten is way more of a concern. And I’ll come back to that in a second.

But there are a lot of environmental goitrogens―and when we say goitrogen, we just mean an environmental factor that can cause goiter, which is a sign of depressed thyroid function. So there’s heavy metals, there’s pesticides, there’s plastic compounds―dioxins, PCBs―there’s medications―there’s antibiotics, NSAIDs and anti-inflammatories can be potentially goitrogenic, diabetic drugs, statins, cholesterol-lowering drugs, etcetera. So those probably play a way more significant role in terms of their goitrogenic effects than any foods do.

And then gluten―well, we have gluten and iodine, which we haven’t mentioned yet. There is a correlation between gluten intolerance and autoimmune thyroid disease. It’s pretty small, but we have ot keep in mind that the testing for gluten intolerance has been really limited until recently, and we’re going to see an explosion in detected gluten intolerance because now we can test for, not just alpha gliadin and transglutaminase, but we can test for all the other forms of gliadin, all the eight types of transglutaminase, we can test for glutenin, we can test for WGA, we can test for deaminated gliadin. You know, there’s over a hundred compounds in wheat, and people can react to any of them!

So, when the studies say there’s only a five-percent correlation, that’s just for alpha gliadin and transglutaminase, the ones that are elevated in celiac. But if you’ve been reading any of the articles on my blog lately, you know that celiac’s just the tip of the iceberg when it comes to gluten intolerance. And for every one person that’s diagnosed with celiac, there’s eight people who are undiagnosed. And that’s just celiac! We haven’t even gotten into all the intolerances to the other proteins I just mentioned. In my clinical practice, I see a huge correlation between gluten intolerance and thyroid disease, and I see huge benefits when people remove gluten.

Danny Roddy: So, Bonnie, you can keep eating your raw spinach. Just don’t eat the wheat.

Chris Kresser: Exactly. And one more thing on that. Be careful with iodine. Because although in the developing world, iodine deficiency is the primary cause of hypothyroidism, and in the US it’s Hashimoto’s―which is, of course, the autoimmune thyroid disease. And iodine can trigger and flare up Hashimoto’s. So if you’ve got Hashimoto’s, or even if you don’t know you have Hashimoto’s, what the research shows is that about eight to nine out of ten people with hypothyroidism in the US do have Hashimoto’s, so you pretty much assume that you do if you’re hypothyroid, unless you’ve had your antibodies tested and you know that you don’t. So be very careful with excess iodine, and supplements, and seaweed, and stuff like that.

Danny Roddy: Agreed. Awesome.

Why Do I Continually Need Higher Doses of My Thyroid Medication?

Danny Roddy: Okay, let’s go to our next question. This one is from Sherry:

I have a question. I was diagnosed with hypothyroidism in 1997, and I’ve been on Synthroid since then. My dosage started at 75 micrograms then escalated to 100, then to 125, and here in the last six months I’ve gone from a steady 200 micrograms to 212 micrograms and, just recently, to 250 micrograms. I am concerned to why the sudden increase in my dosage. I know that the levels must require this, but why? I just wondered if you could advise.

Chris Kresser: Yeah, that’s another common story, unfortunately. The increase in dose obviously indicates some kind of decline in her thyroid function, but the question she’s asking is, why? Why is it declining? Why is it declining so rapidly?

I just mentioned Hashimoto’s in the last question, and as I said, most hypothyroidism is due to Hashimoto’s in the developed world. The reason most people don’t even know they have Hashimoto’s, and that most conventional doctors don’t test for it, is that it doesn’t really change the course of their treatment.

So if you go in to a doctor and you have hypothyroid―your T4 or T3 is low, or your TSH is high―they’re basically going to give you thyroid hormone replacement, that’s the end of the story. They don’t really care if you have the autoimmune version of it, they don’t really care what’s causing it, because it doesn’t affect the outcome of their treatment. The problem with that approach is that the underlying cause of the problem isn’t being addressed. So the immune destruction that is destroying the thyroid gland, and therefore destroying the thyroid’s ability to produce thyroid hormone, can just go on unchecked. And as that immune destruction intensifies, more and more of the gland gets destroyed and the thyroid is less and less able to produce hormone, and then the dosage of the medication continues to go up and up.

Danny Roddy: The first time I heard that, I was just flabbergasted. You have an autoimmune disease, and the course of the treatment doesn’t change at all. It’s just the same protocol for whatever’s going on with your thyroid, and it just astounds me.

Chris Kresser: Yeah, it’s wacky. I mean, part of the deal is that for other autoimmune diseases like Crohn’s or rheumatoid arthritis, they’ve got things like pregnezone, which are really potent immunosuppressive drugs that they do use to treat―of course, it doesn’t address the underlying cause, but it does something to dampen the inflammation.

But in the case of Hashimoto’s, in their mind, the risk-benefit―the risk is too high for those drugs. With Crohn’s, and rheumatoid arthritis, and lupus, and some of those other autoimmune conditions, they’re potentially fatal, so the stakes are higher, and so they’re willing to use the sort of carpet-bombing drugs. But with Hashimoto’s, they’re not really willing to do that, because it can be a really nasty disease but it’s rarely fatal. So they’re not willing to bring out the big guns, and conventional medicine doesn’t really know what to do, otherwise, with autoimmunity. They’re totally behind the research, which we’ll talk about later, I think. They just don’t know what to do, so they just don’t test for it, ’cause they don’t know what to do with it.

But what should be done is the autoimmunity itself should be addressed, and the inflammation that the autoimmunity causes should be addressed. Because inflammation decreases thyroid function in so many ways. Number one, it depresses conversion of T4 to T3. I see a lot of people in my practice with normal T4 but low T3 levels, and they’ve got systemic inflammation. That’s one thing.

