ZOE Science & Nutrition - Antibiotics: The surprising truth about probiotics and what to do instead

Episode Date: August 17, 2023

Antibiotics are one of the greatest discoveries of the 21st century. Since their inception, they’ve saved countless lives, but these miracle drugs come at a cost. In some cases, they can seriously affect your health or can even be life-threatening. In today’s episode, Jonathan puts himself under the microscope. After an injury forced him to take antibiotics, he shows you the effect they had on his own gut bacteria. Jonathan’s joined by Dr. Will Bulsiewicz and Prof. Tim Spector, who explore the impact of different types of antibiotics, how they affect your bacteria in the short and long term, and how we can reverse the unwanted effect of these drugs.  Download our FREE guide — Top 10 Tips to Live Healthier: https://zoe.com/freeguide Timecodes: 00:00 Intro 00:15 Jonathan’s Intro 00:50 Quickfire round 01:40 Jonathan’s accident  04:00 Unpacking clindamycin 11:40 Antibiotic-associated diarrhea  14:45 Side effects prevention advice 22:20 Jonathan’s gut at 7 days  27:50 Fermented foods 27:00 Tips for building your gut back up 41:30 Benefits vs. risks 48:00 Summary  51:20 Outro Mentioned in today’s episode: Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT from Cell Saccharomyces boulardii: What makes it tick as successful probiotic? From the Journal of Fungi Follow ZOE on Instagram. Episode transcripts are available here. Is there a nutrition topic you’d like us to explore? Email us at [e-mail] and we’ll do our best to cover it.

Welcome to ZOE Science and Nutrition, where world-leading scientists explain how their research can improve your health. Now today's episode is a little different. I recently fell victim to an unfortunate series of events. But as they say, every cloud has a silver lining. And my incredibly painful accident means that today, with the help of Zoe's microbiome testing technology and expert team, I can show you what happened to my gut microbes before and after taking antibiotics. Joining me to unpack this topic are two world-leading gut experts, Dr. Will Bolsiewicz and Professor Tim Spector. Tim and Will, thank you very much for joining me today. It's very exciting to have you

physically in the same place. Well, you know the drill. Are you ready to start with a quick fire round of questions? Yeah, hit us. All right. Maybe starting with Will, do antibiotics save lives? Definitely. Can antibiotics damage my gut microbiome? Yeah, hit us. All right. Maybe starting with Will, do antibiotics save lives? Definitely. Can antibiotics damage my gut microbiome? Definitely. If my gut microbiome does take a hit after taking antibiotics, can this damage be long lasting? Unfortunately, yes.

Okay, Tim, will probiotics help my gut microbiome to recover after taking antibiotics? Unclear. All right. We're definitely going to get into that. Last question. Are there specific foods that can help my gut microbiome recover? I believe so. All right. So Tim and Will, I want to start, we don't normally do this, but actually telling a little

bit of a story. I went through, as you both know, rather an exciting start of the year. So I was messing around in the house, rushing from one meeting to another, and I decided to quickly clean up the kitchen, and I knocked over this massive teak bench straight onto my toes. I won't get too graphic, but let's say it was a little bit like popping two grapes open. So I don't recommend it to anybody who's listening at home. Luckily, my wife was nearby. I called her up and said, honey, could you possibly come around and give me a hand?

She wrapped me all up and we went off to a hospital because I'd actually not just broken it, but sort of smashed the whole thing up and open. I ended up having to have a minor operation to clean it all out and sew it up. And the doctor told me that the technical diagnosis was I had smashed my toes to smithereens, which I don't know if that's an American diagnosis or only a British one will. I think it translates in both countries pretty well. So they did a fantastic job. They cleaned it all up. They sewed it all up. And because it had been an operation, I had been in a operating theater. They said,

you need to go on a course of antibiotics. And rather luckily, I have two of the world experts on the microbiome sort of in my phone. And I remember because I messaged both of you and Will, because it was still early evening in the East Coast, you immediately replied when I explained what had happened. So I'd love to go back to that point and maybe tell me what you were thinking at the point that I explained what had happened and said, like, what do you think I should do? Part of the context that was really relevant and important to me as a gastroenterologist was you shared that you have a history of your old bowel syndrome and also that you've

had issues with diarrhea in the past and so that made me think this is a person with a gut that may be more vulnerable um and then you shared the antibiotic that you were on and i have to tell you that this i was not happy when i heard the antibiotic that you were taking. I'm pleased to say you didn't really say that exactly to me at that point. No, I wasn't scared. Yeah, well, I don't want to scare you. So, I mean, I very directly gave you advice without sort of explaining the entire sort of logic behind what I was doing. But let me just say that.

Unpack it for us now. Yeah, let's unpack this specific antibiotic because it kind of froze me in my tracks and made me go, whoa, okay, hold on. We have to make sure that we're handling this properly. The antibiotic is called clindamycin. And clindamycin, just to explain this for people at home, the reason why you were prescribed this antibiotic is to protect you from skin infections.

