How to Restore Healthy Gut Flora Over the Long-Term
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RHR: How to Restore Healthy Gut Flora Over the Long-Term

by Chris Kresser

Last updated on

We received a question about how to restore the gut microbiome when unable to tolerate probiotics and fermented foods not likely due to histamine allergy. This is a great question, it’s one that I get a lot, and it turns out there are several potential reasons why somebody may not be able to tolerate fermented foods or probiotics, and one of them is histamine intolerance.

Note: The Prescript-Assist supplements discussed in this article are no longer available. Please click here to learn more about a substitute, the Daily Synbiotic from Seed.

In this episode, we cover:

4:58 4 reasons why you may not be able to tolerate fermented foods or probiotics
12:32 How to improve your tolerance for fermentable fiber and prebiotics
22:38 Is it better to eat fermentable fibers in whole food, or is it better to use supplements?


Full Text Transcript:

Steve Wright: Hey, everyone. Welcome to another episode of the Revolution Health Radio Show brought to you by I’m your host, Steve Wright from, and with me is integrative medical practitioner, New York Times bestseller, and healthy skeptic, Chris Kresser. Chris, how’s the weather in California?

Chris Kresser: Well, it’s schizophrenic, actually. A couple days ago it was 95 or something and so hot we could hardly even sleep. None of the houses here really have air conditioning because you don’t need it most of the year, but there are a few days where I wish we did have it, and that was one of them. And then yesterday and today it’s been in the 50s. This is kind of how it can be in June in the Bay Area.

Steve Wright: Mother Nature’s playing tricks on you.

Chris Kresser: How about Colorado? Beautiful Boulder?

Steve Wright: Well, it’s been pretty steady here, 75 or 80s, sunny, and we’ve had a few rainy days, but we are getting into what I hear is the best part of Colorado.

Chris Kresser: Nice.

Steve Wright: This will be my first Colorado summer. I don’t really know what to expect.

Chris Kresser: Nice. Well, I’m headed to Tucson tomorrow to participate in this event called Revitalize that MindBodyGreen is putting together. They actually rented out the entire Miraval Resort, which is this super chichi eco-resort kind of place, and I’m really looking forward to it because there are going to be a lot of great folks there. I’m speaking on Saturday morning, and it’s going to be live streamed. By the time this podcast comes out, I think it will have already happened, but there will probably be a recording of some type. They invited a hundred thought leaders, both health experts and authors, but also actors, musicians, CEOs, and people of all different backgrounds who share an interest in health, so it’s kind of like a horizontal focus on health from people in a lot of different industries. We’re going to be there for three days hiking, hanging out, and doing these talks, which will be live streamed, so I’m looking forward to that except when it comes to weather, being in Tucson in June is probably not my first choice. They’re like, you can expect it to be 80 or 85 to 105, and I’m thinking, yeah, 85 is probably at 4 in the morning, right?

Steve Wright: But they probably have air conditioning.

Chris Kresser: Yeah, you’re right. They definitely have air conditioning. They have infinity pools and massage therapists and all kinds of stuff set up for us, so I’m not complaining. I’m really excited to go. It’s going to be great.

Steve Wright: Well, it sounds awesome. I’m definitely not going to shed a tear for you if it gets up to 100.

Chris Kresser: All right.

Steve Wright: Before we roll into today’s awesome topic, what did you have for breakfast, Chris?

Chris Kresser: I had some chorizo. We just got another half pig from a local farmer, Freestone Ranch, who is awesome. We had some chorizo from that and then also some plantains and then some sauerkraut and a little bit of beet kvass. I made that for Sylvie before we took her to preschool, and that’s what I had, too.

Steve Wright: Well, that sounds a lot more delicious than my black coffee.

Chris Kresser: Well, I do that sometimes as well, as you know.

Steve Wright: Yeah.

Chris Kresser: We’re going to answer a question I think a lot of people are interested in today, so let’s do that.

Steve Wright: OK, well, before we get into that, I just want to let the listeners know if this is the first time you’re listening to this awesome podcast or you’re a longtime listener, we thank you, and we want to let you know that Chris has created a membership area on his site at where he’s categorized and he’s made it really easy for you to digest – pun intended – all of his awesome info on paleo weight loss, thyroid health, gut health, everything that Chris has been doing over the last many years he has created inside of his membership site. So you can go over to and join. As of today, there are over 103,000 people who have already signed up for the membership site, who are in there, who have access to these expert interviews with people around the world with the eBooks that Chris has put out for free. So if you haven’t checked that out, definitely head over there and get signed up.