Inflammation also causes thyroid receptor site resistance. So you could have enough thyroid hormone circulating around your bloodstream, but the receptors don’t want it or can’t let it in. It’s similar to insulin resistance. And then, inflammation can also depress pituitary function, so that the pituitary’s not adequately communicating with the thyroid gland and telling it to produce enough hormone. So, basically, inflammation inhibits thyroid function at every turn. And conventional treatment―or conventional testing―doesn’t look at it, doesn’t take it into consideration, they just give you a thyroid hormone and call it a day.

Danny Roddy: So Sherry should seriously reevaluate whatever she’s consuming. She doesn’t say what she’s actually eating here, but the fact that she’s going up on her meds is not a good sign.

Chris Kresser: No. Definitely get some help. Because the long-term consequences of that are not pretty.

Kelp’s Effect on the Thyroid

Danny Roddy: So let’s jump to our next question. This one’s from Claire Harris:

My doctor is suggesting a partial thyroid-ectomy on the right lobe because multiple nodules are growing. Having tried kelp, which only managed to send me hypo, and I am wondering, really, what can I do about this? Can I avoid surgery or is this actually necessary?

Chris Kresser: Well, you know, of course I can’t answer that question. In some cases, surgery is necessary, especially if there is a malignant growth. That’s an evaluation that would have to be made knowing more about her case, and with her doctor, of course.

What I can say is that, just hearing that little bit about kelp, just has me thinking about iodine. She said she got worse when she started the kelp, and I’m guessing that she has Hashimoto’s, and the kelp, which has iodine in it, probably triggered her Hashimoto’s and made it worse. One thing that I always advise patients to look into when they’re facing―well, I advise almost every patient with Hashimoto’s to look into this anyways, but certainly if they’re facing surgery or something like that―is a drug called low-dose Naltrexone.

Of course, I’m not a doctor, I don’t prescribe this. It’s not within my scope of practice to prescribe medications, but I can certainly educate patients about the available options. Low-dose Naltrexone is a really, really exciting medication in the treatment of autoimmune disease.

Basically, it’s a very low dose of a drug called Naltrexone that was used, for many years, with opiate withdrawal and alcoholism. What happens is, if patients take a very low dose of Naltrexone, it provides a blockade of the opiate receptors in the brain, and it kind of temporarily tricks the brain into thinking that opiate levels are low, and it better hurry up and produce more. And then, because it’s such a low dose, it leaves the body―so it doesn’t continue to blockade the receptors―but the effect has already happened, where the brain kicks in with this extra production of opiates. And what we know is that opiates play a really big role in regulating the immune system. So, with autoimmune disease, it’s basically an imbalance in the immune system.

Really, kind of an oversimplification would be to say that the immune system has two primary sides or arms. One is called the Th1 side, and this is cell-mediated immunity. This is our first line of defense, like if you get exposed to a bacteria, or a virus, or a parasite, or something like that. You produce T cells, and the T cells go and attack that pathogen and kill it. That’s our first line of defense.

The other side of the immune system is the Th2 system, and that’s antibody-mediated. This is what happens when you get exposed to one of those pathogens, and then the B cells start producing antibodies to it, so that later on, if you get exposed to that same pathogen again, you’ll be immune to it. This making sense so far?

Danny Roddy: Yeah. This is a highly interesting area of the immune system. Continue, ’cause I have a lot to add to it.

Chris Kresser: Okay. So then what happens with autoimmune diseases is that one of those sides becomes dominant. In some cases, both sides become depressed or both sides become dominant, but usually one side becomes dominant. In Hashimoto’s disease, I think it’s about 70% Th1 dominant.

So it’s like the immune system, which should be in a kind of dynamic balance and adjustment, just gets locked into one of those sides of the immune system being dominant. What Naltrexone―or low-dose Naltrexone―does, is it stimulates the production of Th3 cells, which are called T regulatory cells. And the job of the T regulatory cells is to bring the Th1 and Th2 sides of the immune system back into balance. So Naltrexone, so far, seems to be the most potent way of stimulating the T regulatory cells and bringing the immune system back into balance.

There are other things that stimulate T regulatory cell production, like vitamin D, for example, glutathione―which is the master antioxidant in the body―and then things like acupuncture have actually been shown to stimulate Treg cell production.

So, you know, getting back to Claire’s original question: I would definitely look into low-dose Naltrexone and try to find a local physician in her area that works with it. There’s a growing number of people that do because there’s so much exciting research being done in this area. And I’ve seen dramatic results with it, with my patients.

Danny Roddy: Chris, with your patients, have you seen some of them getting worse by taking specific supplements that boosted Th1 or Th2? Like, unwittingly, if they were just taking a garbage bag of supplements–

Chris Kresser: Yeah, that can definitely cause problems. I know that some practitioners take a really specific approach where they test the various Th1-stimulating supplements, and various Th2-stimulating supplements, and then try to figure out―remove all the ones that are stimulating the dominant side and emphasize the ones that are stimulating the non-dominant side. So far, my approach has been to really focus on the T regulatory cells, the Th3, and there’s a couple of reasons for that.

Number one, I think the immune system is really, really complex and sophisticated, and we’re just beginning to scratch the surface of understanding how it works. My approach is always more focused on supporting the body in doing what it knows how to do best, than it is to kind of get in there and mess with the wiring ourselves. You know what I mean?

So I’m a little wary of that approach, even though I don’t deny that it works and that it can work, I’m just a little wary of it myself. So I’ve chosen to focus more on the T regulatory cells, and making sure everyone’s got enough vitamin D and glutathione, and referring them out―I have someone I refer out to for LDN, low-dose Naltrexone―and that seems to produce really significant changes. And then, if necessary, beyond that, we’ll look at the Th1- and Th2-stimulating supplements. But I think there’s a lot we haven’t learned yet about which substances stimulate which pathways, so I’m a little reluctant there.

