RHR: What the Latest Research Says about Probiotics, with Lucy Mailing

RHR: What the Latest Research Says about Probiotics, with Lucy Mailing

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Probiotics have faced controversy before, but recent news headlines have painted them as everything from completely useless to potentially harmful. That characterization in the media is the result of two studies recently published in the journal Cell. So what’s the real story when it comes to probiotics? Are they safe and helpful, or should you take them with caution? Listen as I discuss what the data really suggest about probiotics with Lucy Mailing, a microbiome researcher.

Revolution Health Radio podcast, Chris Kresser

In this episode, we discuss:

  • Why your stool microbiome may not be a good indicator of your gut health
  • Why probiotics aren’t useless
  • How your gut microbiome fights change
  • What really happens when you take probiotics after antibiotics
  • Why you should consider banking a stool sample, if possible
  • Key takeaways from these two studies

Show notes:

Chris Kresser:  Lucy, thanks so much for joining me

Lucy Mailing:  Thanks for having me on.

Chris Kresser:  So this was kind of a big bombshell that was dropped. This study we’re going to be talking about today … and I’m excited that you’ve been able to join us. Because every so often in science and research, we get a finding that completely contradicts what we thought before. And this is, of course, vital to science.

This is part of the scientific method, that we continually challenge our hypotheses and try to falsify them. And if you were to ask the average person on the street, I think, should you take probiotics after take antibiotics, and the average physician and the average researcher, the answer would probably almost universally be yes. But this study suggests that the answer may be no.

Lucy Mailing:  Yep. Yeah, I think you really have to be willing to put your bias aside here and we have to go where the evidence takes us. And sometimes that results in a total paradigm shift and directly contradicts what we thought before, like you said. But I think we need to be open to that and especially honest about it with those who trust us for health information.

Chris Kresser:  Yes, this, of course, was a big topic on my recent appearance on the Joe Rogan debate, where the evidence over many years on saturated fat and cholesterol and their relationship with heart disease changed to the point where even the dietary guidelines in the US and other countries evolved. And yet there’s still a pretty committed group of people that is not willing to question those original hypotheses that were developed in the 50s and 60s. So let’s maybe not make that same mistake in the case of probiotics.

Lucy Mailing:  Yeah, absolutely.

Chris Kresser:  So why don’t we start with just some general information about this study. We wrote, you wrote an article for a website that we published. It’s called “Are Probiotics Useless? A Microbiome Researcher’s Perspective,” and we’ll link to that in the show notes, and some folks may have already read it. But for those who haven’t, why don’t you run us through the study.

  • What were the researchers trying to find?
  • How is it designed?
  • And then what were the findings?

And then we’ll talk little bit more about what to make of all that.

Why Your Stool Microbiome May Not Be a Good Indicator of Your Gut Health

Lucy Mailing:  Yeah, absolutely. So for starters, I think it’s important to go over a little gut anatomy just in case your listeners aren’t familiar. So we can think of the G.I. tract as a hollow tube, and all the inside walls of that tube are coated with this thick, protective gel. And so in this analogy, the gel represents the gut mucus layer, and the very inner center of that tube represents the gut lumen. And each of these regions has a distinct community of microbes, but these are rarely studied because these regions are rather inaccessible unless you undergo invasive endoscopy. And then of course we have the stool microbiome, which is the most widely—

Chris Kresser:  Let me just interrupt you, Lucy, because some folks might not know what that means. So that basically means a tube being put down your throat to look in your intestine. And not very practical on a broad scale to do that kind of testing to assess microbiome health.

Are probiotics really a good idea after taking antibiotics? Will banking our own stool samples to protect our gut health become routine someday? Check out this episode of RHR where Lucy Mailing, a microbiome researcher, describes surprising findings about probiotics. 

Lucy Mailing:  Right, right. And then of course we have the stool microbiome, which is the most widely used proxy marker for the gut microbiome. And you’ll often even hear these used interchangeably, the stool microbiome and the gut microbiome. But the first thing that was interesting about this study before they got really into the probiotics, was showing that, confirming previous findings that the stool microbiome was really not representative of the gut luminal or gut mucosal microbiome. And so that was really …

Chris Kresser:  That’s such an important finding. Again, you said it. It has already been known for some time, but I just want to clarify this for folks. What you see in your poop is not necessarily what’s in the gut lumen, is what Lucy was saying. And that presents a challenge, doesn’t it?