Today, Chris, the pun intended was because we’re talking about digestion.

4 Reasons Somebody May Not Be Able to Tolerate Fermented Foods or Probiotics

Chris Kresser: Yeah, absolutely. We got a question from – I can’t remember where it was from, maybe Facebook or sent in through the contact form, and it was how to restore gut flora and function when unable to tolerate probiotics and fermented foods not likely due to histamine allergy. This is a great question, it’s one that I get a lot, and it turns out there are several potential reasons why somebody may not be able to tolerate fermented foods or probiotics, and one of them is histamine intolerance, which the questioner mentioned in the question. Fermented foods tend to be very high in histamine, and some people have either a genetic mutation that impairs their production of the enzyme that breaks down histamine. Other people have disruptions in the gut flora, which makes them less able to tolerate histamine, and so when they eat fermented foods like cheese or yogurt or sauerkraut or wine or vinegar, they experience all kinds of different symptoms ranging from headaches to hives, skin issues, fatigue, bloodshot eyes, nausea, all of which are mediated by histamine, which is what is involved in the kind of allergic response, like if you get stung by a bee. So that’s one possible reason that people don’t tolerate fermented foods, although that wouldn’t necessarily cause an intolerance of probiotics.

Another potential reason is SIBO, small intestinal bacterial overgrowth, because SIBO sometimes involves an overgrowth of certain types of bacteria that produce lactic acid, and Lactobacillus acidophilus is one of those kinds of bacteria, and that’s frequently included in probiotics, and it’s also in fermented foods. So if you have SIBO, you have an overgrowth of this kind of bacteria, and then you take probiotics or fermented foods, you could actually end up making yourself worse. I’ve seen that a lot, and actually sometimes intolerance of probiotics is one red flag for me that makes me want to look for SIBO and other gut issues.

Have you seen that as well, Steve?

Steve Wright: Yeah, it’s been in a lot smaller population from the case studies and what we’ve seen. It seems like maybe – I don’t know what it is, but it definitely seems like a minority of people who can’t tolerate the lactobacillus strains who have SIBO. Before you were kind of talking about this, sort of our go-to had been a lactobacillus strain that was very pure, and we had seen a lot of good results, but we had seen some reactions to it. As far as my digging goes, there seems to be an issue with the clearance of D-lactate, like a genetic potentially or an environmental trigger that happens. I think it’s interesting. It’s definitely developing. I think, like you said, if you’re having a probiotic intolerance, there is digging to be done there, and there is definitely something going on.

Chris Kresser: Yeah. From what I’ve seen, it depends on the type of bacteria that’s overgrown in SIBO. It also depends on the specific nature of the dysbiosis. You could have not enough good bacteria and too much bad bacteria, and that can cause probiotic intolerance. I’ve seen gut infections cause probiotic intolerance, like parasite infections, particularly. Inflammatory bowel disease can cause probiotic intolerance because in some cases in IBD people react negatively to their own commensal gut bacteria, the bacteria that’s normally in their gut, and if you introduce new bacteria to a really inflamed gut, that can also be problematic even if those bacteria are beneficial.

Steve Wright: Especially if you’re somebody who’s really messed up with a really bad leaky gut where you’re reacting to most all the foods out there when you introduce a probiotic strain sometimes. Jordan, for instance, actually had to start with, like, one strand of sauerkraut.

Chris Kresser: Yeah, exactly, and we’re going to get to that. I have my own story about that, too.

The last thing is FODMAP intolerance. People who are sensitive to FODMAPs, I’ve found, can sometimes be more sensitive to probiotics and fermented foods.

Now, here’s the really tricky thing or the catch-22 about this, which is generally the extent to which you react adversely to probiotics and fermented foods and prebiotics, which we’re going to talk about in a second, is roughly proportionate to how screwed up your gut is. In other words, the more strongly you react to these things, the more likely it is that you need them over the long term, and that’s the tricky thing about working with these situations because it’s always a dance between addressing the short-term issue, like symptom alleviation, making somebody feel better and comfortable, and then making sure that you’re progressing and dealing with the long-term problem, and that always involves restoring healthy gut flora.

Steve Wright: Have you seen that with FODMAPs, Chris? That’s an experience that I’ve seen, is that the more intolerant you are to FODMAPs, typically the more messed up you are and that that intolerance alleviates over time as everything improves.