Danny Roddy: Very interesting. Very, very interesting area of the immune system.

Chris Kresser: Yeah, this is super exciting, because up until recently―I mean, low-dose Naltrexone, a guy named Dr. Bihari started to use it with HIV, I think in the late 80’s―but for quite a while, it was not really well-known, and there were no clinical studies that had been done on it, and now we have good clinical trials. There was a trial done on LDN for Crohn’s disease at the Univeristy of Pennsylvania, I can’t remember the name of the doctor. Jill Smith, I think? Sorry if that’s not correct.

But, it, a 70% remission rate for LDN with Crohn’s. Which, if you know about Crohn’s disease, that’s a remarkable result. There’s no other medication that gets even close to that, and there were almost no side effects. The only side effect was mild―and usually temporary―insomnia that’s a result of the opiate blockade that happens during the night from taking LDN.

But this is big stuff, because as autoimmune disease continues to increase, we need tools to be able to deal with it. And while I’m not usually a fan of taking medications over the long term, I think the benefits that can happen with LDN far outweigh any potential consequences. It’s a very, very low dose. We’re talking about 1.5 to 3.5 grams, and the normal dose of Naltrexone is 50 grams. So it’s a really low dose, and very well tolerated by most people. So it’s exciting, definitely.

Synthroid vs. Armour, What Is the Best Thyroid Medication?

Danny Roddy: Awesome. So let’s go to our next question. This one’s from Jan:

As someone who was diagnosed about two years ago with hypothyroidism, I take Synthroid daily. Would I do better on Armour? I am a nurse, but I never see it ordered. Always Synthroid, she says. And she’s talking about Armour Thyroid, for the listeners.

Chris Kresser: Yeah. And another good question. There are a lot of considerations when deciding what thyroid medication is best. And, once again, disclaimer, I’m not a doctor. This is not medical advice. But, again, I can educate people on what the options are, and I think it’s good if you’ve got hypothyroidism, it’s really good to understand what the options are and why you might need one medication over another. I wish that more doctors did this kind of education, but it doesn’t seem to happen very often.

So you’ve got to know why the thyroid function is depressed, first of all, and how. For example, is T4 normal, or is it low? Is T4 normal and T3 is low? Which would suggest that T4 is not being converted to T3. For those who don’t know, T4 is inactive in the body. It needs to be converted into T3 to become active. So you could have normal T4 levels, but if you’re not converting T4 into active T3, you’re going to have all they symptoms of hypothyroidism.

So people who have this pattern―which I have to say is the most common pattern in my clinical practice. I see a lot of people with fairly normal TSH, maybe a little bit high; totally normal T4, right smack in the middle of the lab range, or even a little bit toward the upper end of the lab range; but then their T3 is quite low. This is common, and going back to what I said before, inflammation is one of the main reasons that T4 doesn’t get converted to T3 and inflammation is just ubiquitous in the modern world right now.

So these folks, who are underconverting T4 to T3―if you give them a T4 medication like Synthroid or levothyroxine, and they’re not converting T4 to T3―you’re going to have to use a whole lot of that medication to reach the destination, right?

Danny Roddy: Yeah.

Chris Kresser: I mean, you might have to use twice or three times the normal dose in order to get them, if they’re only converting a very small amount of it. So those people might do better on a T4-T3 combo like Armour. Armour is a combination of T4 and T3, in a certain ratio, that’s close to the right ratio for humans. So obviously that would be a better choice for people with this kind of pattern.

Danny Roddy: Chris, I’m sorry―Chris, do you have any opinion on the recent change in Armour’s formula?

Chris Kresser: There wasn’t―that’s kind of a little bit of a myth. The formula wasn’t changed. I think it’s always been 4.22 to 1. I can’t remember the exact ratio. But the ratio is still the same. What changed were the fillers. And that’s a good segue into the next consideration with thyroid medication, is the fillers. Because a lot of people with Hashimoto’s and autoimmune disease, a lot of people with hypothyroidism have Hashimoto’s.

Autoimmune disease is often caused by leaky gut, which we’ll talk about more, I think later in the show. And when you have a leaky gut, that means you’re often reacting to certain proteins in foods, especially corn and gluten. And these medications oftentimes use things like corn starch, and some even use gluten in their fillers.

So I think what happened with that formula change had nothing to do with the ratio of T4 and T3 changing, it had to do with the fact that some people were fine on the previous formula, they weren’t reacting to the fillers in the previous formula, but when it switched to the new formula, they started reacting to the fillers. So that’s another consideration.

And even beyond that, some people with Hashimoto’s produce antibodies to actual thyroid hormone, T4 and T3. That’s not common at all, it’s rare, but it happens. And in those cases, synthetic thyroid hormone will be better, because they’re less likely to react to it. So there’s a lot of considerations, as you can see. It’s not so simple.

Danny Roddy: Yeah, we always want to kind of have a format of exactly what to do, but, I mean, for all the reasons you just listed, it seems like you have to really specify case by case.

Chris Kresser: You do. And like I said, it would be great to find an endocrinologist that you can work with and who’s willing to explain all these nuances to you, but I think what happens with some practitioners is they kind of also want it to be easy and just to have―I’ve heard practitioners say, I really like Synthroid. Or, I like Armour. And I’m thinking, what do you mean, you like Armour or you like Synthroid? It completely depends on the patient’s presentation. You can’t just like one or the other, because it comes in a cool package or something, or it’s easier to use.