And the specific type of bacteria that we want to protect against is Staph aureus. Staph aureus can cause an infection in this area. And if it did, it would be catastrophic for you. And this would be like a really bad thing to happen. So we need something that's going to treat that. And clindamycin is one of the ones that does, but there's unfortunately like clindamycin

is a fairly broad spectrum antibiotic. And can you explain what that means? Yes. So what that means is that it's not just something that will destroy Staph aureus. It will destroy many, many more microbes than that. A very broad range of microbes. So when we say broad spectrum, we're referring to the range of different bacteria that are vulnerable and susceptible to the antibiotic. Clindamycin has this unique property where it can treat, now I'm going to be a little bit nerdy for a moment, so please, I apologize, because these are terms that I know Tim knows, but I think many people, I don't even know, Jonathan, if you've been exposed to this, but there's these bacteria that we call anaerobes. Anaerobes means that they don't breathe

oxygen. They can't survive in an environment where there's oxygen. But our body is actually filled with these types of bacteria, and clindamycin is the antibiotic that you would use to destroy anaerobic bacteria. Now here's the problem. The vast majority of the microbes in our gut are anaerobes. So when we're trying to protect you from this one skin bacteria, we are simultaneously going to have this additional damage that takes place with the destruction of anaerobic bacteria with the recognition that our gut microbes are mostly anaerobic bacteria. So this becomes our gut microbes are mostly anaerobic bacteria. So this becomes very relevant because the reason why I have, as a medical doctor,

a knee-jerk reaction to this antibiotic that I don't like, it makes me cringe, is because this, if you were to ask me, Dr. B, what is the antibiotic that increases our risk of a gut infection called C. diff, Clostridioides difficile. This is a nasty infection. I'm happy to unpack that in more detail, but if you were to ask me, what is the one antibiotic, give me one name that's going to increase my risk, it's clindamycin. It's the antibiotic that you were prescribed, John. It just often shows that the doctor that was treating you had a very short term view of what he wanted to do, right? He wanted to get you out of there, make sure that you weren't getting an infection. He probably knew he didn't have to see you again, just made sure that you weren't going to die or get an infection. He didn't really think about all the other things that might happen months down the

line because that wasn't going to be his problem. And that's generally the problem of short-term thinking within medicine and why he actually chose a drug that, as Will says, is designed to clear out your gut of anaerobic bacteria. It's often used in that way for people who want to reboot the gut in a way. It's a bit of a blockbuster. Pretty heavy duty. When you told me, I was pretty shocked. Clindamycin, wow, that's usually last resort. That is something that, oh, we know he's resistant to this. This is a life-threatening illness. I've got a couple of squashed toes, and I need to make sure that this one bacteria doesn't grow on there, which before 1946, we didn't worry about. We just cleaned it and hoped for the best.

So it was a bit of a shock that they'd done this. Did you coax them into it, Jonathan? Did you say, oh, give me the most strong antibiotic you possibly can? You know, I'm keen on being a human guinea pig for science, both of you, so I thought it would make a much better podcast if I don't know that's really not what happened shows the synabotic that that perhaps you may want to share that's right so i told him that there was a suggestion that i might be allergic to penicillin um which was something that came about from 30 years ago and so he immediately said well you know i'm well, I don't think we should take any risk.

And this was, I understand, part of the reason. Could you explain for a minute, I think, because I don't understand this and I suspect many other people don't, if you can in a very simple way, how does an antibiotic work? And also how come I can just swallow it and it will suddenly kill bacteria in my toes as well as my gut? So it's sort of a bit magical. Yeah, well, antibiotics are these compounds that are produced by other microbes. So the first one came from an Aspergillus, which is part of the fungus family. And all the microbes themselves produce chemicals to keep their niche. They're fighting their way.

So basically what we've done in nature is taken what, by looking at various yeasts and fungi and other microbes, what chemicals they produce and do they have some power against other microbes. Then we've magnified it, used genetically modified yeast to produce tons and tons of this stuff that we then synthesize chemically. So we're using nature's defenses in really big numbers to attack these microbes we're unkeen on. But it's only recently we've started worrying about all the casualties, if you like, the bystanders that get wiped out at the same time.

Can you talk me through, like, let's say I'm swallowing this antibiotic, which you said comes from originally being made by, like, a yeast or something. Could you just talk me through what goes on inside my body as a result? So, yeah, so you've got this compound, which is in a capsule, and it goes beyond your stomach. So usually it's not destroyed in the stomach. It passes through to the small intestine, and some of that will be absorbed there

and gets into your bloodstream. And so this is where most things get absorbed in the body, end up in your blood. So you'll start to get levels of that in the blood. And so if you had a blood-borne infection, so-called septicemia, it would start to uh help there and then some of it is also staying inside your gut and goes down to the lower intestine where that chemical will start interacting with your gut microbe community and killing off the friendly guys and the ones the bit that's gone into the blood is also getting close to the skin and so would fight off any staphylococcus which uh this is the one that for you they were trying to avoid that would get into your body through your skin through that wound so it's getting to your toe through this rather circuitous route and as a a byproduct, it's going everywhere.

