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Answers to Your Burning Questions about Digestion


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In this episode I answer frequently asked questions about digestion, covering topics like parasites, stomach acid, the GAPS diet, SIBO and more.

Questions include:

  • How to differentiate between a gut infection and food sensitivities?
  • How to boost your HCL production
  • Can strengthening the immune system take care of parasites?
  • When to call it quits on the GAPS diet
  • Is FODMAP sensitivity permanent, or can it be treated?
  • What causes digestive reactions to carbohydrates?

The next podcast will be our last with Danny. We’ll make it a good one!

Full Text Transcript

Danny Roddy:  Hello everyone, and welcome to the Healthy Skeptic Podcast.  My name is Danny Roddy of DannyRoddy.com, and with me is Chris Kresser, health detective and creator of ChrisKresser.com.  Chris, how are you doing, my friend?

Chris Kresser:  I’m good.  A little sleep deprived, and I can’t blame Sylvie this time.

Danny Roddy:  Well, you just showed me why.  Why don’t you tell everybody listening why.

Chris Kresser:  Yeah, so I’m super excited about this program that I’ve been slaving away on.  You know, I’ve been working with people on health-related issues for a long time now, probably, I don’t know, over 10 years, and there’s absolutely no doubt that the biggest issue that I see in my practice and I hear about from people on my blog and who listen to the podcast is confusion about what to eat.  I’m sure you see this a lot, Danny, too.  I mean, people are basically paralyzed because they don’t know what to eat.  And I have patients that tell me they feel like they’ve got this voice in their head like everything they could put in their mouth is wrong or bad from one perspective or another.

Danny Roddy:  I can find a reason not to eat anything.

Chris Kresser:  Right, except air, right?  You could be a breatharian, but actually you can find a reason not to do that because you’ll starve to death.  So, I created this new online program called the Personal Paleo Code, and it was born of my experience working with hundreds of patients and hearing from thousands of blog readers and podcast listeners around the world, and it includes a 3-step process to help you figure out exactly what works and doesn’t work for your body.  So, rather than following a canned approach, however good of a starting point that canned approach is, it will never be totally customized for your particular body.  So, I have a process that I use in my practice for helping patients to figure out what that is, and the feedback has been so good, and it seems to be so effective that I just wanted to share that with a wider audience.  So, the core of the program is that 3-step process for determining what your own optimal diet is instead of following some guru’s advice, including mine!

And then the second part, which I’m really, really excited about, is we’ve built this meal plan generator.  It’s a web application, and it allows you to create a completely customized meal plan using only the ingredients you want to include.  So, you open it up, and let’s say you’re on an autoimmune Paleo diet, and you want to keep it under 50 grams of carbohydrates.  All you do is select remove nightshades, remove dairy, and then there’s a little button that says keep it under 50 grams of carbs, and then you can generate a single meal, you can generate a one-day meal plan, or you can generate a one-week meal plan.  And then all of those meals pop up on a grid, and they’re hyperlinked so you can click on the recipe and it goes to the single recipe page, picture, instructions, everything.  You can print that out.  You can print out the whole meal plan.  And you can save recipes to favorites.  You can search; it has a full search function.  It has an index so you can look up recipes by category, like if you only want to look at breakfast or you want to only look at snacks.  So, this is just incredible.  My wife, Elanne, is more excited about it than, I think, anybody else, because it’s pulling recipes from all of the, in my opinion, best Paleo recipe sites, like Health-Bent and Nom Nom Paleo and Paleo Diet Lifestyle.  And we’re gonna launch with over 300 recipes, but we are just gonna keep adding recipes as we go each month, so that’s awesome.

And then we’ve got all kinds of extra stuff.  Like, we’ve got guides on fermented foods; on fats and oils, you know, which ones to cook with, which to use cold, which to avoid completely; nuts and seeds, you know, how to properly prepare them, which I’ve written about recently; how to make bone broth, because that’s something I think that’s often overlooked as part of a healthy diet.  We’ve got even a guide on kitchen equipment, like my picks on particular kitchen stuff that’s good to have around.  We’ve got special tweaks for blood sugar and thyroid issues, weight loss, autoimmune disease, and other health conditions, so it’s kinda like being a patient in my practice without actually being a patient, but even a lot more beyond that with the meal plan generator.  And then we’ve got another web app called the progress tracking app, where you can go in there and fill out a questionnaire each week, and then you get to see your progress charted on a graph as you move through the stages of the program.  So, yeah, I’ve been a little busy!

Danny Roddy:  I don’t understand how you have a new child and you put all this together.  It consumed my whole life writing, like, 40 pages, and you get all this done.  Unbelieveable.

Chris Kresser:  I don’t know.  I’ve definitely brought on more help this time around, so that makes a big difference, but I have to say the last several weeks have been probably the most productive period of my life somehow.  I don’t really understand it either.  So, the other thing I want to mention is we’ve finally figured out a name.  You know, we’ve been talking about changing the name of the show, and we’re gonna do that.  It’s gonna be called Revolution Health Radio.  Probably the logo will have some kind of wordplay with revolution, evolution, evolutionary health.  And radio over podcast because I’ve just never really liked the term “podcast,” and this is my show, so I get to choose!  I’d rather have a radio show than a podcast, so it’s Revolution Health Radio.  We’ll have a new graphic, new show title in iTunes.  You don’t have to do anything, dear listener.  You’ll just notice that next week Danny will say, “Welcome to Revolution Health Radio,” and that’s it.

