Antibiotics: The surprising truth about probiotics and what to do instead

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.

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Episode transcripts are available here.

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[00:00:00] Jonathan: Welcome to ZOE Science and Nutrition, where world-leading scientists explain how their research can improve your health.

I'm your host, Jonathan Wolf, founder and CEO of ZOE. Today we'll find out about the serious implications of antibiotics for our gut microbes. 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.

We'll also explore what the broader research tells us about the variable impacts of different types of antibiotics, how they affect your microbes in the short and the long term. And how we might return those good bugs to their former glory. Joining me to unpack this topic are two world leading gut experts, Dr. Will Bulsiewicz and Professor Tim Spector. Will is a board certified gastroenterologist with 14 years of experience and multiple awards as a clinician. He's also a New York Times bestselling author of Fiber Fueled And Zoe's US Medical Director, Tim Spector is one of the world's top 100 most cited scientists.

Professor of Genetic epidemiology at King's College and my scientific co-founder here at Zoe. 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? 

[00:01:39] Tim: Yep. Hit us.

[00:01:41] Jonathan: Alright. I'll maybe, starting with Will. Do antibiotics save lives?

[00:01:46] Will: Definitely. 

[00:01:47] Jonathan: Can antibiotics damage my gut microbiome? 

[00:01:51] Tim: Definitely. 

[00:01:53] Jonathan: If my gut micro microbiome does take a hit after taking antibiotics, can this damage be long lasting?

[00:02:00] Will: Unfortunately, yes. 

[00:02:03] Jonathan: Okay, Tim, will probiotics help my gut microbiome to recover after taking antibiotics?

[00:02:11] Tim: Unclear. 

[00:02:13] Jonathan: All right. We're definitely gonna get into that Last question. Are there specific foods that can help my gut microbiome recover? 

I believe so. 

[00:02:21] Will: Brilliant. 

[00:02:24] Jonathan: Before we begin, I have a favor to ask. 63% of people that watch this podcast haven't hit the subscribe button and 11% haven't hit the bell to turn notifications on.

We want this podcast to reach as many people as possible as we continue our mission to improve the health of millions. Doing us this small favor will really help. So if you've ever enjoyed this podcast, please hit the subscribe button and turn notifications on. Thank you. 

Alright, so Tim and Will, I wanna 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 just say it was a little bit like sort of 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 round and give me a hand? She wrapped me all up. We went off to a hospital because I'd actually not just broken it, but sort of smashed the whole thing up and opened. I ended up having to have a minor operation to like clean it all out and sew it up.

The doctor told me that the technical diagnosis was that I had smashed my toes to smithereens. Which, I dunno if that's an American diagnosis or only a British one, Will?, 

[00:03:53] Will: I think it translates in both countries pretty well. 

[00:03:56] Jonathan: So they did a fantastic job. They cleaned it all up. They sewed it all up.

And because it had been an operation I'd been in an operating theater they said you need to go on the course of antibiotics. Rather, luckily I have two of the world experts on the microbiome, in my phone. And I remember, 'cause I messaged both of you and Will because it was still sort of 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? 

[00:04:35] Will: Part of the context that was really relevant and important to me as a gastroenterologist was you shared that you have a history of irritable bowel syndrome and also that you've had issues with diarrhea in the past.

And so that sort of made me think this is a person with a gut that may be more vulnerable. 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.

[00:05:07] Jonathan: I'm pleased to say you didn't really say that exactly to me at that point, because obviously I was committed.

[00:05:12] Will: Yeah. Well, I don't wanna 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... 

[00:05:21] Jonathan: yeah. Unpack it for us now. 

[00:05:22] Will: 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.

[00:06:08] Jonathan: And can you explain what that means? 

[00:06:09] Will: Yes. So what that means is that it's not just something that will destroy Staph Phos, 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, and I'm gonna be a little bit nerdy for a moment, so please, I apologize 'cause if these are terms that I know Tim knows, but I think many people, I don't even know if 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. And 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 gonna have this shrapnel, 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 very relevant because the reason why I have a, 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, doctor B, what is the antibiotic that increases our risk of a gut infection called c diff -clostridium 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 jonathan 

[00:08:07] Tim: 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 making sure that, you know, you weren't gonna die or get an infection. He didn't really think about all the other things that might happen. Months down the line, 'cause that wasn't gonna 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 an aerobic bacteria is often used in that way for people who want to, you know, reboot the gut in a way. It's, it's a bit of a block, 

[00:08:48] Jonathan: pretty heavy duty.