And I’m being a little facetious and kind of a jerk, but it’s a concern. It kind of makes me mad, so I’m just mentioning it. I know people maybe have some success with one more than another, but that’s no excuse not to keep looking deeper.

Can Antibiotics Cause Autoimmune Disease?

Danny Roddy: Agreed. Okay, so let’s get to our next question. This one is from Mary Russell:

My son is currently 14 and fighting autoimmune dysfunction. He was on antibiotics for a year straight when he was 8, and a year later developed what we now know to be an autoimmune problem. Do you believe that the overuse of antibiotics and the destruction of his internal gut flora could have at least contributed to his current autoimmune problem?

Chris Kresser: Absolutely. It’s so sad. I’m so sorry to hear about that. It’s just, you know, I think autoimmune disease is the disease of the 21st century. It’s really unfortunate, because it’s difficult to treat. We’re just kind of fumbling around with it. It’s so far incurable. We don’t have an idea of how to really get rid of it forever, and it ends up being something that we just manage as best we can. And for anyone who’s dealing with autoimmune disease, they know how difficult it can be to live with and just how challenging it is.

So, getting back to the question. If I say autoimmune disease is the disease of the 21st century, then I think leaky gut is going to be the pathology or the pathological mechanism of the 21st century.

Danny Roddy: Totally.

Chris Kresser: What I mean by that is, we’re just learning so much every day about how important intestinal barrier integrity is to health, and how severe and diverse the consequences are when that gut barrier becomes compromised.

So, just a few basics on the gut. I like talking about the gut, ’cause it’s such an amazing organ system. It’s home to―we have over a hundred trillion microorganisms in our gut. That’s pretty much an incomprehensible number for most of us. Just to give you an idea―one trillion dollar bills, laid out end to end, would stretch from the Earth to the sun and back, with a lot of miles to spare. You can do that a hundred times and it would give you some vague idea of what a hundred trillion is.

Now the human gut contains about ten times more bacteria than all of the human cells in the entire body. So I like to remind people of this, but we’re actually more bacteria than we are human, if you look at it that way. And some people kind of hypothesize that we evolved, basically, as carriers of bacteria. We’re doing their bidding more than they’re doing ours, in other words. And of those bacteria, there’s over 400 known bacterial species.

So I’m just trying to give an overall picture of the incredible vastness and diversity and complexity of what’s going on in the gut, and that we’ve only really begun to understand its importance. But here’s what we know so far.

We already know that healthy gut flora promotes normal digestion, it provides protection from infection, it regulates metabolism―it can actually even influence things like appetite control, and there’s some really interesting research about how gut flora is connected to obesity and diabetes―and it comprises more than 75% of our immune system. So the majority of our immune system is in our gut. That’s really important to understand.

When the gut flora gets screwed up, it causes diseases ranging from autism and depression and other behavioral disorders to autoimmune conditions like Hashimoto’s, Crohn’s, ulcerative colitis, and type I diabetes. And the list is very long, that’s just a few highlights.

So here’s the link between antibiotics and autoimmunity, getting back to Mary’s question. Antibiotics kill all bacteria in the gut, both bad bacteria and good bacteria. But over time, antibiotics kill a lot of the beneficial bacteria in the gut, and one of the roles of the beneficial bacteria in the gut is to keep the pathogenic bacteria in the gut in check, and keep it from overgrowing. So what happens is when you take antibiotics a lot, you end up with an overgrowth of pathogenic bacteria and that’s called intestinal dysbiosis.

These pathogenic bacteria produce endotoxins called lipopolysaccharide. And the lipopollysaccharide’s found in the outer membranes of these gram negative bacteria. And lipopolysaccharide or LPS damage the intestinal tight junctions and destroy the gut barrier, make it leaky.

The gut is designed to keep certain things in the gut, and excreted―meaning they don’t get into the bloodstream―and it’s also designed to let beneficial nutrients in. But when the gut barrier becomes compromised, it just becomes kind of like a sieve, and it loses the ability to keep things out. And then large proteins and food toxins slip into the bloodstream, they trigger and immune reaction―and even worse, some of these proteins, like gluten, resemble human proteins. So the body begins to produce antibodies against those proteins and starts attacking its own tissues in a case of mistaken identity.

So this is the process by which taking antibiotics can actually contribute to leaky gut and autoimmune disease. And, you know, leaky gut used to be a quack diagnosis that was pretty much limited to alternative practitioners with ponytails and new age music in their waiting room.

Danny Roddy: But it seems like just in the last couple years, it’s become legitimate. Because I remember, not that long ago, that―it was before sites like yours, before paleo came―is it mainstream? I don’t know―but before it came more to the public eye. I remember never hearing about leaky gut, and if I did, it was looked at with–

Chris Kresser: Scorn and disdain.

Danny Roddy: Exactly!

Chris Kresser: It was like the guaranteed way for you not to be taken seriously would be to walk into a room of doctors and say, Hey! What about leaky gut?

But now it’s completely mainstream, in the scientific literature, at least. I think, still, most general practitioners don’t know very much about it. But if you do a search on PubMed, for example, which is the database where all the scientific studies are indexed, you’ll see 9,000 results if you search for intestinal permeability, which is the medical term for leaky gut. And it’s about to get huge. Why? Why do I say that? ‘Cause guess what? There’s a leaky gut drug in development now.

Danny Roddy: Awesome. Is it composed of glutamine, or what?

Chris Kresser: It’s actually more sophisticated than that, but it’s designed to deal with―to prevent the tight junctions from being damaged. I learned about this at a recent seminar with Dr. Kharrazian. I can’t remember exactly what he said about what the mechanism is, but like I said in the last podcast, drugs don’t have side effects. They just have effects.