Danny Roddy:  I might screw that up, though, Chris.

Chris Kresser:  That’s all right.  You’re allowed.  You get a couple times before you’re fired!

Danny Roddy:  Good thing I edit this show.

Chris Kresser:  Right!  So, what’s happening with you, Danny?

Danny Roddy:  Nothing much.  Just wrapping up, kinda sitting on the book, tweaking a few things because I’ve actually had an amazing chance to work with a couple people, so it’s really putting a lot of my ideas to the test, and I’m getting a lot of feedback from them.  Like, they fell in my lap, so I’m really thankful.

Chris Kresser:  That’s where the rubber hits the road, huh?

Danny Roddy:  Exactly, like, you get to kinda test out your ideas every day, where I meet with a lot fewer people, or I only really correspond with people over Facebook or email.  So, it’s exciting.

Chris Kresser:  Yeah.  I keep waiting for you to send me the damn book!

Danny Roddy:  I will as soon as it’s finished.

Chris Kresser:  Are you making me pay for it?  Is that what it is?

Danny Roddy:  No!

Chris Kresser:  I’m happy to pay for it!

Danny Roddy:  With that said, do you want to get to our first question, Chris?

Chris Kresser:  Yeah.  We’re gonna do an episode about digestion.  So, I was on the awesome Balanced Bites Podcast.  I hope you guys all go listen to it.  It’s Diane Sanfilippo and Liz — Do you know Liz’s last name?  I feel bad.

Danny Roddy:  I don’t.  I’ve just met Diane at AHS.

Chris Kresser:  Cave Girl Eats, right?  But they have a great podcast, and Diane totally gets the science, but she’s really into breaking it down into an easy-to-understand format and really focusing on the nutritional angle.  It’s an awesome show.  You should check it out if you haven’t already.  And she wanted to have me on to talk about digestion, and I did a blog post soliciting questions about digestion, and we got, like, 60.  So, obviously we didn’t have time to answer them, and I thought it would be a good idea to try to get to some of them, just to do a whole show on digestion, so here we are.

How to differentiate between a gut infection and food sensitivities

Danny Roddy:  Let’s do it.  This first question is from Emm.  She asks:  “I’ve been trying to follow a Paleo diet since I got a bad GI virus in July.”  She puts in parentheses:  “(I didn’t take any antibiotics, just waited it out), and now my stomach is not the same. I get cramping/pain/bloating after eating any food.  That includes meat, veggies, fruits, white or whole grains, fats, both together or alone.”  She continues and says:  “I followed a Paleo diet with just veggies and meat for two weeks, and I felt like I had knives in my intestines.  The only thing I can digest without incident is freshly made veggie juice.  I take a probiotic two times a day with meals.  Note: Drinking red wine with any food relieves all of my symptoms!  Please help.  I’m slowly losing my daily life, and I need to go back to digesting at least some food again!”

Chris Kresser:  Yeah, that’s bizarre.  Drinking red wine relieves all symptoms.  I thought I had it all figured out up until that line.

Danny Roddy:  I could guess why that was happening.  I think red wine might increase gastrin?

Chris Kresser:  Yeah, I mean, there’s a few possibilities there.  One is just the increase in HCl production from the wine.  Another is that alcohol can be mildly bactericidal.

Danny Roddy:  Oh, yeah.

Chris Kresser:  Although, I mean, you hear about people drinking, like, a fifth of tequila or something in Mexico if they get sick with a gut infection.  I don’t know that the same principle applies here.  But let’s back up a little bit and talk about her exposure to the GI virus.  So, I’m not so sure that that was a virus.  It’s possible it was a parasite or something else.  I mean, the symptoms can be really similar, and if she continues to have symptoms after a while, one possibility is that it was a virus that just really altered the gut flora and caused some gut-brain axis issue.  But another possibility is that it wasn’t a virus and it was a parasite or an opportunistic or pathogenic bacteria and that she still has it and that’s why she continues to have the symptoms she has.  That’s actually fairly common in my practice, and when I see somebody who has made all of the dietary changes, you know, they’re eating a clean diet, and they’ve been doing that for a while, and they’re still having crazy symptoms no matter what they eat, that’s a big red flag for me to start going looking for an infection.  And I would do a stool test.  I use Metametrix.  I prefer them over other labs.  And I would try to at least rule that out, if there is something present that’s causing this continuation of symptoms, because that’s definitely my guess.

Danny Roddy:  I’m actually trying to reference it.  Paul Jaminet.  He was saying there was some way, like, depending on if you had really bad gas you could find out what kind of infection you had, but you were saying if it’s persistent, then it’s more likely a parasite.