Lucy Mailing:  Absolutely, yeah. And also not what’s, not representative of what’s most closely associated to the gut epithelium in the gut mucus layer, as well. And those might have the most impact on our health because they’re so closely associated with the actual gut tissue.

Chris Kresser:  Right, and so all these studies that have been done, which are very useful and important, that have correlated the changes in the gut microbiome to health and disease states have been perhaps only seeing part of the picture, is really what we’re learning. And that there may be a whole other side.

Well, there almost certainly is a whole other side to this story that we don’t know very much about yet. It’s almost like the ocean covers two-thirds of the earth’s surface and we know quite a bit about what’s happening up near the surface, but we know almost nothing about what’s going on down in the depths. And in some ways we know more about space off of the surface of our planet than we know about the deep oceans. And I wonder if that’s an apt analogy for the microbiome.

Lucy Mailing:  Yeah, I think so. They even showed that if they look at the total genetic information in the gut, so the metagenome, as it’s called, there was only 20 percent correlation between the stool microbiome and the gut mucosal microbiome. So we really can’t necessarily use the stool samples to predict what is actually going on inside the gut.

Chris Kresser:  That’s again an important point, and it’s one that’s been so frustrating for me as a clinician, and I’m sure for you too, Lucy. That’s what we have access to as practitioners is stool testing.

Lucy Mailing:  Right.

Chris Kresser:  Of course, there is a big variation in the quality of stool testing that’s available. Some is better, some are better than others and then there … stool testing can still be very helpful for things like identifying pathogens.

Like, for example, I got recently caught up in an outbreak of Cyclospora in the Bay Area here, which folks on my staff know, but some listeners may not. It’s a parasite. It’s an acute pathogenic organism. I also had in that same food poisoning episode, I contracted enteropathogenic E. coli. And so stool testing can be really helpful for finding, I did some testing and identified those pathogens and I was able to treat them.

So it’s really helpful for that kind of thing. But what you’re saying is for identifying what the presence of “good versus bad bacteria” and the overall microbiome, stool testing may not be able to tell us all that much.

Lucy Mailing:  Yeah, absolutely. I think, yeah, I think you said it really well there. It’s definitely still useful for identifying pathogens. But any bacterial abundance I get, whether it’s from a comprehensive stool analysis, biome thrive, I’m always taking that with a huge grain of salt now. Because it’s really not necessarily representative of what’s happening in the gut environment. And so stool testing can be one piece of the puzzle, but we kind of need a consortium of tests to get a better idea of the total gut environment.

Why Probiotics Aren’t Useless

Chris Kresser:  Right. So another thing this study found, which we’ve talked about before on my blog and in the podcasts, is that probiotic, when you take probiotics, the effect that they have is transient. I think there’s been this notion that, I refer to it as like a gas tank analogy, where if your tank is empty, like, you don’t have much good bacteria and then you take probiotics, you’re kind of filling up the tank, and then once the tank is full you can stop. But that’s not really how it works, is it?

Lucy Mailing:  No, no, definitely not. I mean, this is not a new finding, but of course it sent the media crazy all over again.

Chris Kresser:  Probiotics are useless, right?

Lucy Mailing:  Yeah, exactly. We have hundreds of randomized placebo-controlled trials in humans that have shown safety and efficacy of many different probiotic strains. So to just … outright, those media headlines saying “probiotics are useless,” they’ll maybe strip some probiotics, but there are certainly many probiotics that have been shown in randomized controlled trials to have beneficial effects.

Chris Kresser:  But what this is saying is they’re useful in a different way than we thought before and that maybe many people still think, right? So instead of working on that gas tank analogy where you’re filling up your tank with good bacteria, what are they, how are they actually benefiting us as they transit through the G.I. tract?

Lucy Mailing:  Yeah. So they found that there wasn’t really significant colonization. They did this in both mice and humans. So there wasn’t any significant colonization in mice. In humans, it was very individual. So some people did have some colonization, and those people, they turn into permissive colonizers, and other people were completely resistant to the probiotic colonization. And so, but it didn’t really matter because when they lumped them all together and looked overall, there were significant changes in the gene expression in the small intestine in those that were taking the probiotic.

So this is in alignment with many studies we’ve seen before, where probiotics don’t really colonize the gut, but they’re having really beneficial effects in transit, including modifying gene expression, eating and digestion, lots of these different things, stimulating the immune system. And so just because they don’t colonize in this case, in some humans, they did. But even if they don’t colonize, they’re still having benefits.

