ZOE Science & Nutrition - 3 gut bacteria that protect your heart–and what to feed them | Prof. Tim Spector & Prof Nicola Segata

Episode Date: September 18, 2025

There's an unseen world inside you, teeming with trillions of tiny inhabitants. Just like any ecosystem, some bugs inside your gut microbiome are beneficial, while others wreak havoc, quietly disrupting your health. What if these disruptive "invasive species" are silently driving the rise of cardiometabolic diseases, the leading cause of illness and death in Western countries? This episode reveals groundbreaking new ZOE research, soon to be published in Nature, that maps this hidden world. We’re joined by Professor Nicola Segata, the study’s co-author and a pioneer of this new technology, alongside ZOE's scientific Co-Founder, Professor Tim Spector, one of the world's top 100 most-cited scientists. Together, they reveal the top-ranked gut bacteria – both good and bad – that influence your health. Discover three powerful "good bugs" and how feeding them can suppress the "bad," transforming your gut ecosystem and paving the way for better health and potential therapeutic breakthroughs. Learn actionable tips for boosting your beneficial bacteria, starving the detrimental ones, and why gut testing is forever changed. 🥑 Make smarter food choices. Become a member at zoe.com - 10% off with code PODCAST 🌱 Try our new plant based wholefood supplement - Daily 30+ *Naturally high in copper which contributes to normal energy yielding metabolism and the normal function of the immune system Follow ZOE on Instagram. Timecodes 00:00 Introduction  01:05 The most common misconception about gut health 04:04 Your gut bacteria are like mini pharmacists 08:12 Why your gut microbes are as unique as your DNA 14:23 How ZOE is revolutionising health with a new research model 19:39 Groundbreaking research that featured in Nature  22:21 The new, simpler way to measure your gut health 24:25 Meet newly discovered good bugs 28:06 The microbe that thrives when you eat nuts and seeds 32:40 Why only eating kale won't make you healthy 34:25 The 'ancient' gut bug discovered in mummies (and one of our scientists!) 36:37 The future of probiotics 39:17 The shocking truth about store-bought probiotics 42:17 What makes a 'bad' bug bad for your health? 43:45 Could your gut microbes be making you crave junk food? 46:29 The diet your bad bugs love the most 49:10 The future of personalised nutrition for your gut 52:22 How to 'pivot your ' to feed your good bugs 53:55 Is it okay to eat occasionally? 55:53 Tim Spector's simple 'fridge raid ferment'  📚Books by our ZOE Scientists The Food For Life Cookbook Every Body Should Know This by Dr Federica Amati Food For Life by Prof. Tim Spector Free resources from ZOE Live Healthier: Top 10 Tips From ZOE Science & Nutrition Gut Guide - For a Healthier Microbiome in Weeks  Mentioned in today's episode Gut microbiome species indicative of cardiometabolic health are modulated by diet in large and interventional cohorts of over 34,000 individuals, forthcoming in Nature, (2025) Gut microbiome species indicative of cardiometabolic health are modulated by diet in large and interventional cohorts of over 34,000 individuals, Published in Nature Microbiology (2025) [3] Research progress of gut microbiota and obesity caused by high-fat diet, Published in Fronteirs in Cellular and Infection Microbiology (2023) Have feedback or a topic you'd like us to cover? Let us know here.Episode transcripts are available here.

Welcome to Zoe, Science and Nutrition, where world-leading scientists explain how their research can improve your health. Deep inside your large intestine exists another world, teeming with life. Trillions of bacteria crawling around your gut form the complex ecosystem known as your gut microbiome. And just like in the world where you and I live, some inhabitants help their environment while others harm it. Some gut bacteria support the immune system, create anti-inflammatory compounds, and help maintain the gut lining. Others, meanwhile, are more like invasive species,

disrupting their ecosystem with nasty chemicals. If these disruptive bugs grow too numerous, they can significantly increase our risk of getting the most serious conditions, like heart disease and diabetes. So, is it possible to understand how our ecosystem is balanced, so we can start to tip the balance in our favor and stop these diseases before they start? Today, we reveal groundbreaking new research that dramatically advances our understanding of what bugs live in our gut. This research, a collaboration between

the University of Trento and Zoe, and recently published in the Science Journal Nature, has taken us much further to map out this hidden world, identify more of the bugs helping us, and more of those that are causing us harm so we can better nurture our microbiome with the right foods and improve our health. In today's episode, we're joined by Professor Nicholas Agata, co-author of Zoe's new study. His lab uses world-leading technology to map and analyse the trillions microbes living inside us. He's joined by another pioneer in microbiome research, Professor Tim Specter. Tim is one of the world's top 100 most cited scientists, professor of epidemiology at King's College London and my scientific co-founder at Zoe. Nicola, thank you so much for being here.