Chris Kresser:  Yeah, I think it’s more likely a parasite or bacteria than a virus that was just passing through.  Like, stomach viruses tend to be transient, you know, just in the same way that you get a cold.  But parasites tend to stick around unless you treat them.  That’s what they do.  I think what you might be thinking of is Paul, when he was on the show, was talking about how ketones can feed yeast, and a ketogenic diet can actually be harmful when someone has a yeast infection, and I think that’s one of the perils of the GAPS diet, and we’re gonna talk about that later in another question.  But for now, I would say to Emm the first thing to do would be to get a Metametrix stool test.  Usually you have to work with a practitioner for that because they don’t deal with the public directly, and at least rule out some type of pathogenic infection that’s still present, because that would be my guess, hearing those symptoms.

Danny Roddy:  Cool.  Good stuff.  I’m looking at Paul’s thing.  It was the difference between bacteria.  He says bacteria tends to produce more acute transient postprandial symptoms like gas and bloating.  OK, I’m thinking of fungi.  And he says fungi tend to produce more chronic, slowly varying symptoms, like from circulating toxins.

Chris Kresser:  Systemic, yeah.  I would agree with that for the most part.  There are certainly chronic bacterial infections that can produce chronic and slowly changing systemic symptoms, but in general, that’s a fair characterization, I think.

Danny Roddy:  Would there be a way of telling if it was a parasite or a fungus, or is that where testing would be really helpful?

Chris Kresser:  Yeah, that’s where testing would be helpful, but some of the cardinal symptoms of parasitic infections are cyclical symptoms because parasites have specific life cycles.  So, if I have a patient that is basically fine or does pretty well for 10 days and then has an intense flare-up of symptoms for a few days and then does well for 10 days and then has an intense flare-up and it’s pretty regular like that, that can be a real sign of parasitosis.  Extreme hunger even after eating is another typical sign of parasitosis.  Skin stuff can be either fungal or a parasite.  A strange test in the mouth, like a bitter or metallic taste, can be parasitic.  So, there are some things that make me think in that direction, but it’s difficult to do without a test.  And let me just say that you don’t need to go to a third world country to get a parasite infection.  In fact, most of my patients that have parasite infections have not done third world travel, so they’re all around us in the environment, even here in the highly sterilized first world country we live in.

How to boost your HCl production

Danny Roddy:  OK, this is the next question.  This is from Daisy, and this is a related question:  “How can I boost my HCl production?  From what I understand, we all lose the ability to make enough as we age and lack of it is the root of all sorts of issues.”  And she notes:  “Excess gas, bloating, general belly discomfort after eating, candida overgrowth, recurrent UTIs.  Have I understood right, and if so, is there an alternative to lifelong supplementation?”  She she adds:  “I know it’s a good idea not to drink loads of water while eating because I might choke :), but could low level, chronic dehydration have an effect on stomach acid production?”  What do you think, Chris?

Chris Kresser:  OK, so in order to answer the question how can I boost my HCl production, we, of course, always want to ask the other question, which is what’s causing the decline in stomach acid production?  There are some common causes of that.  The most common ones would be obviously drugs that decrease stomach acid production.  So, those would include the obvious PPIs and over-the-counter acid-suppressing drugs, but they also include drugs like antibiotics and birth control pills.  And the second thing would be H. pylori infection.  So, H. pylori, Helicobacter pylori, is the bacterium that has been shown to contribute to ulcer formation, and this was a pretty interesting story. . . thinking if I want to go there. . . no, I don’t.  We probably don’t have time.  I like to ramble off on those tangents sometimes, but basically I’ll give you the short version because it is pretty cool.  It used to be thought that ulcers were caused just by stress, and there was a guy in Australia, a doctor who came to believe that they were actually caused by a bacterium called H. pylori.  Nobody believed him.  He presented this data at medical conferences.  He was basically laughed off the stage, and growing increasingly desperate over the years, he finally decided to swallow a vial full of H. pylori.

Danny Roddy:  Shut up.  Really?

Chris Kresser:  I’m not joking.  This is 100% true.

Danny Roddy:  I didn’t know that’s how —

Chris Kresser:  This is commitment to science, OK?  Or being right!  I don’t know what was driving him, but his name is Dr. Marshall, I think.  And he swallowed the H. pylori, and lo and behold, he developed an ulcer, which he did not have before.  And then the coup d’etat was that he treated himself with an antibiotic and cured his ulcer.  So, even after that, believe it or not, people were still skeptical for a while, I mean, which is just crazy.  Shows you how hard it is to change the dominant paradigm.  So, he ended up winning the Nobel Prize for Medicine, so he got the last laugh, right?  Anyways, we know now that H. pylori does contribute to ulcers.  It’s a very common infection.  By the time we’re 55 years old, one in two people have H. pylori.  Some people believe it’s a normal resident of the digestive tract, and the evidence that supports that is that H. pylori has been shown to have some pretty positive immunoregulatory effects.  So, we evolved over millions of years with pathogens, and some of those pathogens actually exist in a symbiotic relationship with us, so they tune our immune system, they affect our genetic expression.  Actually a lot of what used to be called junk DNA, which is now called noncoding DNA, is thought to have been originally derived from retroviruses.  So, essentially a lot of our genetic code is from viruses that we evolved with over time that came to play an important role in our genetic evolution.  H. pylori, however, when it becomes overgrown, that’s when it is an issue.  So, for a lot of people who carry H. pylori it’s probably not an issue if they have a good balance of gut flora and a healthy gut environment, but when it becomes overgrown, just like when anything becomes overgrown in an ecosystem, that’s when all hell breaks loose.