Chris Kresser:  They’re still doing a lot of good, and that’s why I’ve often told my patients to think of them almost like immune regulators or balancers because of the impact that they have there. And I mean in the same way that makes sense because, historically, a lot of our exposure to these kinds of organisms came through food. And so eating those foods was something that we would do on a regular basis, not just a few times, until we got what we needed. We had this kind of ongoing exposure to these organisms.

Lucy Mailing:  Right, right, yeah.

How Your Gut Microbiome Fights Change

Chris Kresser:  So another interesting finding, which again was not necessarily new, but I think is something that surprises people, is that our normal microbiome kind of wants to stay the way it is and doesn’t necessarily, isn’t easily changed. So tell us a little bit more about what they found here.

Lucy Mailing:  Yeah, so they did a really cool experiment in mice where they use germ-free mice, which are basically raised in a sterile incubator with no exposure to microbes, basically in a giant bubble. And so they gave these sterile mice the same 11-strain probiotic, and they found that in the absence of a normal microbiome, the germ-free mice had massive colonization of the probiotic strains. So this suggested to them that it was the commensal microbiome, the normal microbiome, that was inhibiting the colonization of the probiotic strains.

Chris Kresser:  And that’s interesting too in light of the way that human microbiome colonization happens, right? I think we used to think that a baby’s gut was completely sterile when they’re born. Now I think we know that that’s not the case and there may be some colonization that happens in utero.

Lucy Mailing:  Yeah, I think it’s still controversial.

Chris Kresser:  Still controversial.

Lucy Mailing:  Yeah, still controversial.

Chris Kresser:  But anyways, even if there is some colonization, it’s extremely minimal, right?

Lucy Mailing:  Right.

Chris Kresser:  It’s not, like, a baby is not born with a fully colonized gut and that doesn’t even happen until later in childhood. So this seems to mimic what we understand about how the human gut develops is that that colonization happens early in life and that’s why exposure to the right organisms through breastfeeding and vaginal birth is so important.

Lucy Mailing:  Yeah, absolutely.

Chris Kresser:  So another finding you talked about is that the probiotic colonization in humans is individualized. So you mentioned this in the context of some people being … what was the exact term? It was—

Lucy Mailing:  Permissive.

Chris Kresser:  They had a permissive microbiome. So they were more likely to experience colonization. But that wasn’t the only individual difference. What else happened there in the study? So I think it was not all of the probiotics colonized equally or were not …

Lucy Mailing:  Correct, yeah. So there were, they looked and they found nine of the 11 strains colonized.

Chris Kresser:  Yeah.

Lucy Mailing:  Significantly enriched in the mucosa, especially, but there were some people who had significant enrichment, and some people who really didn’t have any. And that was where they made the distinction between the permissive colonizers and the resistant colonizers. And they did look into some different factors that might explain the permissive or resistant.

But they really had a fairly small sample size there, so they weren’t really able to tease out anything. Although it looked like the baseline microbiome, certain characteristics of the baseline microbiome were able to determine whether, predict whether they’d be permissive or resistant.

Chris Kresser:  Right. But again this, as you pointed out, this doesn’t mean the probiotics didn’t have an effect. I want to read a part of the paper that you highlighted:

Nonetheless, when all probiotic consumers were considered together, probiotic consumption led to transcriptional changes in the ileum with 19 downregulated and 194 upregulated genes noted, many of which related to the immune system, including B cells.

So again we’re seeing changes in gene expression and immune function, even though there isn’t colonization.

Lucy Mailing:  Yep, yep, and it did colonize in some people, which was contrary to what we probably thought before.

What Really Happens When You Take Probiotics after Antibiotics

Chris Kresser:  Right, right. So now we’re getting into some of the really surprising perhaps parts of of the paper, which is that probiotics may slow recovery of the normal microbiome after antibiotics. I think this is the most, again, the most surprising part of the paper and the part of it that conflicts most with maybe what was known before. So tell us a little bit more about that.

Lucy Mailing:  Yeah, so like you said earlier, probiotics are widely used and prescribed during or after antibiotics, often suggested by the physician with this idea that flooding the system with “good bacteria” can help prevent the, some of these adverse effects of antibiotics.