[00:08:50] Tim: When you told me I was pretty shocked. Clindamycin? Wow. That's usually the last resort. Yeah. You know, that is something that, you know, oh, we know he's resistant to this. You know, this is a life-threatening illness. Not “I've got a couple of squash toes and I need to make sure you know that this one bacteria doesn't grow on that.” Which, you know, before 1946, we didn't worry about, we just cleaned it and hoped for the best. So it, this, it, it was a bit of a shock that they'd done this. You know, did you coax him into it? Jonathan, did you say, oh, gimme the most strong antibiotic you possibly can? 

[00:09:23] Jonathan: Well, 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, no, there's really not what happened, 

[00:09:31] Will: there was a reason. Like that, that perhaps you may want to share. 

[00:09:35] Jonathan: That's right. So I told him that there was a suggestion that I might be allergic to penicillin which was something that came about from 30 years ago.

And so he immediately said, well, you know, I don't think we can, should take any risk. And this was I understand part of the reason. Could you explain for a minute? I think, 'cause I don't understand this and I suspect many other people don't like, If you can in a very simple way, like how does an antibiotic work?

And also how comes I can just swallow it and it will suddenly, like, kill bacteria in my toes as well as my, my gut. So it's sort of a bit magical. 

[00:10:11] Tim: 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 it used 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, you know, 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 sort of genetically modified yeast to produce tons and tons of this stuff. That we then sort of synthesize chemically. So we're using nature's defenses in really big numbers to attack these microbes. We're un keen 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. 

[00:11:09] Jonathan: And can you talk me through, like, let's say I'm swallowing the, the, 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? 

[00:11:20] Tim: So, yeah, so you're, you've got this compound, which is in a capsule and it goes beyond your stomach. So usually it's not destroyed in, in, in the stomach. It passes through to the small intestine and some of that will be absorbed there and gets into your bloodstream. And this is where a lot of the 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 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 is the, is the, the one that for you that we're 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, 

[00:12:33] Jonathan: and as a byproduct, it's going everywhere and it sounds like, does a lot of it end up in, 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 everywhere? 

[00:12:46] Will: Well, we be, we know that the downstream effect that it's gonna 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 here is we're, 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, 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, but basically what's happening, Jonathan is, and this c diff is, 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 colon infection. That can be life-threatening for people.

[00:13:49] Tim: It can 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, 'cause it gets worse. So it's actually caused by antibiotics. The first usual old fashioned treatment was more antibiotics.

Yep. And they only worked in about 20% of cases and it made worse and worse than people's lives. You know, it was often fatal. You were going the toilet so much, you just couldn't you were losing so much fluids. 

[00:14:18] Will: I had patients that had to have their colons removed because of this infection. I mean, this was a very serious.

[00:14:23] Jonathan: 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, um 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 like 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, I'd love to, to share and then get you to, to help to explain a bit a bit more. Um, so I knew that when I'd done the very first test we did as part of our first Zoe predict studies, my My ZOE gut health score was about 50 out of a hundred, which put me sort of like in the middle of the population.

It's already much better than it would've been, I think a decade earlier. Will, when you were talking about sort of the the real digestive health issues that 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 got all the way to 78 out of a hundred.

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. I'm feeling really good. Um, and so I thought, well, one thing I'm definitely gonna do is I'm gonna start retesting very frequently and see what happens. And I was nervous that after like all of this hard work, it was going to be smashed away.

So I think you've talked a little bit about the like the immediate concerns about what might happen before I maybe share like what, what did happen over the next week. Would you both just maybe share with me, like what did you tell me to do at that point and why? 

[00:16:00] Will: My concern was you're, you have this IBS  history, you have a history of diarrhea.

You, 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 sacrimisis boulardii and at 500 milligrams once a day.

Um, and the thought process there was to protect you from developing diarrhea and. 

[00:16:39] Tim: And my advice, I think I asked you, do you get bad problems after taking antibiotics? And we, we talked about your penicillin problem. I said, it's likely to be complete nonsense. You did. The doctor should have just ignored that and given you, you know, the more standard less super strong antibiotic, vast amount of people who think they have a person allergy don't when they're tested.

And I think that's important, important lesson that, you know, As we're running out of antibiotics, people don't exclude 80% of them. Um, and the second thing I said, you didn't get diarrhea after antibiotics, so I said, well, 'cause I, 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, if you take them. At the same time, they'll 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 that showed that probiotics in, 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 are better off not taking commercial probiotics, but just taking fermented foods. And so I, 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. 

[00:18:41] Jonathan: So I was really struck by this is like, I'm really lucky, right? I've got two of these world experts available.