In the case of H. pylori, one of its survival strategies is to suppress stomach acid production because one of the purposes of stomach acid is to protect us from pathogens.  Pathogens can’t live in a highly acidic environment.  Most of them can’t, anyways.  So, H. pylori is pretty clever.  It goes in the stomach and suppresses stomach acid production so it can survive.  So, I think for people, especially people over 50, one of major causes of declining stomach acid production is H. pylori.  And so, in that case, I would want to treat the H. pylori, but the way I do it is a little bit different than the conventional approach, which is to eradicate it completely.  The more I work with people, the more I think it doesn’t need to be eradicated completely for the reasons that I just said, you know, if it’s a normal resident of the digestive tract and it’s a question of optimizing and normalizing the environment or the ecosystem instead of total eradication, which can actually cause a lot of other problems.  The number of antibiotics you have to take and the intensity of that course of antibiotics you have to take to fully eradicate H. pylori is gonna eradicate a lot of other stuff too, good stuff, good bacteria that we need to perform all of the functions that good bacteria does, like digesting food and regulating the immune system.

So, I would say, obviously don’t take any drugs that suppress stomach acid production.  I would say treat H. pylori.  I would say another cause is stress.  So, acute stress can actually increase stomach acid production, and most people probably experience that, but chronic stress has the opposite effect; it decreases stomach acid production over time.  So, taking steps to manage stress is important.  And then, eating fermented foods, using apple cider vinegar and, to some extent, alcohol, as we talked about in the last question, can promote stomach acid production.  So, those are some ideas.

Danny Roddy:  What percentage of your patients do you think have H. pylori?  I remember Stephan’s article, and he pointed to some article on PubMed that said, like, 80% of Americans or some ridiculously high number.

Chris Kresser:  Yeah, I’ve seen different estimates.  I’ve seen everything from 1 in 2 to up to 80% to 90%.  I think the better question is what percentage have a pathogenic load of H. pylori.  And that’s fairly high, because I have a questionnaire that’s designed to identify low stomach acid production, and like I said, there are other possible causes of that, but I think in a lot of cases it’s H. pylori.  And I would say about 60% to 70% of my patients have low stomach acid.  So, it is definitely a big deal.  The last part of her question, the reason it’s not a good idea to drink a lot of water while eating is that it can dilute the stomach acid, right?  So, if you fill up your stomach with water, then the stomach acid is not gonna be as effective as it would be if you’re just eating the food.  Chronic dehydration effect on stomach acid production — I’m not aware of any particular link, but dehydration can cause so many problems that I wouldn’t be surprised.

Can strengthening the immune system take care of parasites?

Danny Roddy:  Good stuff.  This next question is from Brianna, and she asks:  “Can strengthening my immune system alone take care of a parasite issue?”

Chris Kresser:  It’s possible, but I rarely see that.  Parasites need to be treated, in my experience.  And I might surprise some people here when I say this, but I think in a lot of cases drug treatment for parasites is actually a better choice than natural treatment.

Danny Roddy:  Bite your tongue!

Chris Kresser:  Yeah, exactly!  You know, my philosophy on medicine has always been whatever works and causes the least harm.  I’m really not that dogmatic.  Of course, I prefer natural approaches because I think they satisfy that criteria more often.  They work well, and they’re less likely to cause harm, so I prefer them.  But if a drug satisfies that criteria and I think it’s a better choice than a natural alternative in that it causes less harm and it’s more effective, I’m gonna recommend that, and that’s true, like in cases of people with Hashimoto’s, I think taking thyroid hormone is a good idea for most people.  Low-dose naltrexone we’ve talked about a lot on the show, and I think that’s one of the classic examples.  I mean, if you can take a very safe low dose of a drug like that and avoid life-altering drugs that are common in conditions that people take LDN for or the intense suffering and increased risk of complication for other diseases, then I’m all for it 100%.  And with parasites, it’s not a hard-and-fast rule, and it’s a case-by-case decision in my practice, but in some cases with certain parasites, particularly the ones that are really difficult to treat, like Blastocystis hominis and Dientamoeba fragilis, I will often refer a patient out to a doctor to do a particular antibiotic protocol that I’ve learned about from the clinic in Australia that is more experienced treating parasites than just about any other place I know about, because what I’ve seen is that those drugs work and they work pretty quickly, and so, yes, there is some damage to the gut flora, but often with herbs for parasites, you have to take them for a really long time for them to completely get rid of the parasites, and even then they don’t necessarily always work for the more virulent ones.  And that means that over that entire time, you’re taking pretty intense antimicrobial substances that are gonna have an effect on the gut flora and that are gonna be really depleting.  So, in my experience personally, a lot of people know that I got into this whole thing, medicine and my blog, because I was infected with several parasites when I was traveling in Indonesia back in 1998.  And it was a long, multi-year process of figuring out how to deal with it, and I took a lot of herbs during that time because that was my inclination and I was studying Chinese medicine, and the herbal formulas that I took kind of wrecked me more than the drug treatments that I ended up doing, and they didn’t work as well.  So, once again, it’s never black or white.  That’s why I try not to be dogmatic about things.  Whenever I think I have an approach that works, there’s always an exception that comes up.

