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Testing and Treating Digestive Issues in Children


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Diagnosing digestive issues in children can be difficult. Find out when you should pursue testing for pathogens or gut issues and when to take an approach that rebuilds the gut.

Revolution Health Radio podcast, Chris Kresser

Over the last three or four weeks in my practice I’ve seen four or five kids of varying ages from about 2 years old to 10 years old, with digestive and other issues, so this has been on my mind recently. As a father myself, I know it’s just so difficult to be in a situation if your child is sick and wanting to help and not being able to help as much as you’d like to be able to.

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In this episode, we cover:

2:00  Goodbye and thank you to Steve
4:22  Pre-enrollment for clinician training program
10:42  Which tests to use for diagnosing children
22:03  Rebuilding the gut

Steve Wright: Good morning, good afternoon, or good evening. You are listening to the Revolution Health Radio Show. I’m your host, Steve Wright, co-author at SCDlifestyle.com. This episode of RHR is brought to you by 14Four.me. This is a 14-day healthy lifestyle reset program. This is for you if you’re someone who is trying to put together all the pieces of great health that Chris talks about, things like diet, sleep, movement, and stress. It can be hard to incorporate all these things into the modern lifestyle, and what Chris has done is created a step-by-step, hand-holding program, where in 14 days he’s going to walk you through how to fit them all into your life so that you can continue to make progress on your health issues, whether that’s weight gain, whether that’s fatigue or any autoimmunity, things like that. If you’re struggling with any of those areas, I’d encourage you to check out 14Four.me.

All right, on with the show. With me today is integrative medical practitioner, healthy skeptic, and New York Times bestselling author, Chris Kresser. Chris, how are you doing?

Chris Kresser: Pretty well. How are you, Steve?

Steve Wright: I’m excited.

Chris Kresser: Yeah? What are you excited about?

Steve Wright: My shoulders have been really messed up pretty much this entire year, and I’ve finally gotten to the place where I can work out on a regular basis, so it’s just great to be able to be exercising on a daily basis again.

Goodbye and Thank You to Steve

Chris Kresser: I bet. I bet. Well, we have a couple of big announcements to make before we go forward with the question for this episode, and the first is that after several years of being a fantastic host on this show, Steve is going to be moving on. This will be our final episode together, and then there’s going to be a short break for the show and we’ll come back in a new format. I’ll be hosting myself, but I’ll also be having more frequent guest hosts, like Dr. Amy Nett from CCFM and others, and then more interviews with experts, researchers, people that I’m interested in talking to that are exploring various things that I’m looking into or passionate about or want to learn more about. Yet another new chapter in the evolution of Revolution Health Radio, and I just feel a lot of gratitude and appreciation for Steve and everything he’s brought to the show over the years. We’re definitely going to miss you, Steve.

Steve Wright: Yeah, thanks, man. I’m going to miss doing the show, too. This is, I think, going on our fourth year of doing this together. Believe it or not, when we started, I was still an engineer back in Michigan, doing the SCD Lifestyle thing on the side, trying to make that work, and you don’t know this yet, but I used to take all of my vacation time, every time you wanted to record I’d take a half day of vacation to go home and record because I had to work those two jobs.

Chris Kresser: Wow. I didn’t know that. Well, that just makes your commitment even more impressive. You’ve certainly come a long way since then, and we’re sad to lose you, but I know you have lots of really interesting things going on, and of course, we’ll stay in touch.

Steve Wright: Yeah, definitely. This has been a labor of love, and it’s been amazing to just get to work with you on a regular basis. I tell this to people who ask me about it. I say basically I get to go to school for an hour every week with Chris Kresser and pick his brain, so it’s been an honor to do the show and to be able to be the guy that gets to ask all my questions.

Pre-Enrollment for Clinician Training Program

Chris Kresser: All right. So that’s number one, a pretty big announcement, and number two is another pretty big announcement, which is that after really kind of several years of development, I’m finally excited to be getting very close to opening pre-enrollment for the clinician training program that I’ve talked to you about several times now.