Thank you. It's a pleasure. And Tim, thank you also. Looking forward to it. So Nicola, we have a tradition here at Zoe where we always start with a quick fire round of questions from our listeners. We're very strict rules. You can say yes or no. or a one-sentence answer if you absolutely have to. Are you willing to give it a go? Let's try. Good. All right. Are diseases like heart disease and diabetes on the rise?

Yes, they are. Could some gut bacteria protect us from these diseases? Yes, some protect us, some actually can actually be against us on this, yes. And could the wrong balance of gut bacteria push us towards disease? Yes, absolutely. It's not only about single bacteria, but the community of them. And Tim, can we change our gut microbiome composition

in a matter of weeks? Absolutely. Can scientists now link individual bacteria to your likelihood of getting sick? We can now, yes. And lastly, what's the most common misconception about our gut health? It's probably that we think it's so complicated

we can never really understand it properly. and our research, certainly over the last year, has really changed that so that we can now really define what the healthy gut, an unhealthy gut looks like, and we can start to tease out the key players there like never before. It's really exciting. It's amazing, and I'm very excited to have you both here. Now, just before the show, our team did some research, and apparently around the world, heart disease, type 2 diabetes, and other cardiometabolic diseases are now the number one cause of illness and death. Now, your new research reveals that gut bacteria may play a big part in our level of risk for these diseases. Now, there's nothing we like more than to discuss

new science on this show, but it's even more exciting this week because these breakthroughs are actually a result of Zoe members who listen to this podcast and who have actually contributed to this research themselves. So I'd like to diet. in. But maybe just to set the scene, Tim, what are these cardiometabolic diseases and why are we seeing cases climb? Well, it's a group of disease that we used to think of as really being separate. So things like heart disease, stroke, high blood pressure, diabetes, obesity, central obesity, and resulting metabolic problems from them. And we now know that there's a common causality. There's pathways that are all causing increased risk of all of these diseases together

that are coming from an interaction between microbes and the immune system and producing inflammation, upsetting the way we handle glucose, upsetting the way we handle fats. And it's all coming together that these things interact in a way we weren't aware of just a few years ago. So it means that Just by changing something as simple as our gut microbiome, we can actually impact all of these diseases and reduce our risk of all of them by interfering in a way with these pathways and reducing inflammation and impacting our immune system. And Nicola, can you help us to understand what are gut bacteria and what do we know today about their role in diseases like the ones that Tim's talking about? Yeah, so gut bacteria are trillions of single microorganisms present in our. our gut, thousands of species, more or less, in each of us, and they are part of an ecosystem that are an interface between the food we eat, our environment, and our health.

So the diet that the food we eat is broken down by gut bacteria, that they are in terms producing molecules, small molecules that are then arriving in our blood and in our system, and so they are having an impact on us. I call them mini-pharmacies, is the way I describe. Yeah, mini-pharmacies, yes. In addition, they also interact with our cells, with our immune system. So they're directly touching and interacting with us. And so if you have the good bacteria that are able to produce good, little molecules

because metabolites is good, otherwise not. So it's like an amplifier of our diet. The good bugs are amplifying the good effect, the positive effect of an healthy diet, and vice versa, they can actually be detrimental for our health in another situation. So we need to push, increase our gut ecosystem to be an ally for us. So you want to improve, have more of these good pharmacies, and you want to have less of the bad ones, you know, doing the breaking bad type home chemistry

and producing these nasty chemicals. And is this real? Is there such a thing as like a good bug and a bad bug? It's not so much black and white. And also in our research, we see that there are bacteria that tends to be associated with better health and better diet. But we also need to consider that our gut microbes are very personalized to each of us. So it's only with big, big numbers that we can tell apart which tends to be good in which situation

from those that are likely not to be there. But as Tim was saying is also about the diversity of them, because the more we have, the more good function they can bring to us. There is no single bacteria that can make all the work that is supposed to be done. the gut. So some of them, bad ones, for example, may be quite harmless in small numbers, but when the conditions are bad, they're fed the wrong foods, they have an so-called inflammatory environment, maybe the acidity changes slightly, then they can grow to an extent that they produce chemicals that influence everything around them, and they become bad guys. There is

this transition, and so it's best to think of this as a bit of a war between the good guys and the bad guys. The more good guys you've got, the more you can squeeze out the bad guys so that it doesn't matter if they're around because they're in small numbers and they're just playing around and really any chemicals they produce are just so diluted, you don't really feel the consequences. But the real problems are when you lose your good bugs and suddenly the bad guys multiply and then you're really in trouble because you're producing all kinds of chemicals that attract even more unhealthy microbes and the whole thing starts to go downhill very fast. The three of us sitting here, will we all have roughly the same bugs inside our gut?