Danny Roddy:  Well said.  At least in the case of thyroid, is it true that traditional diets used to contain a fair amount of thyroid, so in a sense, taking something like Armour or desiccated thyroid you are kind of getting back to the roots of a traditional diet that would have contained — I think I read something that almost 1/2 grain of thyroid would have been consumed daily?

Chris Kresser:  I haven’t read that.  I haven’t thought about it that way, but that’s interesting.  I think yes and no.  I know a lot of people are supplementing with or taking thyroid hormone, and I’m a big fan of that when it’s necessary.  I’m not such a big fan of just kind of the idea that everybody should take thyroid hormone, and there is that idea out there in natural medicine.  A lot of patients come to me and they’re taking Armour or something, and I say:  Oh, so you have hypothyroidism?  And they’re like:  No, I was just seeing a naturopath and they thought, you know, since I was having some trouble with weight loss that I should take Armour.  And I’m not really a fan of it in that respect, because taking thyroid hormone when you don’t need it can really trash your adrenals, and I have a lot of patients in that category who have been on thyroid medication for a long time, they didn’t need it, and that really kind of worked over their adrenals because it up-regulates your metabolic rate, and it’s kinda like having the idle of your engine of your car turned up too high for too long, and that’s gonna shorten the lifespan of the engine and cause other mechanical problems.  So, I think eating actual thyroid gland and even maybe taking some glandulars for people who might have a subclinical hypothyroid condition, there’s something to be said for that, but — and I’m not saying you were suggesting this, Danny — but just I see a lot of people in my practice who are taking thyroid medication that don’t need to be.

Danny Roddy:  Totally.  I wouldn’t suggest it either.  And also taking thyroid can increase the need for almost every nutrient, so if your diet isn’t in place, it’s really —

Chris Kresser:  Bad news.

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When to call it quits on the GAPS Diet

Danny Roddy:  Playing with fire, yeah.  All right, this next question is from Kaitlyn:  “I’ve been following your recommended diet for about 1-1/2 years now.”  I didn’t know you had a recommended diet!  “Started GAPS Intro four months ago but can’t comfortably move on to Full GAPS.  I feel like I have more constipation and more bloating problems as I’m purposefully trying to heal my gut flora than I ever did before starting GAPS.  How is that possible?”  So, she’s having more issues since going GAPS.  She goes on to say:  “Pretty frustrating.  My husband has been eating the same as me and also can’t move on to Full GAPS.  He now has persistent bloating and diarrhea but never had either before GAPS.  We both consume plenty of fermented foods, Bio-Kult, and fermented cod liver oil.  I take magnesium supplements each day to try to prevent the constipation, but my husband does not use magnesium since his digestion tips the other way.”  I don’t know what. . . oh, OK.

Chris Kresser:  Because they were using magnesium for constipation, but if he’s having diarrhea, he obviously doesn’t want to do that anymore.

Danny Roddy:  Got it, and she asks:  “Are all of these symptoms just part of the long healing process, or is something else going on altogether?”

Chris Kresser:  OK, this is a great question.  I’m so glad it came in, because we can cover a lot of important practical and philosophical issues.  So, let’s start with the philosophical.  You know, it’s already a theme in this episode, and I think people know this about me just from listening to my podcast and reading my blog, is that there is no one-size-fits-all approach.  And of course, that’s the whole purpose behind the Personal Paleo Code program that I just created, because I think a lot of the confusion about diet, like people saying:  Well, is white rice OK, or is dairy OK?  The answer is always it depends, and any prescription that claims to be appropriate for the 6-1/2 billion people on Earth is always gonna fall short.  [baby crying in background]  It sounds like Sylvie’s having a little meltdown out there!  So, yeah, I mean, I just can’t emphasize that enough.  And I think that my, sort of, mission is to try to alleviate some of the suffering and confusion out there about diet by getting the message across that the only diet that is the right diet is the one that works for you.  And so, with GAPS, I think the GAPS diet is great.  I use it in my practice.  It’s really helpful for certain people, but it doesn’t work for everyone, and it doesn’t work forever even for somebody that it does work for.

So myself, I was on the GAPS diet for about eight months, and then at the end of that eight-month period, things started to shift back in the other direction.  I just started to have some digestive symptoms again, and I started to feel lower energy.  I just wasn’t feeling as good overall, so that was my trigger to start adding things back in.  The first thing I added back in was starch, and I had absolutely no problem with it at all, and I felt great.  It was awesome to start eating sweet potatoes and potatoes and yuca and taro and all of that stuff, and it increased my energy levels, and it made my digestion better.  So, I could have at that point, if I would’ve gone on the Yahoo group for the GAPS diet and said:  Geez, guys, I’m having all these problems.  What should I do?  I guarantee they wouldn’t have told me to start eating starch.  They would’ve said:  Oh, maybe you should be doing more enemas or maybe you should cut back more on the fruit.  Or whatever it is, it would all be in the context of, like, you’re not doing the GAPS diet right and you should try harder, because when people adopt a certain approach, I mean, this seems to be some kind of human tendency, right?  Like being part of a club.  It’s ubiquitous across human culture, and people get really wedded to a particular perspective or approach, and then it’s like that old saying when you have a hammer, everything starts to look like a nail.  And so, if an approach stops working, then rather than saying:  Hmm, maybe this approach isn’t the right one for me, it’s like maybe I’m doing it wrong or maybe I should do it more or harder or better, and I see that a lot on the Internet and within all of these communities around dietary approaches.