I’m creating a new training body organization called the Kresser Institute for Functional and Evolutionary Medicine. The next announcement, we’re sending an email, if you’re subscribed to my email list, on Tuesday, July 21. I think this podcast is going to come out on the 23rd or something like that. But if you’re not on the email list, you can head over to KresserInstitute.com and watch a short video of me explaining what’s happening and what to expect in the next month or six weeks, and there’s also a little sneak peek there of what the training will entail, how enrollment will work, and a few other things that you should be aware of if you’re interested in taking part in this training. It’s going to start in January of next year, and it’ll go for one year with four breaks during the year, kind of almost like a trimester system, and I just can’t tell you how excited I am to finally be bringing this to fruition. It feels like probably one of the most important things I’m going to do in my life professionally. There’s just such a growing and unmet demand for functional medicine practitioners with an ancestral perspective, and there really isn’t a training that offers that, at least until now, so I can’t wait to share more with you.

For now, just head over to KresserInstitute.com, watch the video. And if you are interested, make sure to sign up for the early notification list. The number of people we can accept in the first course is limited to about 125, I think, possibly 150, and the last time I checked there were over 2200 people on the early interest list. Unfortunately, we’re probably going to sell out, and there may not be space for everybody, so if you want to be among the first to be notified, after you watch the video and check out the page, if it looks like something you might be interested in, make sure to put your email address in the box so that we can contact you when enrollment opens up.

Steve Wright: Well, congratulations, Chris. I know this has been something that you’ve been thinking about for three or four years and working really hard on in the past year, and it’s something that’s going to plug a big hole in the market, so I appreciate you doing all that hard work.

Chris Kresser: Yeah, thanks, Steve. And we’ll be back in August when pre-enrollment opens. I’ll spend an episode talking a lot more about it, what the training is going to entail, giving you much more detail about it, and answering some questions that we’ve received a lot of and just try to paint a more clear picture so you can make an informed decision.

But for now, we’re going to go forward with a question from Brooke, so let’s take a listen.

Question from Brooke: Hi, Chris. I have a question regarding testing and treating digestive issues in small children. My son who is almost 3 years old has had loose stool and pretty significant bloating basically all of his life. We didn’t realize there was an issue until a while after he was really eating a lot of solid food, and his stool was still very mushy and soft. We’ve been working with a naturopath since he was 18 months old, and initially the stool tests she did confirmed that he had dysbiosis and overgrowth of E. cloacae and very low good bacteria. We’ve done a lot of different antimicrobial herbs and Chinese herbs, enzymes for biofilms, along with a low-FODMAP diet and probiotics. These approaches greatly reduce his bloating, but as soon as we veer from the diet whatsoever, the poor guy gets so bloated he looks like he’s pregnant, in his third trimester. His symptoms also seem very similar to SIBO-type symptoms. My question with all of this is what sort of testing you suggest for digestive issues in small children — he’s just learning to blow, so breath tests probably aren’t really possible yet — and specifically for bacterial overgrowths, what sort of treatment you might suggest for SIBO or bacterial overgrowths when confirmed on testing. Is there a point at which one would need to consider a medication? Thank you very much for your insight on all of this.

Chris Kresser: OK. This is a good timing on this question. For whatever reason, the last three or four weeks in my practice I’ve seen four or five kids, actually, of varying ages from about 2 years old to 10 years old in my practice with digestive and other issues, so this has been on my mind recently and something I’m paying attention to. I have been, of course, for a long time, but these particular issues are front and center for me over the past couple of weeks.

Steve Wright: Before you get into the answer here, Chris, I just want to let all the listeners know that RHR is predominantly built for you and by you, so go to ChrisKresser.com/PodcastQuestion to get your question on the show.

Chris Kresser: Great. All right, so first of all, Brooke, I’m sorry to hear that you’re having problems. As a father myself, — Sylvie’s actually turning 4, believe it or not, in a week; it’s hard to believe — but I know it’s just so difficult to be in a situation if your child is sick and wanting to help and not being able to help as much as you’d like to be able to help, so I’m sorry that this is happening.