And so in this study they wanted to see how probiotics, how taking probiotics after antibiotics impacted the long-term trajectory of the gut ecosystem. And so what they did first, they treated a group of mice. They did this in mice and humans again. So a group of mice and a cohort of healthy human volunteers with a single course of the broad-spectrum antibiotic ciprofloxacin and metronidazole. And that was just to kind of wipe out the gut bacteria.

Chris Kresser:  Carpet bomb.

Lucy Mailing:  Yep, exactly. And both of those antibiotics have been shown to have widespread devastation of the gut ecosystem.

Chris Kresser:  Those are the two worst I can think of, cipro and Flagyl, okay. Yeah, so okay, continue, please.

Lucy Mailing:  Yeah, so then they split the mice and the humans into three groups. So group one was just allowed to spontaneously recover over time. Group two was supplemented with the same 11-strain probiotic that they used in the first paper for four weeks beginning right at the end of the antibiotic treatment.

And then group three underwent what’s called autologous fecal microbiota transplant, or aFMT. And that one’s a mouthful, and I think we’ll come back to that group in a second. We’ll focus on group one and two at first.

Chris Kresser:  Such a well-designed study, and I love the autologous FMT part of it. I think that was really a smart way to do it. Why don’t we just go ahead and explain what that is. Basically, it means that they took a sample of the microbiome prior to the intervention, and then they put that back using a fecal transplant after it. So it wasn’t a fecal transplant using another donor’s stool. It was a fecal transplant using the own individual’s stool.

Lucy Mailing:  Yep.

Chris Kresser:  All right, so what happened? We got these three groups. What were the results?

Lucy Mailing:  So most interestingly they found that treating the gut with probiotics delayed the return of the normal microbiota for as long as five months after stopping probiotic treatment.

Chris Kresser:  Wow.

Lucy Mailing:  Yeah.

Chris Kresser:  What have you made of this and other people in the field? Like, what’s the chatter? I know you work in a microbiome lab. I imagine this was kind of like a big day for all of you and a lot of discussion amongst your colleagues about this. So what do you make of it?

Lucy Mailing:  Yeah, I mean to be honest, when I saw the headlines and I dove into this paper, or these two papers, I was prepared to say there’s got to be something wrong with the methods here. Like, probiotics have to be good. We’ve known they’re good for so long.

Chris Kresser:  Right.

Lucy Mailing:  And so you know, but I really tried to put my bias aside and really, like, look at it very critically. And I just couldn’t get over this biotic treatment. And microbial diversity remained low for that five months as well. It was significantly lower at that five-month time point. Even lower than the spontaneous recovery.

Chris Kresser:  Right.

Lucy Mailing:  Which the spontaneous recovery group had no major differences in the stool microbiome within 21 days post-antibiotics.

Chris Kresser:  That’s the part of it that I’m still not clear on because I know previous work has shown that, and I haven’t gone into great, I haven’t looked closely at these studies. So maybe there are methodological issues with these studies. But a single course of antibiotics can alter the gut microbiome for up to two years or even longer.

So it seems like they didn’t find that in this case. And in fact, with no intervention, I think you just mentioned was about five months that they went back to normal, is that right?

Lucy Mailing:  Yeah. So I’m unfamiliar with the studies you’re referring to, the previous studies, and that was with ciprofloxacin as well. In those studies they found that it closely resembled the pretreatment composition fairly quickly in terms of overall composition of the microbiome. There were a few taxa that failed to recover within six months or two years.

Chris Kresser:  I see.

Lucy Mailing:  So those previous studies, we’re still seeing the microbiome is still very resilient and so we’re still seeing this bounceback. We might be missing a few taxa, but we’re not preventing the return of the bulk of the normal microbiota for more than five months.

Chris Kresser:  So has there been any speculation on what the mechanism is in terms of the probiotic inhibiting the natural recovery of the microbiome?

Lucy Mailing:  Yeah, so they did a really cool follow-up study to this, where they essentially took the probiotic pill and they cultured it in a bunch of different growth conditions that each supported the growth of each of the, there were four different genera in the 11-strain probiotic. And so they cultured it in such a way that one of the cultures had a lot of Lactobacillus and one of them had a lot of Bifidobacterium.

And so after 24 hours of culture they collected the supernatants, or kind of the soups that there are surrounding the probiotics on the dish. And then they took that and they kind of added it to a vat of a culture of human fecal microbiota. And they found that the soups, if you will, that had come from the plate with Lactobacillus, with a lot of Lactobacillus showed the strongest inhibition of the native human microbiome.