Chris Kresser: Absolutely. That’s absolutely true, and the same principle applies there with FODMAPs and prebiotics. Most people who have a screwed-up gut are really sensitive to prebiotics and FODMAPs, but fermentable fibers, which is what FODMAPs are and prebiotics are, are absolutely crucial to restoring healthy gut flora over the long term. In fact, I’ve mentioned this before, but the most recent research has shown that probiotics do not quantitatively affect levels of beneficial bacteria in the gut. So you could take probiotics all day long, and it’s not going to increase the levels of certain bacteria like bifidobacteria and lactobacilli over the long term. Probiotics seem to have more of an immunoregulatory effect, so you take probiotics, they have a tuning and regulating effect on the immune system and the gut immune system, which is incredibly beneficial and important, but they don’t necessarily fill up the tank, so to speak, in terms of the beneficial bacteria you have in your gut. That’s what prebiotics, fermentable fibers, do, things like resistant starch, non-starch polysaccharides like inulin and fructooligosaccharides and galactooligosaccharides, those kinds of things. They provide food for the beneficial bacteria in your gut and can increase their levels by orders of magnitude. So it’s another catch-22 where you have someone with FODMAP intolerance who can’t handle any kind of fermentable fiber or prebiotics, where in my work with them I will very, very gradually introduce those things over time so that eventually they become less intolerant of FODMAPs and fermentable fiber because their gut flora is in a better situation.

How to Improve Your Tolerance for Fermentable Fiber and Probiotics

Here are the basic steps that I would use in this situation: The first thing would be, if possible – and I know this isn’t always possible – hook up with a functional medicine provider and get some testing done to see if you have SIBO, dysbiosis, gut infections, FODMAP intolerance, etc., because knowing what you’re dealing with can really accelerate things in terms of what kind of treatment you want to do. But even if you can’t do that and if you do, do that and you find you have some SIBO or overgrowth of bacteria in your gut, you can do a herbal, botanical antimicrobial protocol for SIBO. I’m going to be writing a post on this soon, but I just came across a study which I was really excited about that showed that botanical protocols are more effective than Rifaximin, which is the drug of choice for SIBO, and not only are they more effective, they’re, of course, much safer, they don’t tend to produce as many side effects, nor do they have as negative of an impact on the gut flora, and they’re even effective in people who have done Rifaximin and haven’t had success with it. This is exciting, and it means that a lot of the herbal preparations out there – there are many different varieties. There’s GI-Synergy or H-PLR from Apex, which I use a lot in my practice. Pretty much every major brand name like Thorne or Pure Encapsulations or Apex or Innate Response – all of these companies that are high quality supplement manufacturers have an antimicrobial protocol with many of the same botanicals in them, and these can be effectively used in many cases to deal with SIBO.

That’s the first step. You find out what’s going on. The second step is you can use a protocol to knock back some of the bacteria in the small intestine that may be making you intolerant of these probiotics.

Steve Wright: Chris, I have to jump in really quick.

Chris Kresser: Yeah.

Steve Wright: I just want to add in that there’s a really sexy – just coming from my own experience, and maybe you can relate to this – but there’s a sexy idea here that somebody’s going to be able to just execute these protocols with skipping step one and just going to step two and treating. And while I guess I’m saying that’s not the worst case in the world, I would caution and say that in my own health history as well as a lot of the people that I’ve worked with, SIBO doesn’t just grow by itself. When you have a really messed-up gut and therefore the more intolerant you are to a lot of these things that we’re talking about here today, the higher the likelihood that you have a deeper infection that maybe a general SIBO protocol is not going to take away. Especially those of you who are super sensitive, don’t skip over step one, which is getting testing and working with somebody who gets this stuff.

Chris Kresser: Yeah, I wish it was easier for people to find someone to work with because I often hear from people when I go speak elsewhere – you know, I just did a one-day seminar with Robb in New Jersey, and so many people came up and said, how can I find someone who has this kind of perspective to work with? It’s really difficult. I’ve been trying for a long time, and it just seems impossible. So I totally agree, Steve. For sure, the ideal would be to find a practitioner like that, and I also know that that’s not possible for a lot of people.

Steve Wright: Yeah.

Chris Kresser: And I think that many of the botanical protocols are generally safe, and even if you don’t necessarily get to the full root of the problem with it, you might get some improvement.

Steve Wright: Totally.

Chris Kresser: I’ve also talked about Lauricidin, which I like, on the show before, and then there are some prebiotics and probiotics, and we’ll talk about that in a second.