And it sounds like does a lot of it end up in your gut as a result? Or is it sort of doesn't matter? It's just like it's everywhere and it's powerful enough that it has its impact. Well, we know the downstream effect that it's going to have on your gut. Because again, if we go back to what is the likelihood of you having diarrhea associated with an antibiotic, which of course the diarrhea, like basically what's happening what is the likelihood of you having diarrhea associated with an antibiotic, which of course the diarrhea, like basically what's happening here is we're disturbing the balance within our microbes to the point that they actually are no longer functioning the way that they're supposed to, right? So if we look at what are the antibiotics that are putting us at

the highest risk of developing antibiotic associated diarrhea, this is right at the top of the list. And then if we look at what happens where someone develops this C. diff infection that we've been describing, basically what's happening, Jonathan, is this C. diff is commonly associated with taking antibiotics. Basically, the good microbes that currently reside in your gut are protecting you from this C. diff. The C. diff may be there, but it's not functional or capable of doing anything. But when you take out the good guys, then what gets left behind is this bad guy. And the bad guy, he can now take over and dominate

within that space to the point of actually causing a cold infection that can be life-threatening for people. In the last years, so we're not talking about a trivial gut infection. This C. diff becomes recurrent C. diff and normal antibiotics don't get rid of it. So every time you give an antibiotic, it gets worse. So it's actually caused by antibiotics. The first usual old-fashioned treatment was more antibiotics and they only worked in about 20% of cases and it made it worse and worse. And people's lives, it was often fatal. I was, as you can imagine, sitting here feeling a bit paranoid. Thankfully, Will didn't give me all of this level of fear, but I was feeling a little bit paranoid about it.

And in part, that was because I'd also had this fantastic experience over the previous four years with Zoe of steadily improving my microbiome, which, you know, I was in the unusual situation where I'd had a whole series of full shotgun sequence microbiome tests over the previous four years. And so we actually have some data, which I'd love to share and then get you to help to explain a bit more. So I knew that when I'd done the very first test we did as part of our first ZOE PREDICT studies, my ZOE health score was about 50 out of 100, which put me sort of like in the middle of the population. So already much better than it would have been, I think a decade earlier, Will, when you were talking about sort of the real digestive health issues I was having,

but still sort of middle. And by the time I actually happened to have it tested literally four weeks before I broke my toes, and my score had gone all the way to 78 out of 100. So I was basically sort of in the top 20%. So it's sort of been getting steadily, steadily better, which I was really pleased about and feeling really good. And so I thought, well, one thing I'm definitely going to do

is I'm going to start retesting very frequently and see what happens. And I was nervous that after all of this hard work, it was going to be smashed away. So I think you've talked a little bit about the immediate concerns about what might happen. Before I maybe share what did happen over the next week, would you both just maybe share with me, what did you tell me to do at that point and why? My concern was you have this IBS history, you have a history of diarrhea, there's the family history with your grandmother C. diff infection. I was worried about you potentially developing this infection C. diff because of the fact that you're on the antibiotic that is so well known with this happening. So my recommendation to you was that you take a

very specific probiotic at a very specific dose. And that was Saccharomyces boulardii at 500 milligrams once a day. And the thought process there was to protect you from developing diarrhea and sedative inflection. My advice, I think I asked you, do you get bad problems after taking antibiotics? We talked about your penicillin problem. I said, it's likely to be complete nonsense. The doctor should have just ignored that and given you, you know, the more standard, less super strong antibiotic. A vast amount of people who think they have a personality don't when they're tested.

I think that's an important lesson. As we're running out of antibiotics, people don't exclude 80% of them. And the second thing is that you didn't get diarrhea after taking antibiotics. So I said, well, because you also asked, do I take a probiotic? And the evidence shows that probiotics do prevent post-antibiotic diarrhea in randomized controlled trials. There's quite a few of them. If you take them at the same time, they will reduce it. But I didn't recommend probiotics for you because of this one Israeli study of only eight people, but really thoroughly done and with mouse models and intensity that showed that probiotics in many people, if given at the same time, can actually make the recovery

slower. The reason we don't totally understand is that by having a sort of powerful induction of some extra new microbes, it in a way stops your old community getting back together again. And I didn't want to have that. And because there aren't any randomized controlled trials of people taking antibiotics to improve their gut microbes, I was saying at the moment, the current evidence suggests you're better off not taking commercial probiotics, but just taking fermented foods. And so I said to you, take as many fermented foods as you possibly can, a whole variety of them, and hopefully that will do the trick. Hi, I'm Zoe's US Medical Director, Dr. Will Bolsowitz, and I'm excited to tell you about

a free resource that's going to kickstart your journey to better gut health. If you're a regular listener, you probably already know how a healthy gut microbiome is important for digestion, immune support, and mental well-being, and that a high-fiber diet is a great way to improve your gut health. But where to start? And what exactly does a high fiber shopping list look like? With 95% of US adults deficient in fiber, clearly this is not common knowledge. Zoe's Gut Guide has the answers. To get yours for free, simply go to zoe.com slash gut guide and start feeling the benefits of a healthier gut today so i was really struck by this is like i'm really lucky right i've got two of these world experts

um uh available i thought you were both going to suggest me to take this really broad mix of probiotics and in fact um neither of you did maybe we'll starting with explaining why did you basically suggest this one particular probiotic um and why not a broad thing and i think that's really interesting to um to understand yeah well and i think that first of all it's important to say that you know tim and i were looking at the exact same literature and the cell study from 2018 from the weizmann Institute is something that I was thinking about as well. It suggested that surprisingly to all of us, the use of probiotics may actually negatively affect the recovery of the gut. But on the flip side, a different, a different question