Not really. I think we have around 30, 40% of species in common. And at the level, when you get even below the species level, the subspecies level, it's probably even less than that. We're only sharing of 10 to 15%. So all of us have a unique set of some microbes that the others wouldn't have. And even if you took a thousand people, you'd find nearly everyone has something unique to them. So there's a broad pattern that might be similar, but the more fine detail you get, the harder it is to find things in common. Even in, as we discovered, Nicola and I, when we look to this, even in identical twins,

who have identical genes in every cell in their body, but their microbes, are really only slightly more similar than unrelated people. And probably they are more similar because they live together because we see that we are transmitting our gut microbes, you know, or our all our microbes. It's like pathogens. If we live together, we are going to share some of these subspecies, some of these specific strains or variants like we know for infectious diseases,

no? You're saying that between myself and Nicola and Tim, at least 60% of the bugs that I have are different. different from the bugs that each of you have? Well, another is yes. We talk often about DNA, right? I think everybody listening has become very familiar with that. How does our DNA compare?

Is that also about 40% the same, 60% different? No, we'd be over 99% similar in terms of our DNA. Over 99% in DNA? Yes, your human DNA really is very similar, and we're talking about tiny little differences between humans that get us very excited at the sort of human genetics level. But when you start comparing it to the diversity of the genes in our microbes, it's night and day.

I mean, you know, we're talking, as you said, the difference between less than 1% and these 70%. And this is a real insight because up to this point, we've been depended on genetics to say, okay, we're all really quite similar. 99.5% the same. therefore, you know, identical twins, et cetera, must be identical. But what this tells us is that huge amounts of our DNA that is actually producing chemicals and vitamins are very different between us.

So there is this huge personalised aspect, which really wasn't apparent 10 years ago. And I think this is a real breakthrough in science. So firstly, just all the bugs inside me are really different from the bugs inside everybody else. But also even when it seems like we might have the same bug, it's a bit like saying, well, we both have a dog, but you know, I might have an Alsatian and you might have a chihuahua, they're pretty different. And they behave quite differently, yes. Absolutely, yes.

That's right. Always worry for the chihuahua, right? And even if you had two chihuahuas, one would be aggressive and the other would be nice and docile. So having listened to all of this, is this just because people aren't eating a very healthy diet, Tim? So if someone is listening to this and saying, well, that's interesting, but I know I eat healthy. so therefore I will obviously have a healthy microbiome, a healthy set of bacteria inside my gut,

and therefore it's going to be protecting me from heart disease and these other things. So if someone out there is eating as healthily as they think they can for their gut, generally following, say, all my advice and Zoe's advice, on average they will have a healthier gut score, on average they will be living longer, et cetera, but they can't be sure they don't have the microbes that are maybe predisposing them to certain risks of disease or others they're lacking that could prevent them from having disease. And the only way to be sure about that is to do a gut microbiome test using this sophisticated genetics that Nicola has been working on. Nicola, is it only food that affects the makeup of my microbiome?

It's not only food. The microbiome is a complex system that is modified by a number of things, like food for sure, but your lifestyle, the activity you do, the interaction that you have, the sleep that you have and so on and so forth. But also, as we were saying before, the interaction. We have studies, for example, of babies at the daycare that they acquire from their peers at the daycare so much microbes that they are reprogramming completely their microbiome. And this is also in adults, two students that are starting to live together after two, three years, they share quite a bit of their microbiome. They didn't share before. So, yeah, there are a lot of effect on the microbiome. Also, you know, pollutants, the environment we live in. So tons of effects on the microbiome. Thank you for sharing this. I always think it's amazing hearing about this, like, sort of ecosystem inside me. And it's a bit like this coral reef inside you with all of these different species. It's not an ecosystem inside you. You are an ecosystem. You are part of the ecosystem. You are the coral reef. They just happen to be, you know, one part of it. You've got the human part. You've got the microbial part. And they're interacting. And the coral reef is the, you know, the human's shell, really. You wouldn't work without your microbes. So you are your microbes. I love it. I am the coral reef. I feel more elegant already.