From a dietary perspective, a low FODMAP diet can be really helpful. If you’re not tolerating probiotics or fermented foods, it’s likely you have FODMAP intolerance or dysbiosis of some kind, and a paleo version of a low FODMAP diet can be really helpful.

Now, in terms of probiotics and prebiotics, as I said, even though taking them in normal doses might cause problems initially, that doesn’t mean that you don’t want to take them at all and that you should just write them off forever. What I suggest instead is starting at an extremely low dose and building up very, very slowly over time. Steve just mentioned that Jordan had to start with, like, a single strand of sauerkraut. Some people even just start with a tiny bit of the juice from the sauerkraut, like maybe a half a teaspoon of the juice once a day. When I was really restoring my gut, I started with a half of a teaspoon of kefir, and it took my nine months to build up to the point where I could have a full cup of kefir a day. Now I could drink, you know, three glasses of kefir in a day and feel great, but it was rough initially. I had a lot of reactions, there was a lot of starting and stopping, two steps forward, one step back, and unfortunately that’s just how it often has to be to begin with when you’re dealing with a situation like this because you’re really dramatically changing the composition of your gut flora, and because the gut flora affects virtually everything, that can produce a lot of different symptoms. So I suggest starting with very low doses, being methodical about it. One of the mistakes I often see in my practice is people will get excited, understandably, about being able to tolerate more and they’ll go too quickly, so just be very slow and methodical about it.

Steve Wright: Just to kind of differentiate here because we’re speaking on Jordan’s story with sauerkraut, your story on kefir, and we’ve also mentioned probiotics and prebiotics, is there a pattern that we should look for, because for instance, kefir might be a worse choice due to potentially the milk casein issue. Sauerkraut, you’re dealing with a FODMAP for sure, so the source of the fermented food has a role here, and then, of course, there’s also choosing a standardized commercialized product.

Chris Kresser: Yeah.

Steve Wright: Do you have sort of any thoughts on differentiating which one to start with?

Chris Kresser: I don’t think there’s really much of a FODMAP issue with sauerkraut because the sugar in cabbage is what is the FODMAP component, and when sauerkraut is made that sugar is consumed mostly by the bacteria, so there shouldn’t be much sugar left in cabbage, which means that it wouldn’t really be a FODMAP anymore, so I do think sauerkraut is a good starting place for a lot of people for that reason. Dairy kefir, as you pointed out, can be problematic if people are intolerant of the proteins; however, if you have lactose intolerance, dairy kefir is not an issue if you make it at home and you ferment it for at least 24 hours because all of the lactose will be gone, and in fact, there are some studies which suggest that you can cure lactose intolerance or at least significantly improve it by consuming fermented dairy products like yogurt and kefir. So if you know that the dairy proteins aren’t a problem for you, as I did, then dairy kefir can actually be very healing. Another option is water kefir. You can get water kefir grains from someone like, and you just make it with sugar and water. The cultures consume all of the sugar, and then you can flavor it with a little bit of fruit, and that has a very therapeutic effect as well. Beet kvass is another great fermented beverage that I’ve found to be pretty therapeutic, and then, yes, you get into the commercial probiotics.

My experience, especially over the last year, is that a lot of people who don’t tolerate lactic acid-based probiotics do tolerate soil-based organisms and often very well, and I know you guys have had the same experience. I’ve talked to a lot of colleagues who have had the same experience. Prescript-Assist, which is the product that I sell in my store, is by far my favorite right now as a general use product, and I think it’s safe to use in SIBO probiotics. It works well for people with constipation, and those people often tend to be the ones who don’t respond well to probiotics. It also works well for people with loose stools or diarrhea, too, but it’s really versatile and really safe and well tolerated and really effective, which is why I find myself using it a lot. If you’ve tried other kinds of probiotics and fermented foods and you don’t react well to those, you could start with Prescript-Assist, but instead of taking two capsules a day, which they recommend on the bottle to start with, you would take maybe a third of a capsule. You actually open the capsule, pour a third of it in a little bit of water or just directly into your mouth – it tastes fine – and take it that way and then just gradually build up to one capsule, then gradually build up to two capsules and stay on that dose for maybe two to three months therapeutically, and then you can go back down to one capsule as a maintenance dose. You can, of course, do that same approach with any kind of probiotic, but if you’re having trouble tolerating them, I definitely would recommend starting with something like Prescript-Assist.

Is It Better to Eat Fermentable Fibers in Whole Food, or Is It Better to Use Supplements?