So if you shut down that one function, it’s almost guaranteed you’re going to be shutting down other functions, because proteins usually don’t just do one thing. They do other things, too. So who knows? Maybe it’ll be a miracle drug, but I’m not holding my breath for it.

My point was that once the big pharma gets involved and starts developing drugs, then the pharmaceutical sales brochures will be printed that have all this information about leaky gut, and then the pharmaceutical sales reps will get in their Ford Tauruses and canvas the doctors, and take them to Aruba and Whistler and ski trips and show ’em flashy PowerPoint presentations about leaky gut, and then everyone will know about leaky gut! But they’ll only know about it in the context of this drug that’s available to treat it. Anyways, yeah, you can tell―don’t get me started on that.

The next frontier, too―little sidenote here―is going to be leaky brain, because the blood-brain barrier is the other crucial barrier system, in the brain. And we know that the same things that cause leaky gut―the environmental toxins, the food toxins, stress, antibiotics, etcetera―can contribute to leaky brain. They often go together, which is why we see behavioral problems, and then things like Alzheimer’s and Parkinson’s and ataxia associated with gluten intolerance. But I’ll save that for another podcast.

Most of the research now suggests that, to get an autoimmune disease, you basically have to have a triad of factors. You’ve got to have some genetic predisposition, you’ve got to have some presence of environmental triggers like gluten, for example, or other food triggers or other environmental toxins, and you’ve got to have a leaky gut. Each of these is a risk factor on its own, but the bulk of the research suggests that those who develop full-fledged autoimmune disease tend to have all three.

Specifically, I’m referring to Alessio Fasano’s work, who’s a fantastic researcher, he’s one of my favorite, and he’s really established this connection between leaky gut, genes, environmental triggers, and autoimmunity.

So, that’s the connection, and I’m going to be writing a lot more about this in the months to come and we’ll be talking about it, I’m sure, almost every podcast.

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What Is the Best Diet to Heal the Gut?

Danny Roddy: It’s fascinating. That actually leads us perfectly into Matt’s question. Let me go with it. Okay.

Do you have any recommendations for an optimum diet for good gut health? Especially when dealing with dysbiosis, candida, leaky gut, exhausted adrenals, etcetera, ensuring the body is well-nourished with the right macronutrient ratios. Pretty much every candida diet out there will recommend low-carb based on the assumption that anything that converts to sugar/glucose/fructose will feed the candida.

There seems to be a lot of confusion over carbs, something I’m finding it hard to negotiate around. A paleo diet would include some starches, such as sweet potatoes and yams, but could these be irritants due to their density? Fruits are promoted in a diet such as SCD, however they could be problematic for blood sugar levels, fermentation in the gut, and fructose content. Grains and beans have much slower sustained carb release, but are notoriously difficult to digest, with all those antinutrients.

In your clinical experience, where would you compromise with carbs ensuring the least burden on the digestive tract, avoiding things like hypoglycemia, and having the least negative impact on the adrenals that perhaps too low on a low-carb diet can induce? Many thanks.

Chris Kresser: Yeah, there’s a lot in there. We could probably spend a whole podcast on that one. But I think I’d like to start―rewind a little bit to the first part of the question, which is―and I don’t mean this directed at Matt specifically, but when somebody comes into my office and says, I have candida, the first thing I say is, How do you know? Because I’m a little bit wary of that diagnosis. It’s thrown around a lot when people can’t figure out what’s going on otherwise.

Danny Roddy: Seems kind of like a scapegoat.

Chris Kresser: It’s real, there are certain people who have it. It’s real, but it is also a kind of scapegoat or a kind of a diagnosis of exclusion, like we’ve excluded all these other diagnoses, and we can’t really figure it out, so it must be candida.

You can test for candida, and I know some people will say the tests aren’t accurate. I think if you do a DNA PCR screen for candida and it doesn’t come up with significant yeast, it’s maybe not that likely that candida’s the issue. But anyways, it’s kind of a moot point because the treatment for leaky gut and for bacterial dysbiosis and yeast overgrowth is pretty similar, regardless. But I don’t like the idea of people carrying around the notion of candida unless it’s really there.

And the other problem is that then people tend to go and research candida diets online, and I think a lot of the candida diets are misguided. So, anyways, that’s just my little candida rant. But I think the best diet for healing the gut is something called the GAPS diet. That stands for Gut And Psychology Syndrome. I wish she would come up with another name for it, because it doesn’t really get what it’s doing completely, but―it was created by―it’s kind of a different version―an updated and proved, in my opinion, version of the specific carbohydrate diet that was created by Elaine Gottschall.

And Dr. Natasha Campbell-McBride, who I think is a genius and way ahead of her time, developed this because her son, I think, had autism. She was a physician in Russia―she’s in the UK now―and she researched the treatments that were available and just wasn’t satisfied at all. And the more she researched, the more she figured out that there was a connection between the gut, leaky gut, and brain―which we just talked about as becoming known in the research. She’s been at this for years, and early on, people were just dismissing her theories but she’s definitely been vindicated at this point.

So the GAPS diet removes all the primary food toxins, like grain seed oil, fructose, and soy, of course, but it goes a few steps further. It also removes all polysaccharides, which are the longer-chain sugar molecules. So this is where it differs from the paleo diet a little bit, because the starchy tubers which are allowed on the paleo diet, are not on the GAPS diet. Because the theory is that people who have compromised gut function can’t break those longer-chain sugars down into the single sugars that get digested. And then they become food for pathogenic bacteria in the gut and cause the problems that people are trying to treat with the GAPS diet.

The GAPS diet does not remove fruit, berries and things like that, so it differs from the sort of standard candida diet―or some candida diets, that remove those things. It also doesn’t remove nightshades specifically, which can be an issue with people, especially with autoimmune inflammatory conditions.