But it also shows that because of this interaction with other. and how you acquire new microbes, you do need to pick your friends and partners very carefully. You really want to have the healthiest ones around you, not the most unhealthy ones. So it's good I'm spending so much time hanging around with you, Tim. Exactly. I should charge for my time, really. So I think the thing that it feels is really new is understanding more that these sets of bugs really can either keep us healthier or actually push us towards disease.

You mentioned already, Nicola, there are trillions of bacteria. That's a lot of bacteria. That's very complicated. And I think it's part of why Tim, you said, you know, historically, people haven't been able to sort of decode this and really understand what's going on. So I'm incredibly excited about this new study that I think is providing really unique insights into some of these most influential bugs. Nicola, could you tell us about what your research has been doing? Yes. So in our study, we look at 34,000 individuals for which we know their dietary habits, their microbiome and their cardiometabolic health.

And so we identify the microbes, we identify the food, we identify their potential risk for disease, and we correlate everything. And so at the end of the day, because of these big numbers that have not been done this scale so far, we can link which foods are pushing or favoring or decreasing which microbes. which microbes are associated with favorable or unfavorable cardiometabolic market. So we did this map of interaction and this ranking of which are the species, the bacteria, that are more or less associated with favorable diet and favorable cardiometabolic health. How did we get these samples, these 34,000 people in the first place? And why haven't we done this 10 years ago?

Up to now, most of the microbiome research has been done in universities or hospitals, hospitals where they've collected 50 or maybe 100 people with a disease and looked at 100 people who are controls and either been paid volunteers or part of a university grant or project. But what's different about this one is we've used Zoe data. So these are people who have had a gut test done by Zoe in order to get their own information. And at the same time, we've asked them to complete dietary questionnaires and questions about their health and their health risk. And this is what's unique about what we're doing is because we're using a more commercial model to do the science, which allows us to do it at 100, 1,000-fold the scale that you could do with the old-fashioned academic model.

And it's much faster and it's much more efficient. And we know that we need these big numbers, you know, tens of thousands, hundreds of thousands of individuals, and we've now collected samples on nearly a quarter of a million people that we will be analysing in the coming months. So you're saying that basically people who are getting their microbiome tested as customers of Zohy are actually able to participate in the scientific research? Absolutely. So everyone who gets ZOI test kit is asked if they want to take part in research as well.

And a vast majority of people are giving their approval for this, which means. means that we can use the data to publish papers and make this data publicly available. So it's a real overlap between the normal commercial model and the scientific academic model, which means that we can use the speed and agility of commercial companies to really move science forward at a much faster pace. And how much bigger is this than whatever has been previously published, Nicola? This is extremely exciting. I remember a couple of years ago, we were here talking about the first study with 1,000 individuals, which was the largest at that time.

So a couple of years ago, 1,000 individuals was the biggest. And can you remind us how big this is? This is 34,000, and we are already working on a much largest sample size, as a team was mentioning, 250,000 more or less. So in a year from now, probably we are here even more excited with this larger number. So it's important because we are not just doubling the number of individuals each year here. We are doing 10 times more. It means like a leap forward in the science we can do with these numbers.

I love how excited you both are about the idea of 34,000 poop samples. Yeah, they're not all in my room, but you know. And so what does this enable us to do, Tim? I think you're helping to explain a bit about why that's different to get at this scale. Because I think a lot of people listening might be like, why does it matter? Why wasn't a thousand people already enough? Well, we have to learn this through trial and error. That's how science generally works,

because to be a scientist, you've got to be an optimist, otherwise you wouldn't be in that job. So you always think that whatever experiment is going to give you those answers. And when it doesn't, there's lots of reasons why not. But I'm lucky that I went through the genetics revolution first, which preceded the microbiome one by 10 or 20 years. And I'm seeing exactly the same patterns. So in genetics, we got very excited when we could do the most basic genetic test on 100 people

and would publish papers on this showing that some gene area was related to a disease. It turned out that for 10 years we were publishing results that turned out not to be true, that were later completely shown to be false once you'd got 10 times the number. And this took a long time for people to realize that they needed these very big populations to do the job in order to tease out all the individual genes in the human genome and they're associated with disease. And that's sort of where we've been in the past, in the early days of the microbiome. Many of the studies that people relied on were based on,

too small a group of people to be actually useful. And so it's only now we're in this new phase where we know the results are robust and they're going to be replicated by others. And that's really one reason why we're putting this out there in the public because we want everyone to share in this new science, this new way of looking at the gut microbiome. It's not only about the size, no, it's also about the representation. So studies done in the past were done with a specific population, you know, London population around an hospital.