This brings us to the same question that you asked, Steve, about prebiotics: Is it better to eat fermentable fibers in whole food, or is it better to use supplements? Well, over the long term, I think, you’ll probably guess what my answer is. I think it’s better to get it from food. But in the short term, I actually find that it’s easier to use supplements to start, and the reason for that is that prebiotics tend to really cause problems for people who have a screwed-up gut, and I’ve found that it’s easier to adjust the dose and build up really slowly and cautiously over time with a prebiotic powder than it is to do with food. It’s just harder to control the exact amount of prebiotic fibers you’re getting when you’re eating whole foods than it is using a powder. We’ve talked about resistant starch as one potential prebiotic that you could use to do this, and potato starch is the version that’s most often used, and then there are things like Prebiogen, which I also sell in my store, which is a blend of non-starch polysaccharides, and I actually recommend that people use both because they stimulate the growth of different kinds of bacteria in the gut. Resistant starch will stimulate growth of a certain type of groups of bacteria, and then the non-starch polysaccharides will have an effect on other types of bacteria.

But let me remind you again that starting at the full dose which is often recommended, like one or two tablespoons twice a day, is absolutely not advised for people with gut issues! I just talked to another patient last week who ended up in the hospital because she was so certain that she was having appendicitis or some major issue in her gut, and what had happened is she had started taking one tablespoon twice a day of resistant starch, and on the second or third day, she was curled up in a ball on the floor for hours until she went to the hospital. It turned out it was just gas pains that were causing that pain. They can be super, super intense, and some people who are listening might have experienced this. That really triggered a flare for her that lasted about two and a half or three weeks. That’s not a typical response, but I just tell you that story to emphasize the importance of starting slowly with any prebiotics. I would say, like, a half of an eighth of a teaspoon, like, a sixteenth of a teaspoon, an eighth of a teaspoon, and then just really, really slowly build up over time. That way, I think, you’ll eventually get to reach the goal, but it could take months or even years to finally get to where you’re going, but you’ll see improvement all along the way, so that’s the bright side.

Steve Wright: Yeah, in case people are wondering, I think Chris and I just giggle a little bit about doing these experiments on yourself and the negative consequences that can happen, so we won’t say anything about the woman that Chris was talking about, and hopefully trying to let you know that, in general, you definitely want to ramp up all the time, whether it’s prebiotics or something else. As we’ve talked about on the show numerous times, essentially you’re changing your gut flora with every bite that you take. Resistant starch is kind of like rocket fuel for your gut flora. If you dump a bunch of rocket fuel down there and you haven’t been running that kind of octane in the engine for a while, there can be some serious consequences.

Chris Kresser: Absolutely. All right, so that’s today. I hope that answers your question about how to restore healthy gut flora when you don’t tolerate probiotics or fermented foods well, and we’ll be back next week with another question.

Steve Wright: Yeah. Thanks, everyone, for listening. If you want more information from Chris in between episodes, definitely check out, but you can also get more tidbits on and


Join the conversation

  1. Good discussion but I feel something important was left out. Can you use spore forming organisms to help stimulate the growth of your own beneficial strains? and what if you have severe histamine intolerance and cannot tolerate even a teaspoon of sauerkraut juice, kefir, etc?

  2. Once a person heals leaky gut, are they more prone to it returning? If so, what should they generally do to maintain a healthy gut and ward off backslides?

  3. Interesting article – I learned a lot from the facts ! Does someone know if my assistant can get a fillable NZ INZ 1200 version to work with ?

  4. Hi Chris,

    I was hoping you could comment on some reading I’ve discovered online about SBO being potential pathogens. I started taking PA after reading your articles and listening to digestive health podcasts.

    I’ve never had any trouble with BMs in the past but have become very constipated after starting PA for a couple weeks. I plan to stick with it, but in trying to find out some info online I’ve found some claims that SBOs can do more harm than good.

    Just wanted to know if these claims have any legitimacy and I should be worried about developing constipation as a sign that these may be pathenogenic in my gut and the potential to cause harm to my system.

    • I’m having the same problem! I started KS’s SBO s and I’ve become constipated and now have an inflamed appendix they want to take! I’m mad and need to beg for a antibiotic now- I started a gaps diet to bring down the inflammation but I’m not sure I’m going to make it in time- my appendix hurts now!

    • Hi
      Same here. I took a digestive enzyme containing bacillus subtillis and now it seems my intestines are not moving and loss of peristalsis making me constipated.
      I tried antibiotics to kill the bacteria no help. Resolor is not helping me too.