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Which Tests to Use for Diagnosing Children

I think there are a few things that I would say here. Number one is a breath test for SIBO would be excellent. I understand that at 3 years old he may not be able to blow on demand yet, but in my experience, most kids acquire that ability right around this age, so keep practicing. Maybe turn it into a game. Do some demonstrations yourself. Maybe get a straw connected to a balloon and see if he can inflate that or even just a balloon. There are ways that you can kind of prep for doing the breath test and helping him to develop that capability because it really is the best way to screen for SIBO, and as you mentioned, his symptoms certainly are consistent with that. His symptoms could be related to simply dysbiosis, as you mentioned, or other gut pathogens that haven’t yet been detected, but certainly SIBO would be something that you’d want to rule out.

You didn’t mention any risk factors, whether he was born vaginally or via C-section or if he was breastfed or formula fed or if he had to take antibiotics when he was a baby or if you took antibiotics during your pregnancy or what your gut flora was like when you were pregnant and when you gave birth. Those will all, of course, influence the risk of him developing SIBO early on, and it sounds like it did start basically from the beginning from your description in the question.

The testing that we would do would be breath test as soon as he’s able to do that. We would do two stool tests. We would use Doctor’s Data Comprehensive Stool Analysis, which is a great combination of proteomic analysis and stool culture and has some other very useful markers like inflammatory markers, like lysozyme or lactoferrin or calprotectin, which are good markers for inflammatory bowel disease, some markers for absorption, short-chain fatty acid production, markers for fungal overgrowth, etc., so that’s a really good test. But then we also tend to run BioHealth 401H side by side, and that’s a stool culture, but a very good stool culture. We’ve found that that test will often pick up things that the Doctor’s Data test misses and vice versa, which is why we still run them side by side. It’s a pain and it’s certainly more expensive, but we’ve found it to be necessary.

I would also consider doing urine organic acids testing. I think this is the least reliable or consistent in terms of detecting dysbiosis and bacterial overgrowth of the three methods, and the evidence supporting it for that purpose is thinner than it is with breath testing and stool testing, but I do think it can be useful when it’s combined with the breath and stool testing. I also would say that there are other markers for cellular energy production and mitochondrial function that can be really useful, and in some cases in kids with digestive issues like this, those things can be playing a significant role and actually preventing progress, and if you focus exclusively on the gut and don’t test for these other things that could be contributing, in some cases it can be one reason that progress is not happening to the degree that you would expect.

Steve Wright: Chris, I’m wondering — and I’m betting that other people like Brooke or listeners might be wondering — why is it that we need to do these tests? All the antimicrobial herbs, the Chinese herbs, the enzymes for the biofilms, diet changes, probiotics — this is an approach that a lot of people take rather than spending whatever amount of money, $500 to $1000 or more on those tests. People try this approach, and then they end up in this situation. What is happening here where whatever infections, if they are there, are not going away?

Chris Kresser: Well, it’s hard to say. I mean, there are several possibilities. One is that there is no infection and it’s a question of dysbiosis. I mean, dysbiosis alone can cause all of these symptoms, and really the biggest problem could be a lack of beneficial bacteria, not too much harmful bacteria or bacteria overgrown in the small intestine or fungal overgrowth or a parasite or something like that. That’s one possibility, especially if he had some of the risk factors that I mentioned earlier. And in that case, actually, a low-FODMAP diet, while it might help relieve the symptoms initially, over the long term would not necessarily be desirable because you’re then starving the beneficial bacteria in the colon of what they need to grow.