I thought you were both going to suggest to me to take this really broad mix of probiotics and in fact neither of you did . Maybe Will  starting with explaining why did you basically suggest this one particular probiotic? Yeah, and why not a broad thing. And I think that's really interesting to understand.

[00:19:05] Will: Yeah. Well, and I think that, first of all, it's important to say that, 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 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?

'cause 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, randomized controlled trials involving more than a hundred 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 that there's tremendous value in that. 

[00:20:38] Jonathan: And to make sure I've got that. What you're saying is I potentially, if I had just been on, something lighter you might've 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 

[00:20:50] Will: A hundred percent. That is a hundred percent true, and we don't know what would've 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. 

[00:21:01] Tim: So the only thing to add is to what Will's been saying is that there's 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 been much older or it'd been, you know, a young kid of yours our advice would probably been different as well. 

[00:21:25] Jonathan: So if it'd been my grandmother, you would've said not only that particular single probiotic, which we will, by the way put in the show notes, but also like a broader set of probiotics.

[00:21:34] Will: No, I would use the probiotic that's evidence-based, that has the randomized control trials to clearly demonstrate that we can reduce, like this is a very targeted approach. 

[00:21:41] Jonathan: So you would've stuck to still just that one for you will, like that is the single probiotic. 

[00:21:45] Will: 'cause more strains is not necessarily better.

[00:21:47] Jonathan: So that's really interesting. 

[00:21:48] Will: So ultimately what we want is we wanna lean into where's, 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 and there's value that we find in that. So with that, I would still do this specific 'cause. 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 with what Tim is saying, 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 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.

[00:22:56] Jonathan: So let me advance the story a little bit and sort of tell you you know, where I was a week later. So the antibiotic is actually only five days. So I think as everyone knows who does it, it sort of happens incredibly fast. So it feels, I think as a lay person, 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 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 had 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.

[00:23:49] Tim: Four years of hard work wiped out. 

[00:23:51] Jonathan: Exactly. So that, I was pretty shocked by, but on the other hand I knew that there could be a ,you know, you could have a knock and that sometimes they'd 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 research study that's going on pushing to really identifying the individual, microbes, individual bugs that are viewed as good and bad.

 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. 

So this is like literally this antibiotic had wiped out 80% of these good bugs. So I have to admit, like I was shocked. I shared this data with you guys. What did you think? 

[00:25:10] Tim: I said, well, that's quite a big reaction, but most people, 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 first couple of weeks. Most people recover by eight weeks. But both of these studies and I think between a dozen and 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 you know, and they've got nothing to eat and they're just hoping they can survive long enough to come back up again. 

[00:26:16] Jonathan: And this is a story I was relying on as well, I was like, well, I'm gonna go and like, double down on eating the best possible way and it's all gonna jump back in a couple of months.

Now, before I sort of share, I 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? 

[00:26:49] Tim: 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 are talking kombucha, which is fermented tea kimchi, miso et cetera, et cetera. All these ferments and compared to probiotics, they generally have lower doses, but most of 'em, apart from maybe cheese and yogurt, have, 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 in, once you get to kefirs and kimchi and kombuchas, You can get anything between 20 and 40 different types of microbe, mainly bacteria, but also some yeast. 

[00:27:53] Jonathan: So 20 to 40 versus two or three. So there's like enormously more different types of bacteria in there.

[00:27:58] Tim: Exactly. So my way of thinking is that probiotics, muta capsule, like, you know, sce, it may be very individualized. Whether it's gonna work for you or not, depending on your community. Is it gonna 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 gonna be receptive to this new guy coming in and you know, telling 'em what to do.

Whereas my view is that fermented foods give you a much broader choice so that you've got all these different microbes that are quite happy living together in the food, and collectively they're gonna 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. 'cause that way you get different bugs in your kefir as your, your kimchi and your kombucha. And hopefully some of 'em are gonna work.

Right. I was just throwing the kitchen sink at your problem and saying, well, you know, I, 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 the thinking.

And there have been some studies showing that fermented foods do work in people with gut problems and, and diarrhea, et cetera. It's not as well documented as probiotics, but there's some data. 

[00:29:47] Jonathan: 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 gonna be something that is gonna 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, you know, how did you advise me specifically what to use? 

[00:30:18] Tim: So the first thing is to look at the label very carefully and if it's got so say you're taking kombucha or, or water kefirs, which are generally, so fruit kefirs which are sort of similar.