  5. My question is, how do you know when you’re reacting poorly to a probiotic and when it’s just die-off/adjustment? I have had such bad luck with probiotics in the past, but after reading this I was excited to try Prescript Assist. I have been taking 1/2 capsule for 3 days and my bloating, gas, and difficult bowel movements have gotten worse. I read this is normal and will pass. But what if these strains aren’t right for my body?

  6. Hi,

    Based on recommendations from Chris and everybody else in the Paleo community I started with Prescript Assist a month ago. I didn’t really have any issues I was dealing with I just wanted to try to optimize my health. I took one capsule per day for five days. Since then I’ve been terribly bloated and have pretty bad stomach pains. I’m sure it’s a good product for most people but it really messed me up. I’m writing this to encourage others to be careful and really start slowly. And also, if anyone has a good idea of what happend to me and what to do about it, please ler me know!


  7. How does this topic relate to candida overgrowth in the gut? Can candida cause intolerance to certain foods? Does supplementing with pre- and pro-biotics encourage candida overgrowth?

  8. Thank you so much for speaking on this!!! This gave me so much hope and encouraged me I’m going in the right direction (even though it takes a long time and goes pretty slow sometimes). And, it also gave me some very useful new information.

    Thanks so much! So fun to heal stories of healing this stuff!

  9. I think you’re forgetting about Fructose Malabsorption, where the body cannot physically digest fructose/fructans. Following a FODMAP diet can help people with this issue.

    • Hi Carlo,

      Check out the Rothfeld Center for Integrative Medicine in Waltham. Seeing an excellent nurse practitioner there for my SIBO.

  10. Such an interesting post. I have been dealing with stomach issues for some time. So, my doctor suggested I try a probiotic. I picked up Metagenics IB (60 billion count, a 50:50 blend of Lactobacillus acidophilus and Bifidobacterium lactis). Unfortunately, even knowing my system is sensitive, I mixed one pill into a smoothie. I only took one pill. Two days later, I had horrific diarrhea, nausea, loss of appetite, and really bad heartburn. That last two days. My doctor took blood and my WBC was elevated. The next week it went down into the “normal” range. The diarrhea got a little better each week, however, I am still having issues with appetite (coming and going) nausea, fatigue, food in stools, and, as soon as I wake up, in the morning I have diarrhea. I have lost about 15 lbs. over a two month period and just have a general feeling of being unwell. Also, another really odd thing, I would feel awful in the morning but better towards the afternoon. My doctor did complete a CDSA (through Genova) and it showed things were pretty normal. Although, it shows I no Lactobacillus in my gut. I just went through an EGD and Colonoscopy and was told that everything looked “normal.” They did take biopsies. I just keep associating this issue with the probiotic. Also, I am wondering if I have a parasite (even though the stool sampled showed nothing) or SIBO. I am really starting to lose it. Any ideas or suggestions?

  11. I’ve read repeatedly about the health benefits of probiotics such as kefir. I’ve also read that one of the functions of stomach acid is to kill bacteria. If I have normal stomach acid levels, how do the beneficial bacteria from probiotics make through my stomach intact?

    • Yes, that is exactly my sentiment – stomach acid is non-discreminatory, isn’t it naive to think we need it to kill the “bad guys” but when we eat fermented food – the “good guys” magically get a free pass? I would appreciate if sub could explain this conundrum!!!

  12. Hi Chris,
    I just got my pathology stool report. I have Klebsiella overgrowth in my guts. I was searching for herbal protocol for Klebsiella but can’t find anything ( except, for 1 web-site that recommends Berberin 400mg BID). What is your opinion? Thank you!!!!

  13. Hi Chris. Because you were the first person from whom I learnt about Prescript-Assist (PA), I wanted to let you know about my experience with it. I have suffered from SIBO and leaky gut for several years. I adopted the SCD diet at the beginning of the year and experienced dramatic improvements in my symptoms. Since developing SIBO, I’ve had dysfunctional intestinal motility, with alternating periods of mostly mild C and D. However, after starting the SCD, despite the great improvements overall, I developed moderate (sometimes severe) C. No alterations to the diet seemed to improve the situation, and I’d often go more than three days without a “movement.” A month after starting the SCD, I tried a multi-strain lactobacillus probiotic. After two weeks of horrible symptoms, which initially I assumed was die-off, I gave up and concluded that probiotics were not for me. However, after reading the information you provided on PA, I decided to give it a try. From the second day my bowel movements have been completely normalized; it’s now been over a month and I’m going once a day with no problems at all! I did suffer from a bout of die-off, mainly increased bloating, which peaked at about day 3 and was gone by day 5. Thank you so much for providing this valuable information that has helped me, and many others no doubt, so much!