is risk associated with antibiotics in the short term. The risks of developing diarrhea, the risks of developing a C. diff infection. And these are different things. It's not the exact same thing that we're talking about here. Where do you put your priorities with this? Because you're either going to give a probiotic or you're not. In the vast majority of people, and we can unpack this further if we want to, in the vast majority of people, I don't actually give probiotics anymore after antibiotics. But in this particular case, with your particular history, and with the fact that this was this specific antibiotic, it tipped the scale for me to feel more comfortable with you actually being on this

specific probiotic. And the reason why I chose the one that I did with protection from C. diff, protection from antibiotic-associated diarrhea, the most evidence that exists is with the probiotic Saccharomyces boulardii, the one that I recommended. In fact, there are randomized controlled trials involving more than 100 people that convincingly show us that you can actually reduce the likelihood of developing antibiotic-associated diarrhea or C. diff infection by about 60% by taking this probiotic. To me, there's tremendous value in that. And to make sure I've got that, what you're saying is potentially if I had just been on

something lighter, you might have actually not even said that and only have sort of gone with what Tim was really talking about, which is the package of fermented foods. A hundred percent. That is a hundred percent true. And we don't know what would have happened. All we know is what did happen. And we're all just making the best, using the best available information to make these choices. So the only thing to add is to what Will's been saying is that the risks of antibiotic diarrhea and problems are much greater in young infants and the elderly. And so the threshold for using,

say, probiotics in those situations is much lower. So if you'd be much older or it'd been a young kid of yours, our advice would probably have been different as well. So if it had been my grandmother, you would have said not only that particular single probiotic, which we will, by the way, put in the show notes, but also a broader set of probiotics? No, I would use the probiotic that's evidence-based, that has the randomized control trials to clearly demonstrate that we can reduce. This is a very targeted approach. We have a specific goal. Just that one for you, Will, like that is a single probiotic.

Because more strains is not necessarily better. So that's really interesting. So ultimately what we want is we want to lean into where does the evidence exist that's the most profound and where we're confident. And when it comes to probiotics, I mean, look, like these probiotics, they're not pharmaceutical drugs. So they don't have the phase three clinical trials with thousands of people. So when we get a randomized controlled trial with over a hundred people, we celebrate that that's, and there's value that we find in that. So with that, I would still do this specific as the most powerful evidence for what we're

trying to accomplish with the probiotic is actually behind this single strain. It's a yeast actually, Jonathan, it's not a bacteria. You didn't say that it was, but just making that clear for the audience. So, and you know, with what Tim is saying, you know, in my mind, as I'm clinically processing this, I'm thinking about the antibiotic that you were prescribed, but I'm also thinking about the specific patient and what fits. And you know, what Tim's bringing up is people who are young, people who are old, people who have other medical problems, people who have inflammatory bowel disease, or people who have a history of a

C. diff infection, those are all like if you've had that infection in the past, those are higher risk people. And because they're higher risk, it makes it more valuable to actually give them that enhanced level of protection. So let me advance the story a little bit and sort of tell you where I was a week later. So the antibiotic is actually only five days. So it's almost like, I think as everyone knows who does it, it sort of happens incredibly fast. So it feels, I think, as a lay person, like, well, it can't have had much impact, right?

It's just a couple of days. It does this magic thing, it's gone. I was able to test my microbiome again. And actually I started to test it every week from this point because I thought it'd be really interesting to see what happens. So when I got my results, I was pretty shocked because actually this antibiotic had had a really big impact. So I had got my, my ZOE gut health score up to 78 on this first test, which was just

seven days after I had broken my toe, seven days after I'd started the antibiotics, that score had dropped to 40. So that was below where it was, you know, four years ago, like overnight. So that was like, wow, I've gone from like the top 20% to like the bottom 40% just by popping like 10 of these pills. Four years of hard work wiped out. Exactly. So that was, I was pretty shocked by, but on the other hand, I knew that, you know, there could be a, you know, you could have a knock and that sometimes say like maybe you get more of these bad bugs what was i think particularly shocking and i think also surprising i think even for you is we have this new um research study that's going on pushing to

really identifying the individual you know microbes individual bugs that are that are viewed as good and bad and like when you were at your peak. Exactly. And my peak, which was like, literally, we're now talking about, you know, six months ago, just before, like a few weeks before I broke my toe, which was significantly higher than the number I'd had four years ago. And I only had six of the bad bugs. So that was sort of the situation that I was in. And what had happened in one week is I'd gone from 38 good bugs to six good bugs.