You check there isn't huge amounts of sugar in it. Or large amounts of artificial sweeteners. 'cause we know artificial sweeteners have negative effect on the gut and the gut microbes. So you 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, you know, that it's been pasteurized, so it may be perfectly done. But to give it a long shelf life, it's, it's been just slightly pasteurized, which means slightly dead. And 

[00:30:58] Jonathan: so, so the key thing is like, you've gotta make sure it's alive. You've gotta make sure it's one of the things you said to me, it's like there's a lot of ways that potentially stuff from my... 

[00:31:04] Tim: 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 kefir 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. 'cause that also is a sign that's been ultra processed. And isn't real. And often if you open it it should fizz. I think the one I said, oh, I know Jonathan, you like chuckling goat.

'cause it's really smelly. And it's got a real fizz on it. When you open, it's so really know's live, you know, it's like, and it's got a very pungent 

[00:31:58] Jonathan: taste. So that's right. So I have 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. Um, and it was definitely stronger than the average kefir and I felt really good 'cause it felt like it was definitely medicine. This was definitely taking this properly and you also recommended, I think a kombucha, which again, you'd seen made.

So you were like confident that... 

[00:32:29] Tim: that's right, I'd been to theanti Momo factory in London. I'd seen what was done and it nearly all got a little sediment in it. I knew you were very skeptical of a kombuchas up to that point, but 

[00:32:38] Jonathan: I was, I was all in on anything that was gonna help with the, I was not worrying about my blood sugar at this point. Let's say this was like a hundred percent focus on my gut. 

[00:32:45] Tim: You can be conned very easily in this game. I think that's the message for people. You know, you could 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 really carefully and realize that if it's really cheap, it's also unlikely to be the real thing. 'cause it has a shelf life of a year or so. And they can mass produce it. 

[00:33:09] Will: So it'll often say, live active cultures or live probiotics. And if it says that, then that gives you confidence that, that, you know, it has not been pasteurized.

Sometimes they'll actually list which specific microbes are present and what the doses may be. 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. I mean, the sauerkraut that I grew up on was in a can.

And it was 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 culture or live profile.

[00:34:00] Jonathan: 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.

[00:34:54] Will: Yeah I think if we were to conceptualize like where you started in the beginning let's use the term ubi eubiosis is the term that we would give to a microbiome. That's an imbalance.

And the good guys are outweighing the bad guys. That's what you had.[00:35:13] Tim: It's a stable, healthy environment that is hard to shift. 

[00:35:17] Will: Yeah, it's, 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, 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're, that we did not expect that we're seeing with you is that this is lingering, this is actually getting worse as you're doing serial tests.

Now, a month out, your, your, your measure a month out is worse than it was after a week. And I certainly don't like that. I would've thought that we would be moving in the right direction by this point. Not necessarily back, but at least moving in the right direction. 

[00:36:24] Jonathan: So to bring it up to, to date, which is at this point sort of three months afterwards, my score has recovered a little bit.

There's no more increase in the bad bugs. In fact, they're starting to trend down a little bit. I've got one more good bug, so like a little bit better. But the final summary, you know, for where I'm standing today is this has been a like a really big shift and you know, Tim, and the way you describe, it's like my previous stable microbiome has been sort of smashed up.

And then this is slowly progressing and I think 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 gonna take some time.

What else can I or anybody listening do? 

[00:37:11] Tim: Well, we know from a number of studies including very careful mouse studies that increasing your fiber is really important 'cause 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, in other plants, so it goes back to the general rules for our gut health, which are getting lots of fiber, getting it through plant diversity and reducing as much as possible ultra processed foods, which are, you know, which are stimulating the, the bad guys.

And I, I know, 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 the microbes themselves have a sort of inbuilt laundry service where they do the cleaning at night if they're having late night snacks and things so they can come in and really tidy up your mucosal layer on your gut so it, 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, those gut things. And you've probably got some other tips as well. 

[00:38:35] Will: 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 wanna feed the good guys and you wanna 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 guys, we wanna be cautious to the best of our ability in terms of the things that are feeding them when including refined carbohydrates like sugar, the artificial sweeteners, the ultra processed foods, high levels of saturated fat intake alcohol consumption.

We, I think we wanna be careful with all of these things. And then that 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.

[00:39:21] Jonathan: 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? Like how common is this? You know, what would you be saying? 

[00:39:34] Will: Well, 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 that the vast majority of people, as Tim alluded to, they recovered 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 I C U patient. 

[00:40:12] Jonathan: I'm guessing that's not a good thing. 

[00:40:13] Will: That's not a good thing. So in the depths of dysbiosis and then what you, they had to do is continue to look. So, you know, 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, 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.