And this is not a representative. So what we were saying, that what we see and we put in the paper is what came out to be reproducible in UK, in the US, in different parts of, in different age categories. Yeah, age, sex, pre-postmenopause, different ethnicities, different diets, people with all kinds of conditions. So it's much more useful data than these very limited ones in very narrow studies, which we've been relying on in the past. So it is exciting, and it's certainly not the end.

This is really, I think, just the start of the new era. And you just mentioned paper. So this has just been published. I know that's important to scientists. Where has it been published? And what does that mean? Well, it's been published in Nature, which is the top journal in the world. And this gets scientists very excited because for us, it's like winning the Oscars.

And it's not hard to get a paper published. And the analogy would be like you can film yourself and put it on Instagram and get it into a minor journal. And there might be 100,000 minor journals. But is that film likely to win you an Oscar? No. And so that gives you an idea between an Instagram. Flick and winning the top award. So that's why we're so excited about this,

and that's why our peer scientists are excited about it, because not only is it showing us this link between foods and microbes in great detail for the first time, but it's also telling us a new way of looking at gut health. I love that, and I remember when I first started at Zoe eight years ago, I had no idea that there were all of these different scientific journals, that it was really important. And I have come to learn that this is really directly like your Oscar's analogy, right?

Because it's a sort of proves that the science is really high quality, right? It's very, very hard. It's reviewed by other people. Like, the bar is very high. My other scientists, yes. The work is checked by other scientists before allowed to be published in those journals. So how pleased are you feeling, Nicola? It's great.

You know, it has been a lot of work, a lot of discussion with all the other people involved, but also with the reviewers that, of course, ask question, and we answer the question, we strengthen the work, and it's great to see now public and everyone can read, can also expand on it. And we will, of course, have the link to the paper in the show notes, but for people who don't want to dig through the paper, and the paper is quite hard going, I have to admit, because I did look at it. Tim, could you summarize what the breakthrough from this paper is and what it tells us about impacting our health? Yeah, I think there are two major themes in this paper. The first

is that we've uncovered certain microbes that are associated with increased risk of disease and also are modified by diet and also the opposite. So they're good and bad bugs. So you've got 50 good bugs ranked and 50 bad bugs that we know are correlated with diet and disease. So this is a really good starting point. And we talk about some of those bugs in detail. And the other point is that we've shown that the ratio of the good to bad bugs in everybody, because we picked the hundred that are generally present in most people in the UK and the US,

is a much better correlation of gut health than anything we've had before. So this allows people to take a snapshot of their gut microbiome and say you have a moderately healthy gut microbiome, less healthy, poor, terrible, really good. And it also allows us better than ever before to really track it over time. So in the past, we haven't had a really good measure that works well in clinical trials. It's a bit like blood pressure. If we didn't know how to measure blood pressure, it'd be very hard to know what tablets we should be taking to prevent stroke. Now we've got this great new score and we're hoping that, you know, the rest of the world

will also adopt this so we can move forward and really get some amazing advances, new treatments, exciting, and everything else. For me, that's the really exciting part that we can do something that really advances the field dramatically. Now, I understand that within this, you've also discovered some brand new gut bugs that nobody knew about before. And I think today, Nicola, you're going to share three of these newly discovered gut bugs that could help to reduce our risk of diseases like heart disease.

Correct. So let's start with the bacterium that nobody else saw before. So you cannot grow it in a plate. Microbiologists never see them, saw them, you know, under the microscope or so. This guy, let me read it because I never remember the idea, but he's called SGB 15249. That's very catchy. It is currently called 15249. Exactly. We need to find a better name. But, you know, this is part of a family of bacteria called ruminococassia, which is not telling you much more, actually. But there are some good and some bad bugs in these. So these specific species in the family is the best one. It's the one that is the one that is the most one that is the best one. I think a lot of people listening and say, well, hang

on a minute, how can you have found it, but you also said nobody's ever found it? Could you help us to understand that? That is the power of shock and metagenomics and is the idea of reconstructing the puzzles of each genome, of each genetic content of each bacterium. Each bacteria has a different code, a different genetic code. We read that genetic code and if we find a code, a book, the genome, that no one else saw before and is different enough from everything else that is known to scientists, that is a new species. And this bag was found thousands of times in different individuals, so it cannot be just by chance that we messed up the puzzles. And this is a new species then. So it's like we found a totally new colour in a jigsaw puzzle that wasn't