So, the tricky thing, as Kaitlyn is asking about, is when to know whether it’s just a temporary kind of road bump, a die-off reaction, where maybe you’ve reached another level of healing and there’s another level of bacteria or yeast that are dying and that’s causing the symptoms and you should just push through it or whether it’s actually an indication that this is not the right approach anymore and it’s time to move on.  Unfortunately there’s no easy way to answer that question, and it’s really a case-by-case thing, but I would say in general, if you’ve gone for two, three, four weeks and the situation is just deteriorating, you’re not having any windows of time in that period where you’re actually feeling better, because die-off shouldn’t be just persistently bad without any let-up.  Usually die-off looks like a period of worsening symptoms, followed by a period of improving symptoms, followed by an improving of worsening, like that.  Whereas, something that’s not working, you would just expect things to get worse and worse over time.  So, that’s one possibility in terms of determining when to make the change.

Danny Roddy:  Also, let your body guide you, like your skin and your nails, measuring progress in other ways besides just digestion.  What do you think about that?

Chris Kresser:  Oh, yeah, absolutely.  I mean, all of the symptoms — fatigue, skin, hair.  Mood is a big one.

Danny Roddy:  Totally.

Chris Kresser:  Those should all be considered, and I think she probably is, but it’s a little bit of an art, but I would say that after a few weeks and things are just deteriorating and there is no improvement at all, I would actually start to question whether that approach is going to be valuable over a longer period of time.  Now, more specifically about GAPS, there are a few issues with it and that can make it not helpful or appropriate for certain people.  Number one is that, as we talked about earlier and talked about in more length with Paul when he came on the show, is that yeast can thrive on ketones, and GAPS, especially the Intro GAPS diet, is by definition a very low-carbohydrate diet and will probably be ketogenic.  So, for some people who have a systemic yeast infection, doing a ketogenic diet can actually make things worse, and I’ve seen this in my practice.  What’s a little confusing to me is that it doesn’t seem to always be the case.  Some people tend to improve, so I don’t know how to explain that.  Maybe some species of yeast are more able to utilize ketones than others, I’m not sure.  But I sometimes even use that as a diagnostic protocol.  If you put somebody on a ketogenic diet for a short period of time and they get a lot worse, then that could be an indicator of a yeast infection.  So, that’s one issue.  Another issue is that because it’s a low-carb diet and someone’s on GAPS for a long time, that could affect thyroid function, which we’ve talked about before.  Glucose is required for the conversion of T4 to T3.  There are studies showing that fasting and very low carb diets over a prolonged period can cause a decline in thyroid hormone and conversion of T4 to T3, and T3 is five times more metabolically active than T4, so that’s significant.

A third problem is people who have issues with fat digestion.  Some people when they eat a diet that’s extremely high in fat and low in carbs like GAPS, if they have any kind of gallbladder insufficiency, it can be really, really hard on them.  It causes a lot of bloating and pain, sometimes even vomiting and really difficult digestive symptoms.  So, in that case, it doesn’t necessarily mean that the GAPS approach won’t work for them or isn’t a good idea, but they may need some additional gallbladder support to make it work.  And then the other thing I would say is that my diet, actually you could call it Paleo plus GAPS, or you could call it GAPS plus starch, so I’m not that far from the GAPS diet now in the sense that I eat a lot of bone broth, I eat a lot of fermented foods, which are two characteristics of the GAPS diet, but I do eat starch and starch really works well for me.  And what I’ve seen in my practice is that of all the things that are removed from the GAPS diet, starch is usually the thing that causes the least problems for people.  So, if somebody has been on the GAPS diet for a long time and they are starting to have issues, I would suggest adding more starch back in, you know, if it’s been a while since they’ve had the issues, not two days, but if it’s been weeks, like with Kaitlyn and her husband.

Danny Roddy:  It’s been a while.  Natasha Campbell doesn’t like starch because it passes through the gut lining easier?