[00:40:38] Tim: Yeah. 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 they have no, no real secretly, but, and this is where I think the exciting science is if 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 your surgeon, you said, listen, I'm highly likely to get a long-term reaction to these antibiotics, give me something else, or you know, I'll take more of a risk or gimme 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 are a good responder, a medium responder, a bad responder. And offer much more tailored advice. But I think the other, the other advice is there is epidemiology data showing that overuse of antibiotics does in increase allergies.

And to some extent, weight 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 'em for. 

[00:41:56] Jonathan: And I wanted to ask a bit about that. 'cause 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 'cause I've, and 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 with our kids and things like that as well as for ourselves. 

[00:42:22] Will: So I think 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.

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 they, we, 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 the appropriate antibiotic? 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 minimize our exposure, yet get the benefits that we're looking for.

[00:43:41] Tim: 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 onto antibiotics to try and clear the infection that were taken for two weeks.

[00:44:10] Jonathan: So you would've taken dozens and dozens of courses? 

[00:44:13] Tim: Yeah. Unlimited supply had big supplies at home and obviously, 

[00:44:17] Jonathan: and a value, a value pack of antibiotics in the house. 

[00:44:19] Tim: Often, you know, 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 I 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, It's about one day of symptoms. So yes, statistically they work in trials, but the difference between taking 'em 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 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.

So, and the good news is that having taken many more antibiotics than you in the last 10 years by improving my gut health, you know, 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 you know, I'm, hopefully you can. Get up there in the high eighties and, and beat me on.

[00:45:33] Jonathan: I think it's a brilliant, brilliant story. So you're saying like even with all of the antibiotics you took when you started this journey around the microbiome, you know, like a dozen years ago actually, you've managed to get to this to this great point. 

[00:45:43] Will: Well, and 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 'cause 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, 

[00:46:08] Jonathan: and I feel this happens a lot with children. I, and I'm particularly struck also in different, I remember, like 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...

[00:46:26] Tim: there's 20 courses on average by the time a US kid has reached 18. 

[00:46:31] Jonathan: 20 courses of antibiotics. Oh wow. 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 of, we see basically the worst microbiome scores in the US of anywhere we've, we've tested. Right? 

[00:46:53] Tim: Yeah. And I'm sure that is a major contributory factor. Not only. In that, but it's also in foods as well. And you know, that's another source as well as the antibodies you take.

It's in many meats and, and other products as it's used in agriculture. Interesting. To fatten animals up. Yeah, so that's why the interesting epidemiology shows 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

[00:47:22] Jonathan: antibiotics in order to make them put on weight.

Faster factor. 'cause you 

[00:47:24] Will: can feed them the exact same amount of feed. That's the fascinating thing about this, is that you, 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 of 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. 

[00:48:06] Jonathan: I was gonna say, and I imagine that's worse in the US than elsewhere because we know that the restrictions are.... 

[00:48:10] Will: some, 80% of the antibiotics in the United States are not given to humans.

[00:48:13] Jonathan: Extraordinary. Well, look, I think that it'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 gonna be continuing to track up. And I think, you know, 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. Lemme 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 a hundred years.

So we shouldn't be scared of ever using them, but we need to be thoughtful and we'd really like to make sure, 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 wanna demand this if you don't need it because actually there, you know, there are downsides as well as upsides.

 We explained that there's I guess, two concerns with taking the antibiotics. One is sort of this short term situation where as you're actually ha taking the antibiotics, what might might happen? This real concern about getting horrible infections like c diff having diarrhea. Um, 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. Um, 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, and doesn't live.

Then we talked about like, what do you need to do sort of longer term to, to deal with this and that critically. Pro, 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, think in these. 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, 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 gonna support the good bugs over time. So even if you don't fix this immediately, actually the right long-term diet.

Which Tim is 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 these bad bugs. And then I think a couple of interesting additional ideas. So like time restricted eating to like really reduce the amount of time that you are eating so that you are having no food for 14 hours or, or 16 hours or something in a stretch.

It's something else you can try. And then I think interestingly 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, you know, if you've got something really bad, it's gonna be really effective. But you've gotta recognize that this is not a sort of precision targeted pill. This is sort of having this big impact 

[00:51:37] Tim: Nuclear bomb. 

[00:51:37] Jonathan: It's a nuclear bomb. And I guess we all know you don't want to set them off unless you really need to.

[00:51:42] Tim: Exactly. 

[00:51:42] Jonathan: Okay. Wonderful. Well, look, I love doing this in person. Thank you. And we will, 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 with 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 As always, I'm your host, Jonathan Wolf. ZOE Science and Nutrition is produced by Yella Hewings-Martin, Richard Willan, and Alex Jones. See you next time.