So this kind of points to Lactobacillus in particular might be preventing this recovery. So, and I mean, that’s probably the most commonly used one, Lactobacillus acidophilus.

Chris Kresser:  Absolutely.

Lucy Mailing:  Yeah.

Chris Kresser:  Yeah. I mean it would be really interesting to see what the differential effects of different categories of probiotics would have in future studies. Like, wonder about soil-based organisms or something like E. coli Nissle, or even beneficial yeast Saccharomyces boulardii, which some people are often advised to take after antibiotics.

Of course, we don’t know the answer, but I hope that future studies will be done to assess that. And then I also even wonder about different delivery systems because there are now companies that are, like Seed, for example, and others that are, have developed patented delivery systems which they claim make the probiotics more likely to survive the digestive, acidic stomach and upper part of the small intestine. And I wonder if there’s a different effect there versus just a probiotic that doesn’t have that kind of delivery system. So this study definitely raised even more questions than it answered, I think.

Lucy Mailing:  Yeah, definitely. And the other thing to point out is this was a single combination of antibiotics. Probably the most devastating of the broad spectrum antibiotics, arguably. And like you said, a single oral probiotic supplement mixture. So there’s so many different combinations of antibiotics, probiotics, and even treatment timing.

So in this study they didn’t begin the probiotics until after the antibiotic course was over. But there’s some studies to suggest that if you begin the probiotics earlier, we don’t know anything about how it affects the microbiome, but it certainly can prevent, be better at preventing antibiotic-associated diarrhea and Clostridium difficile infection.

Chris Kresser:  Right. And they didn’t measure any clinical symptoms either during or after the antibiotic treatment, which would’ve been interesting to see if the changes are in the microbiome or the lack of change is correlated with any clinical symptoms.

Lucy Mailing:  Right.

Chris Kresser:  And I think you pointed out that it would have been also interesting to see, like they didn’t, one of the reasons it’s often offered for taking probiotics after antibiotics is as a way of protecting against any kind of opportunistic pathogens, right? Enteropathogens like Salmonella. But we don’t know whether maybe the probiotics would’ve protected against that even though they delayed recovery. So that might be another interesting study to see in the future.

Lucy Mailing:  Right, yeah. And I did dive into the literature a little bit on this to see what’s the degree of the protective effect of probiotics after antibiotics for clinical symptoms or C. diff infection. And there are several meta-analyses, but there’s a statistical concept that I think you’ve talked about before on your podcast or your blog. It’s called the “number needed to treat.” And that’s essentially a measure of the impact or efficacy of a particular therapy relative to the burden of treatment.

And so in this case, based on the most recent meta-analyses, you’d need to treat 13 patients with probiotics to prevent one case of antibiotic-associated diarrhea and at least 43 patients to prevent one case of C. diff. And so in all those other patients we’re potentially delaying restoration of the gut microbiome.

Chris Kresser:  Right.

Lucy Mailing:  And so there’s definitely this trade-off here.

Chris Kresser:  Yeah, yeah. Especially with the 43. I mean 13 is a little more of a gray area in my mind, but 43 it starts to, that starts to be, the calculus is pretty clear there. Although it may depend on the virulence of the pathogen. Like, with C. diff., there are some 30,000 people, I think, are still dying of that in the US each year. So tricky, very tricky.

Why You Should Consider Banking a Stool Sample, if Possible

Let’s talk a little bit more about the autologous FMT because I thought that was one of the clever, most clever parts of the study and is certainly something that I think has a lot of potential in the future. I’m personally a lot less enamored with FMT than I was maybe five years ago as a potential treatment. Certainly I think it still can be lifesaving in the case of recalcitrant C. diff, where someone has failed antibiotics and they’re actually, they could die. In that case I think an FMT is a no-brainer and the research is still really solid on that.

But what I’ve seen clinically is a lot of people have come to think that FMT is some kind of miracle cure for all kinds of conditions, like fibromyalgia or even being overweight and autoimmune disease, etc. And I’ve seen definitely some improvement when people have done FMT and I’ve also seen no change, and I’ve seen people get worse.

Lucy Mailing:  Yeah, yeah.

Chris Kresser:  If we go back to what you said earlier about how stool testing is not necessarily telling us what’s going on in somebody’s gut or what’s in the stool, like, I just don’t know that we have the level, I’m not confident enough in stool testing right now to be able to know that we’re screening donors properly.

