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

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This post was originally published on ChrisKresser.com on June 25, 2014

We received a question about 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.

In this episode, we cover:

  4:58 Four 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 ChrisKresser.com. I’m your host, Steve Wright from SCDlifestyle.com, 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 ChrisKresser.com 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 ChrisKresser.com 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 CulturesForHealth.com, 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. 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. [Update: Chris no longer uses Prescript-Assist and recommends Primal Probiotics instead.]

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.


1 Comment

  1. I found this article/podcast transcript very helpful. I’m actually working with Dr. Amy Nett at CCFM (as of 2 days ago) and will begin an anti-microbial protocol next week when my herbs come. I was given the guidelines, but this additional information is valuable and hearing about potential pitfalls (some of which I’ve fallen victim to before as well – seeing results and ramping up way to quickly, only to be back where I started from after major gas pains again). The timing of this article couldn’t be better for myself really. I know this podcast is a few years old, but the information is still extremely valuable. Thank you Chris!

    PS- I’m heading to the symposium on Functional Medicine in San Francisco on March, 4th. Excited to hear more for you and your peers and possibly meet you in person.