This is like literally this antibiotic had wiped out 80% of these good bugs. So I have to admit, I was shocked. I shared this data with you guys. What did you think? I said, well, that's quite a big reaction but most people you know i would try and reassure you that actually this should improve there are a couple of studies where they've given volunteers antibiotics and every week they've followed their microbes and by eight weeks most people have recovered they've all gone down as you did in those uh first couple of weeks most people recovered by uh eight weeks but both of these

studies and i think uh between a dozen and uh 30 people so smallest studies but they've always been this other group so maybe a quarter of people have not got back to normal but i said okay chances are you'll be in that you'll be fine at eight weeks they're not dead completely you've just they've stopped replicating they've stopped having fun they've stopped eating and they've sort of gone into a little shell like this and they're hiding in your appendix and these little crevices uh you know and they've got nothing to eat and they're just hoping they can survive long enough to to come back up up again when you know and this is a story i was relying on as well i was like well i'm going to go and like double down on eating the best possible way and it's all going to jump back in in a couple of months now before

i sort of share i guess guess, where I am today, could we talk a little bit more about this fermented food? So if probiotics sort of, I've been taking this one pill, which I took for I think about a month or something like that, and then I was like full in on the fermented foods. Could we talk a bit about why fermented foods are so interesting? Fermented foods are basically probiotics, live microbes, but actually in food, as opposed to in a capsule or in some synthetic version. So these are things that have been, we've had them for thousands of years in our diets.

And we're talking about the live cultures, they're in yogurts, they're in cheese, they're in kefir, which is fermented milk. We're talking sauerkraut, which is fermented cabbage. We're talking kombucha, which is fermented tea, kimchi, miso, etc., etc., all these ferments. And compared to probiotics, they generally have lower doses, but most of them, apart from maybe cheese and yogurt, there's many more species, many more types, many more diversity of microbes than you'd find in a probiotic capsule. So the average yogurt has maybe three species

but once you get to keffirs and kimchis and kombuchas you can get anything between 20 and 40 different types of microbes, mainly bacteria but also some yeast. 20 to 40 versus two or three so So there's like enormously more different types. Exactly. So my way of thinking is that probiotics when you take a capsule, like, you know, Saccharomyces, it may be very individualized

whether it's going to work for you or not, depending on your community. Is it going to respond to that guy? Yes or no. And that sort of, we sort of see that in the results not every not you don't get a hundred percent response because you know some people just don't have the gut community that's going to be receptive to this new guy coming in and uh you know telling

them what to do uh whereas my view is that fermented foods give you a much broader uh choice so that you've got all these different microbes that are quite happy living together in the food, and collectively, they're going to have a better chance of having an effect on your gut and restoring it to health. And we know from other studies, randomized controlled trials of fermented food, that getting five or six little portions a day in a few weeks can actually reduce inflammation and boost your immune system. So there is now science behind these fermented foods. So that was my rationale for saying to you, get as many of these different ones you can,

go for diversity, because that way you get different bugs in your kefir as your your kimchi and your kombucha and hopefully some of them are going to work right i was just throwing the kitchen sink at your problem and saying well you know we don't know which ones are the best or not we don't really know yet how to personalize it for you yet hopefully zoe will sort that out in the future but we don't know that yet so that was was the thinking. And there are some studies showing that fermented foods do work in people with gut problems and diarrhea, et cetera. It's not as well documented as probiotics, but there is some data. So I immediately bulk ordered the kombucha and the kefir and the kimchi, Tim, that you recommended. And I was in London at the time. How do you figure out

whether this is going to be something that is going to be full of these live bacteria or actually like it has the stamp on it? And I know that sadly, there's actually, there's a lot of things out there that say, for example, kombucha on it, but don't really meet the criteria. Tim, how do you differentiate that? And then maybe just tell me, how did you advise me specifically what to use? The first thing is to look at the label very carefully.

And if it's got, so say you're taking kombuchas or water keffirs, which are generally fruit keffirs, which are sort of similar, you check there isn't huge amounts of sugar in it or large amounts of artificial sweeteners because we know artificial sweeteners have negative effect on the gut and gut microbes. So definitely don't want anything with that in it. And you also need to check that it hasn't been pasteurized. And it might be in tiny little letters that it's been pasteurized. So it may be perfectly done, but to give it a long shelf life, it's been just slightly pasteurized, which means slightly dead.

So the key thing is you've got to make sure it's alive. You've got to make sure it's alive. It's one of the things you said to me. There's a lot of ways that potentially stuff might... And you can tell it shouldn't have a shelf life of two years, for example. That would tell you it's definitely dead. Some of the kombuchas can have a shelf life of... and keffirs and things and kimchis for a couple of months.

Usually it's shorter than that, but that's the most you should ever get in. And on kombuchas, you should often see a little sediment at the bottom showing that it's actually forming something live. It's real. It hasn't just been so filtered and processed that there's nothing left. And it shouldn't have lots of fruit and other stuff added to it as well because that also is a sign that it's been ultra processed and isn't real and often if you open it it should have a fizz i think the one i said oh i know jonathan you like chuckling goat uh because it's really smelly and it's got a real fizz on it when

you open it so you really know it's live you know it's like and it's got a very pungent taste that's right so i had this experience you have to actually go and look at a video online for how to open it, because when you open it, it explodes so much that like a good chunk of it ends up sort of pouring around the side and you need to collect it so you don't lose it.