If the stakes are high enough that you’re facing death, then I think that, again, that calculus makes sense. But if it’s like you’ve got an autoimmune condition, I’m not so sure. So it seems like autologous FMT where you replace … if there was a time where you were lucky enough to bank a stool sample before you were sick, of course, that’s the big challenge here, the question. That makes a lot more sense to me than a donor that has not necessarily been screened adequately.

Lucy Mailing:  Yeah, absolutely. I think, I mean, certainly we only have this one study to my knowledge, but it certainly seems a lot safer because you’re not going to be re-inoculating yourself with anything that wasn’t already there before.

Chris Kresser:  Right, right. And I mean, in this sort of situation, if someone knows they have to take antibiotics for some reason and they were fortunate enough to bank a sample, that’s a lot more clear, right? But if someone is trying to use FMT to deal with a chronic condition, it’s probably unlikely, at least at this point, that they would have banked a sample.

But there’s no reason that in the future, it wouldn’t be, that couldn’t become something that people just do. That becomes part of our, sort of like when you’re 17 or 18 and you’re healthy, bank some stool samples, and then maybe when you’re 30 and you develop an autoimmune disease, you could get an autologous FMT with your stool sample from when you were 18. Who knows?

Lucy Mailing:  Yeah, definitely. And you can definitely imagine this being a part of normal clinical practice in the future. Like, if you, if you’re undergoing surgery and you have to have prophylactic antibiotics, then save a stool sample the day before your surgery.

Chris Kresser:  Absolutely.

Lucy Mailing:  Get your antibiotics and then you can re-inoculate.

Chris Kresser:  Yeah, that’s a perfect example of where you know that you’re going to be taking antibiotics and it’s not because … and you can plan in advance, basically. Yeah. Well, this is really fascinating.

So let’s break this down. I know some people are probably scratching their head right now or just throwing up their hands, saying, “Oh, my gosh, should I even listen to anything anyone says anymore? It’s just so frustrating, confusing.” And I totally understand that.

But again, this is how science works. We continue to learn, we continue to challenge our own hypotheses, even the most cherished held ones, and it doesn’t mean that that process isn’t valuable. On the contrary, I think it makes it even more valuable, and over time if you look at the last hundred years, I think it’s clear that what we’ve learned during that period of time is just enormous. And so it just means that we have to be willing to be flexible, right? And not hold on too tightly to certain beliefs that we may have had.

Lucy Mailing:  Right, yeah.

Key Takeaways from These Two Studies

Chris Kresser:  So why don’t you take us through some of the takeaways in a practical fashion. What can people take away from these two important studies?

Lucy Mailing:  Sure. So first, I just want to make sure we mention that we described what the autologous FMT is. But it resulted in rapid restoration of the gut ecosystem even within as little as a day to two days after the first infusion. So that was just dramatic compared to the probiotics and the spontaneous recovery group.

Chris Kresser:  Yes. And I’ve seen this in patients with C. diff who were on death’s door, essentially, and couldn’t even walk up a flight of stairs because they were so sick, who within a couple of days after an FMT are like running up the stairs and are well.

So it is pretty remarkable. When it works, it really works. And this aFMT, or autologous FMT, may even be better because it’s, I think, Lucy, you may agree with this, what we’re beginning to understand is there’s no one healthy microbiome. There’s probably more like a fingerprint where each person has their own healthy microbiome. So it makes so much more sense to replace using your own stool than somebody else’s.

Lucy Mailing: Yeah, definitely. There’s so much individual variability from person to person in the microbiome that I think this is a much, this is definitely the ideal choice is to use a sample from your prior, ideally healthy, self.

Chris Kresser:  Great. So what would you advise people now, given these results? I know this is just one study, or two studies, actually, but it seems to me that it was very well-designed. I’ve looked through it carefully and I know you have, and many have as well. And I’m certainly more reluctant to recommend probiotics after antibiotic use on this basis.

Lucy Mailing:  Yeah, I think in most cases, this suggests that probiotic use during or after antibiotics may not be worthwhile. I certainly think it has to be a cost–benefit analysis for each individual person. So someone who’s in a hospitalized environment where they have a greater chance of acquiring C. diff is very different from someone taking antibiotics in an outpatient setting.

Chris Kresser:  Right.

Lucy Mailing:  And so I don’t want to blanket statement we should never take probiotics during or after antibiotics, but I also think this definitely suggests that caution is warranted.