I think the studies are pretty clear now — and this is consistent with my experience in the clinic — that probiotics, in most cases, don’t have a quantitative impact on the levels of beneficial gut bacteria. In other words, taking probiotics doesn’t, over the longer term, increase the levels of beneficial bacteria in the gut. They play more of an immunomodulatory role, which is very important, and they can have a really significant impact that way, and as long as you’re taking them, of course, you’ll have more bacteria there, but when you consider that we have a hundred trillion microorganisms in the gut and even the strongest probiotics are billions or hundreds of billions, it’s a drop in the bucket. So the best way to actually increase beneficial bacteria in the gut over the longer term is to eat fermentable fibers or types of carbohydrates that the bacteria can ferment. We’ve talked about this on the show before. Microbiota-accessible carbohydrates was one of the terms that’s been used in the scientific literature. But these, of course, would be FODMAPs but also other kinds of starches that have a low glycemic index and would survive the upper part of the small intestine intact and then maybe make it to the colon, where they can be fermented by gut bacteria. So that’s one possibility.

Another possibility is that there is an infection present but the treatment so far hasn’t been strong enough or effective enough to get rid of it. Without knowing what of the herbs and other stuff that have been used and what dosages have been used, I can’t really comment on that, but I can say that treating these conditions both in kids and adults, they can be very recalcitrant and difficult to get rid of and can sometimes require pretty aggressive approaches, so that’s another possibility.

A third possibility, as I alluded to earlier in the show, is that even though bloating is the main symptom and gut issues are the main symptom, in some cases there are other problems or conditions that can contribute to these symptoms that aren’t the expected culprit. For example, if he has a thyroid problem and low thyroid function, T3 is required to produce stomach acid, activate intestinal motility and peristalsis, and has a number of other important functions in the gut, so if T3 is low, that can cause bloating and a number of other issues. Hypothyroidism in kids isn’t super common, but it’s not rare either, so it’s something that should definitely be checked out.

Mitochondrial function I mentioned. Mitochondrial disorders in kids are really on the rise, and there are a number of reasons for that. It’s another disease of civilization, and I’m going to have someone on the show in the near future to discuss this. It’s fascinating and also a little bit disturbing, but environmental toxins, in particular, and poor diet and a range of other influences that are just part and parcel of the modern world that we live in can adversely affect mitochondrial function. And then when the mitochondrial function is reduced in the gut, then that can actually produce a lot of symptoms like bloating or gas or changes in stool frequency and consistency and things like that. In some kids, if that’s present, focusing on that will be helpful and necessary in terms of moving forward.

Steve Wright: And the organic acids test will let someone know about that?

Chris Kresser: It certainly provides some important clues. There are organic acids that give you some hints into the Krebs cycle, the citric acid cycle, which is what happens inside the mitochondria to start producing energy, ATP, and whether there’s a defect in the processing of glucose to pyruvate. There’s maybe a problem with aerobic respiration and a consequent buildup of lactic acid because anaerobic respiration is being favored, or if pyruvate is not being shuttled into the mitochondria and oxidative phosphorylation where ATP is produced is impaired, if there’s a problem with the electron transport chain. There are a lot of genetic mutations that can affect all different stages of this process, and then there are environmental factors which can affect all different phases of these processes. All of these conversions that happen in the citric acid cycle, or the TCA cycle, and through the whole transport chain require nutrients. They’re enzymes and they require nutrients to function properly, so if the nutrients are low for whatever reason, then that whole system can get broken, essentially.

Another possibility is inflammatory bowel disease. Especially if he’s had loose stools and it just continues despite all of these different interventions, I would want to screen him for inflammatory bowel disease, like Crohn’s or ulcerative colitis. Those are autoimmune conditions, and certainly they can co-present with SIBO and other gut infections, but if IBD is present, that will probably have to be addressed with additional steps above and beyond just treating SIBO or dysbiosis. Short of a colonoscopy, which is a very invasive procedure, those markers that I mentioned from the Doctor’s Data Comprehensive Stool Analysis — calprotectin and lactoferrin and lysozyme — can be helpful initial markers for determining whether active IBD is present.