So again, my children thought I was mad, but also thought this was really funny. And it was definitely stronger than the average kefir. And I felt really good because it felt like it was definitely medicine. This was definitely taking this properly. And you also recommended, I think, kombucha, which again, you'd seen made. So you were like confident. That's right. I've been to the Momo factory in London. I'd seen what was done and they

nearly all got a little sediment in it. I know you're very skeptical of the kombuchas up to that point, but- I was all in on anything that was going to help with me. I was not worrying about my blood sugar at this point, let's say. This is like 100% focused on my gut. You can be conned very easily in this game. I think that's the message for people. You know, you can be taking the best intentions.

You're taking something that's pasteurized. It's got so many artificial ingredients in it. It's not useful. It's too sweet. You know, if you can't make it yourself, work really carefully and realize that if it's really cheap it's also unlikely to be the real thing because it has a shelf life of a year or so and they can mass produce it often say live active cultures or live probiotics and if it says that then that gives you confidence that that you know that has not

been pasteurized sometimes they'll actually list which specific microbes are present and what the doses may be. The show you're listening to right now that's providing you the latest evidence-based health and nutrition information from the world's top scientists, while making it takes a lot of time, we think it's well worth it, all in the name of improving your health. All we ask in return is this, send a link to this podcast to someone you think would benefit. And if you haven't already, click follow this podcast wherever you're listening right now. Okay, let's get back to the show. The other thing too to look for is not so much with kombucha, but more so when you're looking at fermented plant foods like a sauerkraut or a pickle. The sauerkraut that I grew up on was in a

can and the second ingredient was vinegar. And that is not actually fermented sauerkraut. When you make pickles or when you make sauerkraut, it may surprise some people, but what you want to look for in the store is that actually the ingredients are whatever the plant is plus water and salt. Water and salt is how you actually create fermentation. So, and again, I feel more confident when it says live active cultures or live probiotics on it. So I'd love to run forward just one month. What has happened at this point? And so the good news is that my number of good microbes have doubled at this point. Yeah. I think if we were to conceptualize where you started in the beginning, let's use the term eubiosis. Eubiosis is the term that we would give to a microbiome that's

imbalanced. And the good guys are outweighing the bad guys. It's a stable, healthy environment that is hard to shift. Yeah, it's quite resilient. But unfortunately, the fastest way to cause a shift in this microbiome is actually antibiotics. And antibiotics actually are medically inducing dysbiosis. Dysbiosis is the term that basically means a shift towards an unbalanced microbiome. There's more vulnerability. The microbiome is not able to do its job the way that it's supposed to. So now the problem is that when you reduce the good guys, Jonathan, you're creating a tremendous opportunity for the bad guys to take over where the good guys left space. And so they will actually flourish. That's quite depressing. Well, and that's, and that's to some degree, we expect

this sort of medically induced dysbiosis to occur after antibiotics. The part that we did not expect that we're seeing with you is that this isn't lingering. This is actually getting worse as you're doing serial tests. Now, a month out, your measure a month out is worse than it was after a week. And I certainly don't like that. I would have thought that we would be moving in the right direction by this point, not necessarily back, but at least moving in the right direction. a little bit. I've got one more good bug, so like a little bit better. But the final summary for where I'm standing today is this has been a really big shift. And Tim, in the way you describe it, my previous stable microbiome has been sort of smashed up and then this is sort of slowly progressing. And I guess the obvious question I have is beyond taking the fermented products,

is there anything else that one should think about if one's saying, well, you know what, I want to get to this much healthier microbiome. You know, maybe I have to accept this is going to take some time. What else can I or anybody listening do? Well, we know from a number of studies, very careful mouse studies, that increasing your fiber is really important because that will directly impact the good guys. And if you can get more of those good guys in,

they'll suppress themselves, the bad guys. And the bad guys are living off this inflammatory. They like inflammation. They like a sort of slightly stressed gut and so the more you can put fiber and other good things in there and other plants so it goes back to the general rules for our gut health so which are you know getting lots of fiber getting it through plant diversity and reducing as much as possible ultra-processed foods, which are stimulating the bad guys. And I know you're already doing that, but for other people who might not know about this.

So I think they're the other things. You could try doing more time-restricted eating, give your gut a rest overnight, because we do know that microbes themselves have a sort of inbuilt laundry service where they do the cleaning at night if they're not having late night snacks and things. So they can come in and really tidy up your mucosal layer on your gut. So it's pristine in the morning. And then that seems to help gut health as well in your immune cells. So I think it's a combination of those gut things um and you've probably got some other tips as well i mean just to build off i think that's a great foundation and like the general

concept that you're proposing which i completely agree with is you want to feed the good guys and you want to starve the bad guys right so this is how we restore the balance feeding the good guys with the high fiber foods and then with the bad, we want to be cautious to the best of our ability in terms of the things that are feeding them, including refined carbohydrates like sugar, the artificial sweeteners, the ultra processed foods, high levels of saturated fat intake, alcohol consumption. I think we want to be careful with all of these things. And then the other thing beyond time restricted eating is we know that sleep is incredibly restorative to the microbiome. So getting a good night's rest as much as possible, spending time with exercise, spending time outdoors. These are some of the strategies

that can all help. This is my one individual story. And if people are listening to this, like, how should they think about taking antibiotics in general? Does this mean you should never take antibiotics? How common is this? What would you be saying? I think that before we even go there, your experience is unique to you, but also there is evidence in the medical literature to say that there are people that this similar thing happens to.