there before. And I think that's a decent analogy. And Nicola's Timar really, you know, the best puzzle solvers at the moment in the world. That's amazing. So it's a bit like with, you know, people hunting dinosaurs and you find this like little bone of a dinosaur. And because you're an expert, you figure out there's this whole new species of dinosaur that no one has ever seen before and this is what it looks like. But you're doing this with sort of the DNA. So even that hasn't been grown outside, you actually have found the DNA of this bacteria over and over. And you've been able to see that it's linked to people being healthier because you just have so many samples to look at. Exactly. And you said, correctly said, analyzing this data is a lot

of computer science, is a lot of statistics, there's a lot of artificial intelligence, which is 90% of what we do, because it seems that we are looking at the Microsoft, we are not. We are analyzing DNA, which means just staying on the computer and analyzing big data like is done in other fields. That is the secret here. So as soon as I heard you explain that this was the top bug. I obviously went back and asked the team whether or not I have it. And I think as many people listening on this show will know, I broke my toes two years ago and I ended up having these very intense antibiotics. And it wiped out almost all the bacteria, good and bad, inside my gut. And since then, I've been testing very regularly. So I've tested about 18 times.

And sure enough, straight after the antibiotics, I didn't have this. In fact, I only had six, six of the 50 good bugs. And a year ago, I said, still didn't have this bug either, but it turns out that on my last two tests, I have had exactly this bug. Congratulations. So I'm excited. I still only have about 23 of the 50, which is still quite a bit less. I had 38 before I took the antibiotics, which was the result of quite a few years of it going up. But I do have this one, and now I feel much better about my score than I did yesterday. So thank you, Mr. 15249 for, you know, helping look after me. And I will bet you also have the third microbes in this ranking

because that is a micro that is also more changing when you improve your diet. So do you have the SGB 4964? Oh, I'm going to have to come back and I haven't got the list in front of me. They need some catchier names, Nicola, for me to remember. But I do know that there's a second one that you wanted to talk about today, that you're also really excited. Could you tell us about that? Yeah, the one I asked you, no, and it's called the nuts and seeds, a microbe because

is the microbe that is changing the most when you increase the amount of nuts and seeds that you're eating. Is after the bacterium that grows only with coffee is the second bacterium that is mostly impacted by the diet and is impacted specifically, we think, by nuts and seeds and maybe some particular nuts and seeds we still need to find out. Is that new to understand this link between individual foods and individual bacteria? Absolutely, yes. Before that, we'd just had groups. So we could see changes in, you know, thousands of microbes together as a group, but only because we've got to this number,

this scale of this project that we can now identify an individual microbial species that is strongly correlated with a particular food. So that's why we're making this link. This is why when we saw the coffee microbe, it was a one-to-one relationship. Here, we're also seeing, you know, this microbe, just like me, loves nuts and seeds. And it really doesn't need anything else to thrive. And that's what we're seeing. And it's just this level of detail that wasn't possible before. And this is so much more important than seeing thousands of them, that some of them going in one direction, some of them going in other direction, It doesn't allow you to have that same precision about the advice you can give people and the personalized advice.

And some people listening will be saying, why is there any particular link between the food that I eat and the bugs that I have inside my gut? Well, because the food is feeding also your bacteria. The bacteria are growing. They need food themselves. And specific components of the food are feeding specific bacteria. So fibers is an example that is very well, very well. studied different fibers, you know, are the food for different kinds of bacteria. We do think that things inside the nuts and seeds are the substrate, the food for these microbe. We still need to find which none, like the same with the bacterium that grows with coffee. We don't know whether it is caffeine, whether it is another component of coffee.

Also here, dachshund seeds are still complex foods. So we need to teach apart which are the components. But still, we know for sure that if you increase the amount of nuts and seeds, then this bacterium, on average, will grow. And this is a good thing. You've got to try and remember that any plant has hundreds of chemicals in it, and our microbes might be super-specialized. So of those 800 chemicals, they might only be interested in about 10 of them.