Rebuilding the Gut

So that’s a good place to start, looking into all of those things, getting some additional testing done, and then if you do the breath test and that’s negative and there are no parasites, no fungal overgrowth, no other pathogens, this really could come down to just a lack of beneficial bacteria, and it may be that the approach to getting well is much less about killing and much more about rebuilding. The tricky thing about this is that if he improved with a low-FODMAP diet, that does suggest that at one point there may have been microbial overgrowth, but it’s also possible that the microbial overgrowth or pathogens have been dealt with now but he still has really low levels of beneficial bacteria, and what you need to do at some point is start adding the FODMAPs back in and then start adding other types of fermentable fibers back in. Soluble fibers like glucomannan or psyllium husk or acacia tend to be pretty well tolerated. Then you have the resistant starches, which are potato starch or green banana flour or green plantain flour. And then you have the non-starch polysaccharides, which are the FODMAPs, but can be supplemented with, like inulin or FOS or larch, and you have to be extremely methodical and careful about how you add those in initially because they can cause gas and bloating if you go too quickly. And of course, you’d want to make sure that there aren’t pathogens or SIBO present before you try to do this because if they are still present, then it could get worse.

I’m not sure what probiotics you’ve been taking, but if you’ve only been taking acidophilus and bifidus and those kinds of probiotics, I would definitely recommend some soil-based organisms like Prescript-Assist, some spores. MegaSporeBiotic is a product I really like, and AOR 3 is another good product. You can just rotate these in sequence so that he’s getting a lot of different types of probiotic bacteria. And then fermented foods can be, in my experience, even more potent in terms of rebuilding the gut and modulating the gut immune system. If he tolerates dairy, homemade kefir — so that there’s no lactose in it — can be really, really therapeutic and healing. You can start with as little as, like, a half of a teaspoon a day and then just gradually increase. If he can’t tolerate dairy, you could do water kefir. You can order the kefir cultures from CulturesForHealth.com. A 24-hour homemade yogurt so that the lactose is gone can be helpful, too, although I’ve found kefir to be more therapeutic than yogurt in most cases. Beet kvass can be very therapeutic if he can tolerate that. Raw sauerkraut can be therapeutic, and adding these things back in in conjunction with the fermentable fibers either in foods and/or the supplemental fibers, in some cases that kind of really focused approach is what’s necessary to rebuild the beneficial gut bacteria and heal the gut.

Steve Wright: Got it. So in general, would it also be safe to say that if he’s more on the constipated side than the diarrhea side that the prebiotics might be another plus-one for potentially doing the prebiotics in the short term.

Chris Kresser: Yeah, exactly. They can work for both, but certainly resistant starch can be really helpful with loose stool. One thing, too, Saccharomyces boulardii can be really helpful for loose stool presentations like this. Again, I’m not sure what probiotics you are doing, but that’s something else to consider.

In sum, I think expanding the diagnostic approach to include other tests that you may not have gotten yet, like breath and the urine organic acids, looking at things like thyroid function and mitochondrial function, basic blood markers to rule out any other issues — blood sugar issues, liver function, nutrient status, etc., all of which can, of course, affect gut function — and then if there really aren’t any pathogens or gut issues present, then considering switching more toward the rebuilding-your-gut kind of approach that I described instead of the antimicrobials.

Now, if SIBO is present, then the way that I approach it is with a kind of microbial reset diet, which is a combination of low-FODMAP plus reducing intake of certain starches that are likely to be fermented by the gut bacteria, the ones with the most fiber and the lowest glycemic index. And then we start with antimicrobial herbs and nutrients. We use kind of different tinctures for kids because 3-year-olds can’t typical swallow pills or capsules.

As for the question of whether I would consider medication at some point, it’s tricky. I think it really depends. Rifaximin is the medication that is typically prescribed for SIBO if there’s hydrogen overgrowth without methane. If there’s methane, it’s more effective to use rifaximin plus neomycin. Rifaximin is not systemically absorbed, so it has that going for it, and it’s not a hugely broad-spectrum antibiotic that would be expected to totally wipe out the beneficial gut flora, and it is generally well tolerated and pretty safe, so I might consider that, but I would probably do a lot of other things first, all of the stuff that we’ve talked about, of course, including the reset diet plus all of the natural antimicrobials, before I moved on to that. If you did have to give rifaximin a try, again, it’s better than a lot of other antibiotics, and if you do that, I would just follow up with all of the approached that I mentioned in terms of fermentable fibers and fermented foods and probiotic rotation to help rebuild the gut.

