A streamlined stack of supplements designed to meet your most critical needs - Adapt Naturals is now live. Learn more

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


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), and we’ve launched a new supplement store. Click here for more information. 

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 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 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.

Like what you’re reading? Get my free newsletter, recipes, eBooks, product recommendations, and more!

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 ChrisKresser.com, but you can also get more tidbits on Facebook.com/ChrisKresserLAc and Twitter.com/ChrisKresser.

ADAPT Naturals logo

Better supplementation. Fewer supplements.

Close the nutrient gap to feel and perform your best. 

A daily stack of supplements designed to meet your most critical needs.

Chris Kresser in kitchen
Affiliate Disclosure
This website contains affiliate links, which means Chris may receive a percentage of any product or service you purchase using the links in the articles or advertisements. You will pay the same price for all products and services, and your purchase helps support Chris‘s ongoing research and work. Thanks for your support!


Join the conversation

  1. Thank you for the info. I’m having a heck of a time with probiotics. My dysbiosis is out of control. Prescript Assist was great, but then it’s reformulation wasn’t too great. I’ve recently tried another soil-based probiotic called ProFlora. It’s been a few weeks of my taking a little out of the capsule per day. I am encouraged that being disciplined in this process will eventually benefit me.

  2. 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?

  3. 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?

  4. 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 ?

  5. 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.

  6. 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?

  7. 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!


  8. 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?

  9. 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!

  10. 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.

  11. Like Webraven and Melinda I am curious about how to gauge response when you’re always symptomatic.


  12. 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?

    • Lactobacillus isn’t always a good thing. Bifido bacteria is the main commensal in the gut.

  13. 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!!!

  14. 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!!!!