So what I do with my patients is I usually put them on some version of paleo or GAPS, or some combination, really, depending on their symptoms. I see fewer people having problems with starch than―I actually see people have problems more with nightshades than with starch, so I might be more likely to start with a paleo type of diet, but add the bone broth, which is one of the most important things in the GAPS diet because of the glycene, and it’s collagen-rich, it really helps rebuild the intestinal lining.

And then if they’re not―if I suspect that they need even more support, to be even more strict, I might have them do the actual GAPS diet, but take out nightshades and also limit fructose, because 30-40% of people don’t really digest fructose very well. That becomes pretty restrictive, so I only use that in the kind of a last-resort type of situation when somebody’s really in bad shape and they need immediate intervention.

For example, if someone’s got Crohn’s disease and they’re having 10-15 bowel movements a day, and they’re facing surgery or they’re about to start prednisone or something. I’ll put them on the GAPS diet and they’ll actually just eat meat broth, without even any vegetables, because the vegetables can irritate the gut lining when it’s super inflamed. But that’s not common, that’s only in a real crisis situation. Normally, for me, it’s some combination of GAPS and paleo. May include the starches, may or may not include the nightshades, and generally try to keep fructose pretty low.

You can still eat fruit when you’re limiting fructose. You just have to eat fruits that have about equal amounts of fructose and glucose in them. So that means you’d be staying away from watermelon, stone fruits like peaches, mangos, papayas, I think there are a couple―oh, apples. But berries and a lot of the other seasonal fruits are fine.

Danny Roddy: Yeah, I remember looking at the GAPS diet and was kind of perplexed at the recommendation for fruit and not starches. I didn’t quite get it. But the berries and the equal fructose to glucose makes a lot more sense.

Chris Kresser: I will say that some people don’t tolerate starches well, and I understand the mechanism that she’s proposing. Everything that we absorb, we have to break it down first, right? So theoretically, the longer the chain is of molecules that we need to break down, the more difficult that is going to be for the body.

So I get the theory, and I see that actually, it’s not just a theory, I’ve seen it with patients that can’t tolerate polysaccharides, like starch. However, I see a lot of patients who really benefit from the GAPS diet and seem to be able to tolerate starches fairly well. That’s just my personal experience, I see nightshades being more of an issue for most people. And I could be wrong, but I don’t think that Dr. McBride talks about nightshades much. Maybe she does, but that’s more of a paleo―that’s pretty common in the paleo world.

Danny Roddy: Chris, what’s your opinion on fermented dairy products? Isn’t Natasha Campbell really big on that?

Chris Kresser: Yeah. I mean, from the start, she’s telling you not only to remove the foods that irritate the gut and cause overgrowth of bad bacteria, but to start rebalancing the intestinal environment with good bacteria, and fermented dairy is one of the ways that she suggests doing that. I’m a big fan of fermented dairy, for people who can tolerate it, but it needs to be done carefully.

Obviously, if someone has an allergy to casein, which is the protein in dairy, that’s not going to work. And sometimes you need to wait until your gut barrier heals enough to where you can tolerate the dairy. Because if you’ve got a leaky gut, it’s pretty likely you’re going to react to dairy, even if you don’t have a true allergy to it, because it’s a common cross-reactive protein.

So, what I have people do sometimes is they do the intro diet without any dairy for a period of time, and then they add it back in, but extremely slowly. I actually have people start with a teaspoon of kefir, made from raw milk. And it sounds ridiculous, but it’s super potent medicine! And people will sometimes even react to that. And it might take them six to eight months to build up from a teaspoon to like a half a cup a day or a cup a day, which would be more of a therapeutic dose. But if they try to go any faster than that, they get flare-ups and constipation or diarrhea.

So the good news about gut healing is that we know a lot about how to do it now, a lot more than we did in the past. The bad news is that it can take a long time. If you’ve got a seriously compromised gut barrier, we’re talking about six months, and even longer, on a diet like this before you’re really back to where you need to be. And that’s assuming that the autoimmune condition that caused it isn’t just running out of control all the way through that.

Danny Roddy: It didn’t happen overnight and it’s not going to be fixed overnight.

Chris Kresser: Good point. Exactly right.

Danny Roddy: Chris, that is the end of our second episode.

Chris Kresser: Wow, already?

Danny Roddy: Okay, that’s going to bring us to the end of this week’s episode. Chris, how can we find more of your work on the internet this week?

Chris Kresser: Well, next Tuesday I’m recording a podcast with Robb Wolf and Andy Deas for their Paleo Solution podcast, which I’m really excited about. It’s going to be a good time. I’ll definitely report on the blog when it’s available, I think sometime later next week or the week after.

We did the Growing a Healthy Baby seminar last Sunday. It was really fun, a lot of people showed up. It sold out, actually, which was really exciting. And I’ve had several requests or questions about whether I’m going to be offering it for people who don’t live in the bay area, and the answer is yes. I’m planning right now to offer it as a four-week online class, maybe like an hour each week for a period of four weeks. Still trying to figure out the technical details there and the best way to do that. I’m also considering a DVD. So that’s that.

And then, I’m about halfway through the Nine Steps to Perfect Health series on my blog. If you haven’t checked that out, go to TheHealthySkeptic.org and you can catch up with the articles I’ve already written. I’ve got some good ones on deck.

And I think that’s it for this week.

Danny Roddy: It is a solid series, by the way. I think it’s fantastic. It’s very to-the-point, and any of the people that wrote in would be highly served by reading your articles.

Chris Kresser: Thanks, Danny. I just wanted―it’s kind of an outgrowth of wanting to have one thing to just refer people to. I get all these questions, you know? Like, what’s your theory on this? What do you think about that? And I just want to be able to go, read that! That’s what I think about pretty much everything related to nutrition and health right now.