So there was actually a study that Tim and I have been looking at together where they took a group of people, very nice study, and they found the vast majority of people, as Tim alluded to, they recover by eight weeks. But there was a small subset of people that they could not explain why this was. But these people, their gut took a harder hit and it basically started to resemble the gut of an ICU patient. I'm guessing that's not a good thing. That's not a good thing. So in the depths of dysbiosis, and then what they had to do is continue to look. So we have the data up to three months. Well, in this particular study,

these particular people, they didn't really start to get back to their baseline for about six months they did get back to that place so i think that's that's you know one of the points of encouragement but i think that the the takeaway here is that for some people it may take longer to make that recovery than others yeah and and there are some people that recover totally in two weeks so who just seem to have a microbiome that just bounces us off. And this is fairly trivial, you know, and no real sequelae. But, and this is where I think the exciting science is if we, you know, we at Zoe, for example, can collect enough data, in the future we can start personalizing this.

So, you know, you'd know that when you went to see your surgeon, you said, listen, I'm highly, you know, I'm highly likely to get a long-term reaction to these antibiotics. Give me something else or I'll take more of a risk or give me some topical cream to put on an antiseptic antibiotic cream on the outside rather than poisoning my gut. So I think in the future, we can see how hopefully we can pick whether you're a good responder, a medium responder, a bad responder, and offer much more tailored advice. But I think the other advice is, you know, there is epidemiology data showing that overuse of antibiotics does increase allergies and to some extent can cause weight gain, particularly in children.

And we know that in the US and the UK, we're overusing antibiotics probably about two to threefold from what we actually do need to use them for. And I wanted to ask a bit about that because you, I think, made clear that I had a particularly heavy antibiotic, right? So it sounds like this is much stronger than average. How would you think about, because I've heard you talk about this sort of repeated antibiotic usage versus single antibiotic usage, maybe it's something that is more, you know, not as strong as this. How would you, as people are thinking about this, like weighting the risk? And I think we often think about this, for example, if we're, you know, with our kids and things like that

as well as for ourselves. So I think, you know, Jonathan, from my perspective, when I think about these things as a medical doctor, you're thinking about benefits versus risks. And when a person has an infection

that requires antibiotics, or in some cases, like for example, in your situation, it's not to say that it was wrong to take antibiotics across the board some cases, like for example, in your situation, it's not to say that it was wrong to take antibiotics across the board. When the benefit is there, then we have to consider that. There is, and I don't think I'm being hyperbolic when I say this, the greatest invention in medicine in the modern times was the discovery of antibiotics. There's no specific thing beyond this that added

more years to our life expectancy. If you look at the top causes of death in 1900, they were all infections. Now they're not even close to being the top causes of death because we have these antibiotics, but we have to be thoughtful about their use. And so really what we're getting into here is, do you need these antibiotics are they really required what is what is the appropriate antibiotic how how broad spectrum do they have to be you know it's just be thoughtful if we could with our medical doctors and ask questions what happens if i don't take this antibiotic is this the right antibiotic for me how long do i need to take it and by asking those questions we're trying to really sort of minimize our exposure, yet get the benefits that we're looking for.

I have a personal story here because I've always suffered from sinusitis, which is a nasty, chronic infection of the sinuses, started by bacteria, and then it just becomes a long-term infection. And each time I got a cold, usually it would go to sinusitis. And probably for 20 years, every time my cold lasted more than a week, I would go on to antibiotics to try and clear the infection that were taken for two weeks. So you would have taken dozens and dozens of courses? Yeah, unlimited supply. I had big, big supplies at home.

And a value pack of antibiotics and pills, did you? Often, as doctors do, self-medicating and not doing necessarily the right stuff. And it was only when I really got into the gut microbiome about 12 years ago, that's when I stopped. But also the other reason I don't take them now when I get infections, I still get infections, is that if you look at the literature, often the difference between taking them and not taking them for something like that is about one day of symptoms. So yes, statistically they work in trials, but the difference between

taking them and not taking them might only be a day in symptoms. And so this is true for many, many conditions that do self-resolve. Not all, and as Will says, they're often a good reason to take antibiotics, but there's many like this where it's a bit touch and go. And anyone who now values their gut microbiome more than an extra day of respiratory or nasal symptoms, I think, needs to take note. And the good news is, having taken many more antibiotics than you in the last 10 years, I improved my gut health. I have a really good gut score. So I think if there's a bit of optimism there, it may not come back immediately,

but hopefully you can get up there in the high 80s and beat me on your studies. I think it's a brilliant story. So you're saying even with all of the antipodes you took, when you started this journey around the microbiome a dozen years ago, how have you managed to get to this great point? Well, I think the shift is it's hard for healthcare to move away from what they sort of accept as their standard. You know, the standard is to sort of liberally use the antibiotics and not to see this risk

because the research on the gut microbiome is so new that it really hasn't gotten into the mind of the medical doctor who's conventionally treating a person who has sinusitis or whatever the issue may be. They're not really thinking about that. And I feel this happens a lot with children. I'm particularly struck also in different, I remember I grew up in the States and my mother tells me about the amazing number of courses of antibiotics I had by the time I was like four years old. And even contrasting with my sister, who was born 10 years later in the UK, like many fewer.