Chris Kresser:  Well, the whole principle of the GAPS diet — We probably should have done this before.  I realize not everybody listening to this even knows what the GAPS diet is.  So, the GAPS diet is very similar to the Paleo diet actually, but it goes a step further.  I removes disaccharide and polysaccharide molecules.  Carbohydrates are broken down into sugar molecules, ultimately into monosaccharides like glucose and fructose.  So, monosaccharide is a single molecule of a sugar, and a single molecule of sugar can be directly absorbed from the gut across the lumen of the intestine into the bloodstream without any additional breaking down.  So, when you eat a carbohydrate, it has to be broken down into those single molecules, monosaccharides, to be absorbed into the bloodstream.  Disaccharides are molecules with two sugars, so lactose is a disaccharide.  And then you have polysaccharides, which have multiple sugar molecules chained together, and that would be a starch.  So, when you eat a polysaccharide or a disaccharide, there’s some digestive action that needs to take place to break those longer-chain sugars into the monosaccharides, the single molecules of sugar, so that they can be absorbed, and that involves the brush border enzymes, which are enzymes on the villi, these hair-like projections on the lining of the intestine, and they need to act on those longer-chain sugar molecules to break them into those smaller molecules, right?  So, what happens with people with gut problems is those brush border enzymes don’t work as well, and they don’t break those longer-chain sugars into the monosaccharides, and as a result, they end up floating around in the gut for longer than they should, and in doing that, they become food for pathogenic gut bacteria and yeast.  That’s the whole theory of the GAPS diet.  So, the GAPS diet removes disaccharides and polysaccharides and only allows the simpler sugars like glucose and fructose and fruit.  So, not only does the GAPS diet eliminate grains, which the Paleo diet does too, it also eliminates all starch, so no sweet potatoes, no potatoes, none of the starchy tubers that the Paleo diet does allow.

So, what I’m saying is that what I’ve seen is that if somebody goes on the GAPS diet for a while and they reach a point where Kaitlyn’s reached or I’ve reached and they start adding starch back in, that can sometimes be helpful, and I think one of the reasons behind that is that when you only eat the single-molecule sugars, the monosaccharides, then in addition to starving the bad gut flora, you can also end up starving the good gut flora.  And when you’re eating a lot of fermented food, that may not be a problem, but for some people even who are eating a lot of fermented food, it does seem like it is a problem.  And then adding the starches back in, starches have a prebiotic effect, meaning they stimulate the growth of certain species of bacteria in the gut, and then people’s stools might tend to normalize and their digestive system just starts to work better.  So, yeah, it’s a really individual issue, but those are some of the variables to consider.

Is FODMAP sensitivity permanent, or can it be treated?

Danny Roddy:  Great stuff.  OK, this next question:  “I’m curious why and how a person develops a sensitivity to FODMAP foods, and is there any way you can heal it or if one just has to avoid these problem-causing foods forever.  For me, apples and onions cause a lot of digestion pain.  These are foods I’ve been eating since I was a baby.”  What do you think about FODMAPs?

Chris Kresser:  Yeah, I talked about this a little bit on Diane’s show, but I think FODMAP intolerance is a symptom of a deeper problem usually.  I don’t think anyone is born with FODMAP intolerance, for example.  But I think it’s probably a consequence of small bowel bacterial overgrowth or any other kind of dysregulation of the gut flora, which could also include a pathogen like a parasite or yeast or pathogenic bacteria.  So, my approach, I do use the FODMAP diet in my practice.  I talk about it in the Personal Paleo Code as one possible adaptation to digestive issues, but it’s more of a temporary thing to provide some symptom relief while we figure out what those underlying issues are, and then oftentimes people will be able to add back in at least some of the FODMAPs once those issues are resolved.  It probably bears noting that a lot of the FODMAPs are things we shouldn’t be eating anyways, like wheat flour.  And for those of you who don’t know, who are just swimming in acronym soup right now and have no idea, with GAPS and FODMAPs and all that stuff, FODMAP stands for fructo-, oligo-, disaccharide — What’s the M, Danny?  I always forget the M.

Danny Roddy:  I have no idea.

Chris Kresser:  P is polyols, sugar alcohols like sorbitol and stuff like that.  Anyways, it’s similar actually to GAPS in the sense that there are these certain foods that this theory holds are more likely to be undigested and unabsorbed, and then they become food for pathogenic gut bacteria, and that’s what causes the symptoms.

Danny Roddy:  Here we go:  fermentable oligo-, di-, and monosaccharides, and polyols.

Chris Kresser:  Right.  So, catchy name.  You can see why they’re going with FODMAP!  Yeah, this is, like, fructans and then fructose, not all fructose, just any excess fructose.  Fructose can be well absorbed by the body when there is a sufficient amount of glucose that’s eaten with it.  So, if somebody eats a food like a banana that has equal or greater amounts of glucose than fructose, then they shouldn’t have any problem digesting the fructose, but if someone with FODMAP intolerance eats a fruit like a pineapple that has a lot more fructose than glucose, than that excess fructose is what causes the issue.  Yeah, these are foods that are all aggressively fermented by the bacteria in the gut when they’re undigested, and again, I think it’s a result of already dysregulated gut flora and that if you deal with that, you usually can reintegrate some of the foods, not always, but in most cases in my practice.  And dealing with the pathogen is one step, but also restoring healthy gut flora using probiotics is another.  Let’s go on to the next one.  Got one more, maybe?  We have time for one more.

What causes digestive reactions to carbohydrates?

Danny Roddy:  Time for one more.  OK, let’s get to Niklax’s problem.  He or she says:  “My problem is bloating from carbs.  It doesn’t really make much sound, but it looks like a beer belly although my BMI is OK.  Switching to a VLC diet solves the problem, but I am fed up with eating so much fat all the time.  Also quite fond of rice noodles and potatoes.  Is there a solution?”