And they're the ones that really drive their production and their growth. But the other interesting finding is that there have been some researchers have worked out that of the total amount of food we eat, our microbes are perhaps consuming. between 5 and 10% of it, I used to get told, always leave some food on your plate for Mr. Goodmanos, you know, that was what my Jewish grandmother used to say, well, actually, you know, have an extra 5% for your microbes, and, you know, that's really important because, you know, you're not just eating for yourself. I think that's the other thing. And this specialization, it also means that we need to eat a lot of diverse food. So it's not

about healthy food, but a diversity of healthy food, because these different chemicals in each food are pushing, are improving different microbes. And so the more healthy chemicals you eat, the more good bugs you are probably pushing. And to make sure I've got it, what you're saying is, you know, you've discovered in this paper these sort of 50 good bugs that are supporting your health, they don't all just want the same food. So it's a bit like being in the zoo and like all the animals are very picky about the different things they want.

You might think, why can't they all just eat grass, but that's not how it works. And you're saying it's the same for these bugs. You need to be feeding them different sorts of food if you want to. have not just one or two. I guess the question I might have is, why wouldn't I just want to have lots and lots of your 15249 that's number one? Why wouldn't that be the best thing to do? Because it is buggy, is healthy, yes, but it's going to do one operation, one activity, and this is not enough for you. So you need a lot of activities by different bacteria, different short-chain fatty acids, different anti-inflammatory molecules and so on and so forth.

So it's much better to have a little bit of all these 50 or, you know, 70 good bags than having one of them or two of them that are most of what you have in the gut. Yeah, and that's why people who say only eat kale aren't as healthy as they think they might have been based on the old science. The old science was said, okay, they're getting enough fiber, it's all green, you know, they're getting all the nutrients they need, but they're not. And so it's the people with the diverse diets have the diverse microbes, and they get more of our top contenders, and they're the healthy ones. So coming back to my latest gut health results, I was feeling really smug that I had number one, but I only have 23 of the 50 good bugs. So what you're saying is if I can push that up to 30, 35, 40, then that's going to be even better in terms of supporting my health? Yes. Did you come back to the number you had before the antibiotics?

I haven't yet. I had 38 good bugs before the antibiotics. But when I started Zoe, I actually had about 20 good bucks. So I slowly increased. When I first met Tim, I had about 20. I got it up to 38. Then the antibodies wiped all that good work out in seven days, which is really depressing. But I think what is really exciting, I've been following this is, you know, I went all the way down to six good bugs straight after the antibiotics. It's been steadily going up. I've gone to 23. that's about double the number it was a year ago. But also interesting, I've been looking at the bad bugs, and I know we're going to come to that in a minute, so I'll save that. I would say I have just been looking at the results since now you've told me this other number is really good, and since I do eat a lot of nuts and seeds, it turns out that I do have this bug within my 23,

and you're saying that you sort of predicted that because you knew that I was going to be eating lots of nuts and seeds. Correct. You're confirming our science. I love it. I think you have one more newly discovered gut bug you want to. to tell us about. Yes. I can tell you a little bit more about that guy, because I can present it is this guy here.

It's called cutting bacteria. So Nicola, you're actually holding up a little stuffed animal. Do you want to describe what you've got in your hand? All right. Well, I've been passed it. So it's quite cute, isn't it, Tim? It's got little, like, hairy stuff off the top, two little eyes. I guess that's probably not real.

And it's made in sort of three segments. It's kind of a chain shape, and that's why it's called cutting bacterium, because in Latin chain is catany. We can show this because we saw this bug under the microscope. This is one exception because we saw it with what I told you metagenomics, but then we targeted it and we were able to grow it in vitro and then we are able to study. So this is not one of the 50 good bugs for a reason because it's very rare in our populations in the UK or in the US, but there are a lot of these microbes in what we call non-Westernized populations. So population, so population that are unable to have antibiotics, even when they need it.

They don't have high fat diet and stuff like that. And there's also the microbiome that was, you know, in our gut, 5,000 years ago in our population. Our ancestors, microbes, really. So we probably all had this bug originally. Usually they're good ones, aren't they? Exactly. We saw it in mummies.

Ancient mummies have this bacterium. And guess what? This was a first isolated from my gut microbiome. So I had very little amount, but they were still detectable in my same. myself and this was coming out of my gut. That's amazing. So basically you're saying we found this bacteria in like mummies that are thousands of years old. We find it now in people who are still living sort of non-Western lifestyles. But that anyone listening to this in the US or Australia is very unlikely to have it because of our modern diet and lifestyle. Exactly. So that's why it's

not in the top 50, but this is more long-term science, I would say, because we are trying to study this and try to study whether it's safe to think to reintroduce it in our populations and whether we can then feed them the right food to keep it in our population.