  14. Are the symptoms the same for the possible causes of intolerance to fermented foods and probiotics that you mentioned?

    Also, what testing would be involved in step 1 of the treatment plan you outlined?

    Thank you.

    • Chris, I have no symptoms/issues with fermented foods or probiotics. Sorry, I should have been clearer. I was only interested in what negative affect, if any, alcohol may have on desirable gut bacteria? Great podcast & blog BTW! Thx, Ian

  15. Chris, could you comment alcohol’s effect on gut health? Does moderate consumption harm healthy gut bacteria? Which type of alcohol, if any, is preferable, etc.? Thanks, Ian

  16. Chris,
    I am so grateful, and very happy, that you chose to answer my question in such detail. This podcast theme couldn’t have come at a better time, and the reminder to proceed slowly is definitely needed :-).

    My follow-up questions are:
    – in terms of the pace, what kind of symptoms should one expect to tolerate? I am pretty much always symptomatic, and symptoms vary. Is it ok to progress through some degree of e.g. bloating and discomfort?

    -how to time the antimicrobial regimen so that it doesn’t interfere with, and decrease the effect of, probiotics and fermented foods?

    Thanks again!

    • Good question about how to gauge response when you’re always symptomatic. This is my situation and I’m curious about it too.

  17. I always enjoy your blog episodes and appreciate the wealth of information and insight you offer. I do want to raise an issue however which many might consider nit picking and irrelevant. At the beginning of this podcast you made a reference to the “schizophrenic” weather. As a health professional I would hope that you would choose your metaphors more carefully and be a bit more sensitive about making these kinds of references. It may sound funny and harmless to describe something as “schizophrenic” and certainly the media and public use this all the time. However, all you are doing is to perpetuate this hurtful myth that continues to reinforce ignorance (stigma) in both the health care community and the public. I am a researcher and educator working with individuals with severe mental challenges such as schizophrenia. I am also very aware of the epigenetic factors that are at play, especially when it comes to wheat gluten and nutrient deficient diets. I have referred many individuals who live with schizophrenia to your site because it is my belief they will greatly benefit by making changes to their diet and lifestyle, especially the ones you recommend. So… as a professional courtesy, I would appreciate that you choose your words with a bit more respect.

  18. I am a nutritionist in the midst of trying to solve the mystery of my two year old’s gut. Stool test came up with dysbiosis. ND I worked with had us do 6 weeks of GSE, and then 6 weeks of 100 billion probiotics (Ther-biotic complete) and biotagen. He got better towards end of GSE, but then worse again. –Main issue is that he only has BM every other day, and it’s a HUGE pile of loose stool. I can tell that his temperament can go up and down with this… He’s an awesome eater – in fact wants to eat all the time and is on a paleo diet like the rest of the fam. I’m in the middle of trying GSE, probiotics, and prebiotics at the same time, but not seeing improvement. Considering FODMAP intolerance, so this is my next step. He has a lot of extreme histamine reactions (huge welts that stay there for awhile and/or hives) to bug bites, some herbs (cinnamon & Uva Ursi so far…). What are the best tools for determining histamine intolerance?

    Also, can a toddler take SBO’s (or is he getting this from all the dirt that goes in and on him in the yard?)

    Any thoughts from anybody on all of this? Next steps?

  19. You mentioned sauerkraut, kefir and kvass as good probiotic sources. What about kombucha? Is that a good source? Or, do you have reservations about kombucha?

    • I’m curious about this too. I sometimes make water kefir but it takes quite a while to ferment and buying kombucha is much more convenient.

  20. I’m curious Chris, since you mentioned Apex H-PLR, do you have any experience with or know of the efficacy of mastic gum in the treatment of h-pylori?

  21. Chris,

    Could you share which herbs are effective for eradicating methanogens for people with SIBO? I react badly to Allicin, which supposedly should be effective. What are other options?

      • Thanks John, but I have read everything there, as well as in almost every other site, I have attended SIBO symposium, Siebecker 7-hour class so I know a lot about it. I’m looking for an answer to my question, not a suggestion to look somewhere else.