And so my plan is to turn this into an ebook, which would make it even more accessible, just have everything in one place. And I’m really excited about having it all together there.

Danny Roddy: Awesome.

You can find me at Twitter.com/DannyRoddy and my website, DannyRoddy.com Keep sending us questions at TheHealthySkeptic.org and thanks for listening!

Chris Kresser: One thing about that, before we go! To send a question: When you go to the blog, there’s a category at the top, in the navigation bar, called Podcast. If you click on that, there’s a little thing that says, Click here to send us a question. And when you click on that, there’ll be a form that you fill out, and we’ll get your question. That’s the best way to do it and make sure that we get it and see that it’s a podcast question.

Danny Roddy: Awesome. Yeah, that question will go straight to me and then I will index them. Chris, do you have anything else?

Chris Kresser: That’s it!

Danny Roddy: Cool, man. I’ll talk to you―

Chris Kresser: Thanks, Danny!

Danny Roddy: Thank you.I’ll talk to you soon, buddy.

Chris Kresser: Thanks for listening, everybody!

Danny Roddy: Take care, guys!

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Join the conversation

  1. Hi Chris,

    Thanks for the informative podcast. I was just wondering if you could speak to this: So many people talk about Hashimoto’s disease, but very few people address Grave’s disease, which I have, and I already had the radioactive iodine treatment 7 years ago when I was 19. I was being treated by your average endo for years and only recently became aware of the big picture, now that I’ve declined since then greatly and my medications don’t seem to be helping anymore. Whenever I read information about nutrition and supplements for people with Hashimoto’s I just wonder how much of it will work for me? Do the same protocols help someone who just doesn’t even have a thyroid anymore from radiation therapy? Is inflammation still the main reason why I’m so sick and what is inhibiting my medications from being used properly in my body? Thank you for your help. I’m trying to get my life back together but with so much information out there it’s hard to focus on what will really help my individual case.

  2. I was diagnosed with Hashimoto’s about a year ago and have been taking Synthroid only, but I’m wondering if I should start adding in a T3 med as well as my level is in the low end of the normal range.

    Also, since I started taking Synthroid, I’ve been having horrible insomnia with a weird pattern. Even at a starting dose of 25mcg, I sleep for 5-6 hours and wake up wired and sweaty with anxiety. Some days I can’t fall back asleep and others it takes at least an hour, making my fatigue even worse. I haven’t found anyone else with this issue and I have no idea what’s causing it. My doctor has tested my cortisol levels, but they’re pretty normal except that they’re slightly low before bed. We’ve also been testing my blood sugar, and while it’s low, around 70, and I have hypoglycemia constantly, it’s not ridiculously low when I wake up early.

    If you have any suggestions as to what I could be doing better, or even a doctor in the NJ/NYC area, I’d really appreciate it. Thanks!

  3. Hi Chris can you tell me is naltrexone approved and readily available? Some websites say it’s not but many websites can be quite old.


  4. How long would someone take low dose Naltrexone for Hashimoto’s & Graves disease? 6 months? 1 year? For rest of ones life? Yes… Hashimoto’s & Graves at the same time. Thanks!

  5. Its funny how everyone is so convinced that gluten is the villain here , it seems that glucose intolerance causes all of the same problems you ascribe to gluten. A low gluten diet is also lower in glucose so it would help even if your biochemical theory were wrong. The thing is ,that glucose intolerance explains why the thyroid and sex steroids and growth hormone healing mediators all go to hell , since glucose intolerance causes hyperinsulinemia and the insulin is a proopiomelanocortin derived oligopeptide just like the thyrotropin and the gonadotropin and the insuline-like growth factor. which means that high glucose and high insulin in the blood feed back on all of the hypothalamic-pituitary axis and peripheral receptors for these hormones and gunk them up , thus imbalancing the system even before any autoimmunity gets started , this is the cause of metabolic syndrome. Of course rampant vit D deficiency in the developed world makes the autoimmunity arise sooner but really its not even needed to explain these endocrine problems. So why the gluten fixation?

  6. I am working with my doc to help heal my gut. I started taking ther-biotic probiotics with no reaction. Everything was good. Then I added in Glutagenics and ended up with watery diarrhea a couple days later that didn’t subside until I removed glutagenics. I reintroduced a half dose after some time without any noticeable side effects. She wants me to continue doing this. However, I am a bit skeptical. Why would I have this reaction? Is it safe to continue the half dose of glutagenics? I am consuming 2 cups of bone broth daily in addition to beginning the autoimmune protocol. Wondering if I should just see how this pans out without the glutagenics. Thanks for any advice!

  7. Thanks Chris, this is one of your most informative podcasts about Hashimoto’s and I continue to come back to it to reference as needed. 🙂