It's 20 courses on average by the time a US kid has reached 18. 20 courses of antibiotics. On average. And so presumably if this is my one experience, even though this might be stronger, you can sort of see that even if each individual course wasn't as bad, if you do that like 20 times, you're knocking it down and you're not eating all the foods that get it back. It's not so surprising that we see, in fact, we see some, we see basically the worst microbiome scores in the US of anywhere we've tested, right?

Yeah. And I'm sure that is a major contributory factor, not only in that, but it's also in foods as well. And that's another source. As well as the antibody you take it's in many meats and other products uh as it's used in agriculture interesting to fatten animals up so that's why the interesting epidemiology says that taking too many antibiotics you know actually increase your weight there's lots of evidence from farmers that pay lots of money to give their chickens and things uh antibiotics in order to make them put on weight faster because you can feed them the exact same amount of feed that's the fascinating thing about this is that you can give them the same number of calories and end up with a

with a larger animal and of course at the end of the day when you're selling that animal it's the number of pounds it's the weight of the meat that you actually sell it at but you know there was a study done in 2014 published in the journal Nature Medicine where they put people on five days of a plant-based diet versus five days of an animal-based diet. And one of the big surprise findings is that on just five days of a completely animal-based diet, they actually saw antibiotic resistance develop in the gut. And that's not because of meat. That's because there's residues of antibiotics that are existing within the meat that was being served. And by the way, the study was done in the United States.

Extraordinary. Well, I think that's been a fascinating tour. I think the good news is that I've just done another test, so we'll have the results soon. But I feel very optimistic that those numbers are going to be continuing to track up. And I think Tim's story is really exciting. So we will definitely share my upward trajectory. I'm determined to beat Tim's score in the future, but I recognize it may take a little while. Let me just try and summarize and as always try and please keep me honest. I think we started by saying, look, antibiotics are amazing.

They're probably the greatest life-saving invention in the last 100 years. So we shouldn't be scared of never using them, but we need to be thoughtful. And we'd really like to make sure, you know, particularly for doctors who are thinking about prescribing this, about understanding that there are these side effects. And also, I think as patients that you don't want to demand this if you don't need it because actually there are downsides as well as upsides. We explained that there's sort of, I guess, two concerns with taking the antibiotics. One is sort of the short-term situation where as you're actually taking the antibiotics, what might happen is real concern about getting sort of horrible infections like C. diff, having diarrhea, and that for people who are at risk,

and I think you said in particular, either sort of people who are really young, people who are old, or people who've had previous issues, which is where I fell into, then actually there is one particular probiotic yeast, not even a bacteria, whose name I'm going to mangle, even though I have bought it, Saccharomyces boulardii. And the good news is I didn't get any diarrhea. So as far as I'm concerned, Will's a genius and it worked perfectly. And we saw some traces of it in my first few microbiome tests. And then interestingly, it fell away. So again, it's one of these things that's sort of transient and doesn't live. Then we talked about like,

what do you need to do sort of longer term to deal with this? And that critically, there isn't like these magic probiotics, you know, even though there's shells and shells of them in the stores, you know, neither of you said take any of this. Actually, it's all about this fermented food.

And the fermented food is packing maybe 20 times more different varieties than just a simple yogurt. And even though that might sound less high-tech than getting these pills, actually, this is a much better solution to actually improve our health. And you talked about, you know, these magic things like kimchi and kombucha and kefir. I've been trying the lot. And then on top of that, I think what you said is like, take the things that will really support your gut health in the long term. So really thinking about lots of fiber, because that's actually what's going to support the good bugs over time. So

even if you don't fix this immediately, actually the right long-term diet, as Tim was talking about in his experience, will mean you'll be able to support more and more of these good bugs over time and sort of squeeze down these bad bugs. And then I think a couple of interesting additional ideas, like time-restricted eating, to really reduce the amount of time that you're eating so that you're having no food for 14 hours or 16 hours or something in a stretch is something else you can try. And then I think interesting things just like sleep and exercise, Will, you mentioned might also all contribute. So I think the summary of that is there's quite a lot of things that you can do and none of this takes

away from the fact that this antibiotic is like a huge sledgehammer. And so if you've got something really bad, it's going to be really effective, but you've got to recognize that this is not a sort of precision targeted pill. This is sort of having this big impact. Nuclear bomb. It's a nuclear bomb. And I guess we all know you don't want to set them off unless you really need to. Wonderful.

Well, I love doing this in person. Thank you. And I will keep everybody posted on the state of my guts. Good luck. Thank you, Tim and Will, for joining me on Zoe's Science and Nutrition today. If you want to understand how to support your gut microbiome with the best foods for your good bugs, whether you've recently taken antibiotics or not, then you may want to try Zoe's personalized

nutrition program. You can get 10% off by going to joinzoe.com slash podcast. As always, I'm your host, Jonathan Wolfe. Zoe Science and Nutrition is produced by Yellow Hewins Martin, Richard Willen, and Alex Jones. See you next time.