Chris Kresser:  So, yeah, I think this is closely related to the last question and the earlier question.  Carbohydrate intolerance is almost always a sign of messed-up gut flora because, as I was just explaining, when carbohydrates remain undigested in the small intestine, they provide food for pathogenic gut bacteria, and then when those pathogenic gut bacteria are killed by the immune system, they release toxins.  Those toxins can cause all kinds of symptoms ranging from brain fog and depression to leaky gut, skin conditions like psoriasis and eczema, etc.  Also the process of the bacteria fermenting the carbohydrate produces gas, and that gas is what produces that beer belly type of bloating that he or she is talking about.  So, one possibility is to get some testing done to see if there is a pathogen present.  There’s a small bowel bacterial overgrowth breath test that you can do to test that out, and then dealing with those issues and restoring healthy gut flora would be the thing that you would need to do to increase the carbohydrate tolerance so you can expand your diet and eat a broader mix of macronutrients.  I think that’s it.

Danny Roddy:  Killer, Chris.  That’s gonna bring us to the end of this week’s episode.  Chris, where can we find more of your work on the Internet this week?  What are you working on?

Chris Kresser:  OK, so we talked about the Personal Paleo Code in the beginning of the show.  This show is gonna be released on November 1, so the actual program itself is gonna be ready is about a week from today, you know, today if you’re listening to this on November 1.  But right now, I’m doing a promotion where I’m given away a free iPad 2.

Danny Roddy:  Oh, my god.

Chris Kresser:  Yes.  I hope I win!  No, I’m just kidding.  I’m not gonna win.  So, if you can help me get the word out, I’m really excited about this program, I want to get the word out far and wide, and so I’ve created this page, a landing page that describes the product.  I have a little video of me talking about it and just a couple short bullet points, gives the basic idea.  And if you go there, it’s iPad.PersonalPaleoCode.com, and if you pull that up and you share that page on Facebook or Twitter — you can use either one, and you can change the text.  I mean, there’s some text that’s prepopulated in there, but you can change it if you want.  You share it on your Facebook or Twitter account, help me get the word out, you’ll be entered into this drawing to win the free iPad.  It’s a 16GB black one with Wi-Fi, and the contest is over on November 20.  And then by entering that contest, you’ll also be put on the email list where I’ll send you an email once the product is ready.  We’re gonna be offering a discount for my podcast listeners and blog readers and faithful fans, and that’ll be available for only a couple of weeks after the product launches.  So, yeah, if you’re interested in an iPad, which is actually a perfect way to access this content so you can be in the kitchen and pull up a meal plan on the iPad and check it out before you make some food for the day, I’d appreciate you helping me get the word out, and I wish you luck in winning the iPad!  I’ll be jealous.  Let’s see.  What else?  I think that’s it.  I mean, we’re changing the name of the show next week, like I said, and yeah, that’s it.  I think I’m gonna take a rest for a little while.

Danny Roddy:  You can find all of my work on DannyRoddy.com.  Hopefully, I’ll be releasing my new book, Hair Like a Fox, sometime next month.  The ETA is unknown at this time.

Chris Kresser:  C’mon, Danny, get with the program.  We’ll all waiting with bated breath!

Danny Roddy:  But keep sending us your questions at ChrisKresser.com using the podcast submission link.  If you enjoyed listening to this podcast, head over to iTunes and leave us a review.  Thank you for listening, and thank you for your support.

Chris Kresser:  Thanks everybody.  Good digestion to all of you!

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Chris Kresser in kitchen


Join the conversation

  1. Any new info on Blastocystis hominis? I have a college boy with it who suffers from terrible gas and has for years whose life would be changed with a natural cure. Ginger?

  2. Hello, what protocol would you recommend for h.pylori? I bought Mastic gum, Lauricidine, probiotics and Zinc carnosine and I’m going to buy Interfase plus as well. However, I don’t know how to combine all these, which to take first, with food or on empty stomach. Please, help. Thank you! Renata

  3. Hi Chris,

    I have been a follower of yours for several years now, and I love your excellent and science based content. Thanks for your work and dedication!
    I have a question about parasites. For almost 3 years now I have had worm-like eye floaters. Could it be a parasite? If so, how do I find out? I have been battling gut issues and gut-related symptoms since 2011. Had SIBO last year which I treated. In terms of parasites I have endolimax nana and a mild blasto infection.

    Thanks a lot!

  4. Hi there, I am hoping to find the clinic in Australia that treats Dientamoeba fragilis well: Chris, you mentioned a clinic and program with antibiotics that you would recommend: might I get the name from you?

    Many thanks

    • The Centre for Digestive Diseases is very experienced. I am not sure if that is what Chris is referring to, though.

  5. Hi there Chris,

    I know this blog post is from a long time ago but I was just wondering if you would be able to go into more detail or write a post about how to treat parasitic infections?
    For me it’s at the root a lyme disease + coinfections issue, but I think it’s really parasites that are causing the major pain in the whole body in a very cyclical fashion. Are you familiar with nematodes and how they can migrate through the body? I am going to get an fmt done in a few months, but I am trying to figure out the best parasite protocol to do before getting the good bacteria in. Glen Taylor from Taymount in England says that parasites are the only thing fmt doesn’t fix! But I think the main problem is that for me it could be a combination of intracellular ones like babesia + ‘regular’ ones. Well, any thoughts from your experience or treatment of others would be greatly appreciated.

    Thanks a bunch,