    • Hi Simas,
      I react badly to allicin as you say.
      How did you solve your problem? Did you find some herbs effective on methane rather than allicin?
      I was having big anxiety(i’d say panic), tachycardia and brain fog from allicin.
      I’m supposing this could be related with histamine but I’m not sure, because I don’t know if allicin is a liberator.

  22. Hi Chris,

    Do you have any thoughts about people with autoimmune disease taking resistant starch in the form of potato starch? Do those people need to be more cautious of using it since it is a nightshade?

    • I would like to know this, too. I am curious if that is why I reacted so poorly to potato starch. I have otherwise been nightshade-free for two years.

  23. I have a combinbation of symptoms and get conflicting advice. The symptoms: benign esophageal lesions, hiatus hernia, atrophic gastritis. Is tumeric OK? Fermented dairy? Fats? Is a low-carb diet adequate, or do I need the paleo diet?

  24. Hi Chris,
    Can you speak more about using DAO enzymes? do you recommend them? I’ve also heard of people taking Molybdeum when eating high histamine foods. I have low Molybdeum levels and also react badly to fermented foods.

    • Yes, I occasionally recommend DAO to patients with histamine intolerance. Quercetin + bromelain are also effective in many cases, as is vitamin C, pycnogenol, and nigella sativa.

  25. I am in the process of eradicating SIBO, I have made some progress and my practitioner has me taking both a probiotic and prebiotic (GOS). As far as I can tell I’m tolerating both, but many people in a SIBO discussion forum I belong to are saying that pro/prebiotics should only be used after SIBO is gone. It makes sense to me that one would need the good bacteria in order to assist the digestive system in returning to normal function but I’m wondering if it’s possible for them to hinder progress without causing an obvious ‘reaction’, or if a more obvious reaction (increased bloating or gas, for example) is a better way to gauge things rather than the mere presence of lingering symptoms, which is my case.

    • In my experience it depends on the person. Some are able to tolerate prebiotics during SIBO treatment, while others aren’t. But even for those that tolerate them, I think it makes sense to start at a very low dose and then ramp up as the treatment progresses and the bacterial load in the small intestine decreases.

        • Our CN says the soil based probiotic Prescript Assist is safe to take if someone has SIBO, or if it’s unknown whether someone can tolerate Lactobacillus acidophilus. (My daughter’s tests showed she should NOT have L acidophilus although she tolerates the 15 billion in Metagenics Ultra Flora Balance). So instead she’s switched to the soil based Prescript Assist working up slowly starting with less than 1/4 capsule. It has both prebiotics and probiotics which sounds like Chris prefers. She also has high histamine/ histamine intolerance and thankfully it sounds from this article that soil based are safe for that as well.

  26. I am all confused about stomach problems all I know is I have had two colonoscopies and one dic says diverticulosis another colitis and after six yrs I still walk around with a pregnant stomach and am thn and way h what I eat!

  27. Chris, I find that some people get “addicted to” taking a probiotic supplement each day. So they don’t have SIBO, but they also aren’t able to keep the normal flora sustained. Do you have experience with helping someone wean off a probiotic using prebiotics? Would you use the same extreme caution of 1/16 tsp to start?

    • As I mentioned, probiotics don’t quantitatively increase beneficial colonic bacteria over time. That’s what prebiotics are for. Definitely makes sense to start at a very low dose and build up over time.

      • what about probiotic retention enemas?do they colonize?and if so how much is too much to take because with the numbers of billions of bacteria that some products contain you put a large Number of bacteria inside…it is the concept of fecal transplant therapy as i understand but you only introduce a few strains but in large metametrix test showed zero lactobacillus and zero bifido and a very alkaline stool ph after years of lyme disease treatment(with herbals mostly)..

  28. Chris,

    You have Prebiogen listed in your supplement guide for skin conditions. However, you have acne and rosacea lumped together. Do you tend to treat the two conditions differently?

    In my case, it is unclear which of the two I have and I am worried about inadvertently making my condition worse. My experimentation with resistant starch led to considerable breakouts and I am unsure if I should give Prebiogen a try.


    • No, I don’t treat them differently. RS tends to affect people differently than the non-starch polysaccharides in Prebiogen. I think it’s probably worth a try, but start at a low dose and build up slowly over time.

    • You should keep up with the RS, but drop down to a much lower dose to where no adverse reactions happen. RS shouldn’t cause anybody any problems, but if it does it’s pretty much a sign you’ve got something messed up down there. the worst it should do technically is cause non-scented gas.

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