Chris Kresser:  Yeah, and I mean, another really key aspect of the scientific method is replication. So I really would love to see these results replicated by another research group, again, not because I think there was anything wrong with the way the study was done, but history is full of examples of really interesting findings that on the surface appeared to be totally credible and legitimate that failed to be replicated in subsequent studies.

So I hope that there are other research groups that are working on replicating these findings and that also we have research groups that are considering additional studies that would shed light on mechanisms and also maybe how these results would change if different antibiotics were used or if different probiotic preparations were used, etc.

Lucy Mailing:  Yeah. You and me both. I’m hopeful that those studies will come in the next few years as well, so that we can have more evidence to be able to give recommendations after antibiotics.

Chris Kresser:  Well, great. Thanks so much for joining me. This is, I think, going to be really enlightening for people, and I really appreciate you helping us to work through the studies. There’s a lot of information there. A lot to unpack. And your article was fantastic, and I think this podcast will be helpful. So, Lucy, where can people find out more about your work?

Lucy Mailing:  So you can find me at NGmedicine.com or on Facebook or Instagram as NextGen Medicine. And I just wanted to say thanks for having me on. It’s been incredible working with you over the past few years, and it was your site originally that put me on this amazing career path and helped me heal my skin from healing my microbiome and my gut. So I certainly hope to continue to work together and expand our knowledge in this area.

Chris Kresser:  Absolutely. It’s been a pleasure to have you on board, Lucy. I really appreciate your insight and your keen intellect and your willingness to dive deeply into the research and translate it in a way that people can understand. It’s so important to have that ability and that skill in today’s world because as you and I both know, so much of what’s reported in the media is just not really worth reading at this point when it comes to … I really miss those days where we had actual science journalists that were capable of reading a study with a critical eye and understanding it. Now, unfortunately, we just have, in most cases, there’s still a few good ones, but mostly it’s just pulling stuff off the wire and not really looking into it. Which is so confusing for people, right?

Lucy Mailing:  Right.

Chris Kresser:  It leads to an environment where people are just throwing up their hands and they feel like they’ve lost complete faith in public health recommendations. But I think now science literacy is increasing thanks to people like you who are out there translating your knowledge in ways that people can understand. And a more scientifically literate public is absolutely a good thing, with all the challenges that we’re facing. So thank you for your important work.

Lucy Mailing:  Thank you, and absolutely, your blog is doing the same, increasing scientific literacy.

Chris Kresser:  Okay, everybody, thanks for listening. I hope this was helpful. Continue to send us your questions at ChrisKresser.com/podcastquestion, and we’ll talk to you next time.

  1. There’s always some new hothead that shows up out of the blue and tries to disprove established research so they can start their own health coaching practice and convince people that they have the answers. I am seeing this constantly now

  2. Concern about age: I think it was Dr. David Perlmutter in Brain Maker who pointed out that while young peoples’ flora seems to recover in 6 months after antibiotics, it can take far longer or NEVER for folks over the age of 50 or 60… so in your “dream study” I hope they address the differential capacities of microbiome behavior in varying age groups!

  3. My question is, if it’s worth taking probiotics for their effects in transit, then I would already be taking probiotics when antibiotics are prescribed. Should I then stop probiotics?

  4. I love the information here, but these transcripts have gotten cumbersome. Hard to read…with the interruptions and such.

    How about an edited Main Take away peice, with a link to the transcript. I rarely have time to listen to the interviews, and prefer the text, but rather a distilled down version.

    Heres my takeaway. Pre/probiotics have limited effects, and may even slow down a regeneration of a biome, post antibiotics. And FMT is a good route back.

    But who can actually do the FMT? And how would one even “bank” a stool, process same, and know when to use it effectively? How much out of pocket would that all cost?

    I love the info, love learning new things, but then it wanders off into fantasy land…and leaves me without much of a solution…

    • I agree. Great podcasts, but perhaps someone on staff could write a follow-up article to help us wrap our heads around each one better.

  5. Now I’m really confused. For the life of me I cannot understand how one can possibly do any kind of meaningful study of post-antibiotic treatment with probiotics or even with FMT without also at least taking a good hard look at, and maybe even deliberately controlling for the type of prebiotics and even other probiotics in each subject’s regular diet. And how surprising is it really that if a subject continues to eat the same basic diet both before and after FMT, that an autologous FMT consisting of a microbiome that naturally thrives on their regular diet would produce the most rapid recovery?