  8. I have had hypothyroidism since I was 18 (I’m 38) in 2011 (a year after having my first baby) I developed severe itching and major (like I was in a car accident) bruising as a reaction from thing I was eating. Exactly 2.5 hours after I ate thing I would itch severely but just my legs from my knees to my hips. Sooo weird. I couldn’t figure out my problem. Prior to my prefnancy for a year or so yeast infections were just as regular as my monthly cycle. My dr tested me for diabetes and checked my pituitary and other random things but couldn’t get my T4 n T3 to work together. I was miserable and scared to eat things in fear of itching to death. Then jan of 2012 someone face me the book g- free diet. I read it and had so many of the symptoms that I had to try it. I immediately went cold turkey gluten free ( which felt like a food death sentence) I immediately stopped about 15 lbs in like 8 weeks as a bonus. (I’m getting to my question soon) in week 12 of the diet I went out to eat with my family to a Mexican restaurant. I asked if the chips were made of corn not flour cuz I couldn’t have wheat ( which no one understands) and they either misinformed me or seriously cross contaminate everything without knowing. I threw up for 15 hours hardcore that evening. I’m guessing that the gluten was out of my system and then I ate a bunch of it without knowing. Now I’m just scared to eat anything near it. It’s hard to even eat out socially without bring difficult. I really want to know exactly what it is I’m allergic to but to get tested for celiac u gave to eat those things and have it in your system to test it. I’ve since lost 35 lbs and my t3 and t4 are in perfect harmony haven’t itched bruised or had a yeast infection since I went gluten free. Only problem is Im having a problem getting prego again and my “gluten allergy” ( self diagnosed) raised the eyebrow if my OB . Is there any reason I should try to see what I’m really reacting to? I don’t feel like its an allergy…. Seems like intolerance us different?? So I continue to be blindly gluten free cuz it’s been my best fix. Went back to my doctor a year later so I could renew my thyroid script and he asked what I’m doing to Acheive the good weight loss better numbers and no infections. I told him I went gluten free and he said “oh yes that could be really good for you”. It’s so frustrating that because drug companies do all the research you can’t find a dr that knows anything about the effects of food with disease. Thanks for letting me share… No one understands why be gluten free. Just wondered if I should test myself further somehow? Also wish I could get everyone gluten free cuz u feel so much better! Thanks for your show.

    • The only definitive test would be a DNA test as other tests tend to have a high false negative rate (low sensitivity). People don’t realize that there are glutens in all grains with corn having a high gluten content and rice having the lowest (they’re just different from the gluten found in wheat, rye and barley) but they can keep you from healing. Dr Peter Osborn discusses this in detail on his site http://www.glutenfreesociety.org. Lots of good free information through signing up for his free updates. But I think you and your body already know the answer to your question and don’t need to definitive diagnosis.

    • If you have been gluten free for a substantial period of time don’t bother trying to get a medical diagnosis. The blood test that is supposedly 98% accurate only works if you are currently on a normal gluten containing diet. Same goes for an upper endoscope. Your villi will be mostly healed & most pathologists don’t “grade” the villi as clumped or misshaped; only present or not present.
      Your severe reaction to being re exposed is all you need to know. Now do your homework to understand all the places it can hide. This took me years and I rarely eat out because even restaurants that have GF menus have poisoned me. Some real eye openers were : french fries or any seasoned potatoes.All restaurant frozen fries are rolled in wheat so they won’t stick together & fry crisp. Ice cream: all the cheap store brands and soft serve ones use wheat instead of cream as a cheap thickener. Turkey and cold cuts in general. They are injected with “broth” solution which is usually wheat or MSG. Look for gluten free and antibiotic free or don’t buy it; especially if you are making bone broth from chicken or beef. Read every label every time if you are using prepared foods as they can change the formula any time. Learn the 20+ names for MSG to avoid as well.

  9. Hi Chris,
    I have just started subscribing to your podcasts. I linked to your terrific “eat real food” blogpost today. Great job!
    I’m curious as to what comments you got from the folks at science-basedmedicine.org. I think highly at their work, despite the fact that they’re not necessarily up to date on nutrition. Where are the comments from them? I’d be interested in seeing what criticism you got.

  10. As for Iodine and autoimmune thyroid disorders here is a cut and paste of what Dr. Brownsterin says.
    ================================================== ==============
    Brownstein, D

    “The best results with iodine, as with all nutritional supplements, can be achieved as part of a comprehensive holistic program. As I describe in my book, Iodine: Why You Need It, Why You Can’t Live Without It 2nd Edition, adding magnesium and vitamin C will enhance the effects of iodine. This is particularly true for individuals experiencing a number of factors related to iodine. This article will cover four major factors sometimes associated with iodine supplementation and how vitamin C and magnesium can support individuals with these concerns:

    1. Allergy
    2. Autoimmune thyroid disorders
    3. Detoxification Reactions
    4. Iodism

    “Some physicians feel that iodine supplementation causes autoimmune thyroid disorders. They also claim that those with autoimmune thyroid disorders should not take iodine as it will exacerbate their condition. Before conventional medicine began using radioactive iodine to treat autoimmune thyroid disorders, large doses of iodine was the treatment of choice in treating autoimmune thyroid disorders. There are numerous reports in the literature, some dating back well over 100 years, showing the benefits of using iodine in excess of the RDA to treat autoimmune thyroid illnesses. If iodine was the cause of autoimmune thyroid illnesses, these illnesses should have been decreasing over the last 30 years. The opposite has occurred. In the United States, iodine levels have fallen approximately 50 percent over the last 30 years while, at the same time, autoimmune thyroid disorders have been rapidly increasing. My clinical experience has shown that in an iodine deficient state, higher doses of iodine, as part of a holistic treatment program, are an effective and safe way to treat autoimmune thyroid illness without appreciable side effects.”

    “Iodine can cause a detoxification reaction in the body by facilitating the body’s release of the toxic halides fluoride and bromide. If the body’s detoxification pathways are overloaded when the toxic halides are being released, a detoxification reaction can be triggered. A detoxification reaction can take the form of fatigue, muscle aches, fever, diarrhea, and brain fog, skin rashes, etc.”

    “If one is found to be iodine deficient, it is best to correct other nutrient imbalances before instituting iodine supplementation. Proper dosing of magnesium, Vitamin C and minerals will maximize the response to iodine. Before beginning any nutritional program, the best results can be achieved when working with a health care practitioner skilled in the use of natural agents.”

  11. Chris: is there a definitive diagnostic test to determine if someone has a leaky gut? Thanks

  12. Chris

    What are the ideal T4 T3 numbers?What are the numbers we should see for this in pregnancy?