Steve Wright: Awesome, Chris. Thank you for sharing all that. I think the one question that I’m left with for all the parents out there is, “Awesome, Chris. My doctor might be able to get me a breath test and knows nothing about everything else that was said today,” so is there ability for more people to get in to see you or Amy? Are there other kid functional medicine specialists that you could point these people to that would understand?

Chris Kresser: Good question. I reopened my practice a couple of months ago, and I still am accepting new patients, although I may have to close again shortly because I think I’m scheduling out into November now. Amy is still accepting new patients, and so we would definitely welcome anyone who can come see us in the Bay Area. If you live outside of the Bay Area, you just have to come in for the first appointment in person, a case review appointment, and then we can work via video conference or phone long distance after that. I’m only currently accepting patients who live in California, while Amy is accepting patients that live all over the US.

As far as pediatric functional medicine specialists elsewhere, nobody comes to mind, and this, of course, Steve, is the big problem, right? I get requests for referrals pretty much every day either via email or people calling the office, social media, etc., and there’s nothing I would love more than to be able to have a long list of folks all over the country — or even the world — that my staff or I could just easily refer people to. Nothing would make me happier, and this experience that I’ve had, getting these requests for so long now, is, of course, what pushed me in the direction of creating this clinician training program, and I really don’t think there’s anything else that I could do right now that’s more important because we desperately need more clinicians that understand these things.

Steve Wright: Got it. Yeah, it’s a big problem right now, and I would say that if there are some functional medicine practitioners out there who actually have experience with kids — not that you’re just a functional medicine practitioner — please leave a comment on this podcast. Try to get your name out there, and don’t think that someone commenting is an endorsement from me or Chris for anyone leaving a comment, but at least we can maybe help facilitate trying to get the word out about some people who might specialize in this area.

Chris Kresser: Thanks, everyone, for listening. And, Steve, a very heartfelt thank-you and appreciation again for everything you’ve done for the show over the years. We’re going to miss you, and you’ll have to come back for a visit to say hello sometime in the future.

Steve Wright: All right. Thanks, Chris. And thank you to all the listeners, everyone who has ever said hello to me at a conference or in Whole Foods and thanked me for the work here. I really appreciate you as listeners and making this possible. And, Chris, as always, man, thank you so much for this opportunity. It’s been just amazing, both from learning about health, but also growth and getting to know you, so I really appreciate the opportunity and I’d love to come back every once in a while and do a little guest episode.

Chris Kresser: A little guest hosting. All right.

Well, thanks again, everyone, for listening. Make sure to check out KresserInstitute.com if you’re interested in joining us in this functional medicine, ancestral nutrition revolution and radically transforming people’s health and radically transforming the way that we approach healthcare in this country and the world. I think it’s one of the most important things we can do and devote our lives to, so if you’re ready to take up the charge with me, I would love to have you in the training.

Steve Wright: All right. Thanks, everyone, for listening. Make sure you’re following Chris on social media, Facebook.com/ChrisKresserLAc and Twitter.com/ChrisKresser. And also remember that you could have your question live on this podcast. Just go to ChrisKresser.com/PodcastQuestion.

Once again, thank you all for listening. It’s been a wonderful, wonderful couple of years. Have a great day.

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Join the conversation

  1. Hi Chris. Great podcast! I am a naturopath and functional medicine practitioner based in the UK and am one of very few who specialise in paediatrics. I mainly see kids with gut issues, autoimmune conditions and neurological health challenges. I have been practicing for about 20 years and also have three kids myself. Let me know if you have any enquiries from UK, Europe or the Middle East.