This is sort of a new generation of probiotic intervention potential in the future. This is very early stage. I just wanted to give you an example of where we can go with our science. We might be seeing this chain bacteria in our yogurt in 10 years time. Tim, can you just help us something? What is a probiotic? And, you know, we see them on the

supermarket shelves all the time. Are you telling me that they aren't like really good stuff, like catina bacterium? The probiotics we have in our shops are really the same that we've had for about 100 years. They really haven't changed much. Probotic just means a live microbe that's been shown to be good for your health. And the ones that we're allowed to sell are those that exist naturally in foods. So we've pretty much discovered all the ones we're ever going to find in food. And there are several thousand of them, but we tend to really use the same 10 or 20 over and over again. And what we're seeing here is that with these new discoveries, we can suddenly go to much more important, much more advantageous microbes.

And if we find they're safe to put into foods and into the human body, then that's going to be a massive advance. Because the probiotic field really hasn't changed much at all. We do know they're helpful, but they're not helpful for everybody, and they're not helpful in prevention. They're helpful for specific conditions. But we think we can do so much more with these new bugs that Nicola and the team are finding.

So, Nicola, in this paper, you now have listed sort of the 50 top bugs. Can I buy a probiotic from my supermarket for any of these 50 today? Not yet, absolutely not. But we are trying to cultivate it. Our science here is trying to target these microbes to culture them and think about having a new way of having probiotics. So this is one of the goals. It's much more long-term goal than what we are talking about today,

but it's something we are really working on. I feel like a lot of people would be quite shocked because I think a lot of people have been taught that, well, if you want to improve your gut health, you go and buy a probiotic and you eat it. And now, like, every product in the supermarket says, you know, has probiotics on it and you can get probiotic soda and whatever you want. But I think what you're saying is that none of them,

those probiotics actually are the good bugs that are going to support your health? No, the available, commercial available probiotics have any of those 50 good bugs. No, they cannot have them. So in a way, it's a different mechanism. I think what we're talking about is the probiotics you see classically in foods and yogurts and kaffirs and things been discovered historically a long time ago, and they're not normally part of our gut. So they would come in and they would pass through.

and they might stimulate our immune system, but they're not going to stay there and multiply. Whereas what we're talking about with these ones are these can naturally inhabit and live in our gut for a long time. Therefore, if we can get them into you, then they could have much more profound effects. And Tim, if you're listening to this and you're suddenly saying,

oh, I would like to have more good gut bugs and a bit like, you know, my own personal story, right, which is it went down to six and you get it up to 24, If you can't get it up to 24 by eating a probiotic, what can you do? Well, prebiotic is the other answer. And some people have heard of this term. It really means a fertilizer for your microbes. And it's a broader approach than a probatic, which is just targeting one particular

microbe and hoping that it has other effects. So prebotic is scattering lots of fertilizer in the soil of your. your gut so that the good microbes will grow and they will push out the bad microbes. So we think that the way to improve your good microbes is definitely through fertilizers from the tools that we have at the moment. So we think this diversity of plants on a regular basis is really the key currently. And that's available and it's actually easier to give people these pre-bartics than probatics because there aren't any real risk, health risks associated with it.

Absolutely. We have also to say that they are not enough per se. So probiotics alone or prebiotics alone are not enough because probiotics are living bacteria that are getting your gut, even the next generation ones, but then you have to feed them the right food, otherwise they will not stay there. And the same with prebiotics.

So it's not that you can think of taking pre and probiotics and then eat just junk food all the day. So it has to be a system approach. to get the right environment for your microbes, then maybe you need the specific microbes to be given to you. But this does not mean that, you know, diet is not important. The first thing is diet, then some supplements can really push an improvement. And I think in the future we might be looking at personalized fertilizers,

personalized pre-barics, really to tease apart these different ones. At the moment, we're going for generic. They work really well, but, you know, I think we can do even better in the future. Do you know someone who's worried about heart disease or diabetes? Why not share this episode with them right now? This new scientific breakthrough will give them the right tools to feed their gut so that it can protect them from getting sick. I'm sure they'll thank you.

Now, we talked a lot about the good bugs, but I'd love to touch at least briefly on the bad bugs, the sort of the villains of this story. How are they impacting our health? The bad bugs are, as we've discussed, only bad when they get too numerous. And when they're too numerous, they seem to interact together and they produce a nasty environment. They produce chemicals that irritate the immune system. They cause inflammation. They might cause slight swelling of the gut lining, making it leaky. They might change

the acidity of the local environment. They can mess up your fat transport, interfere with the way your body gets rid of fat, so it's hanging around and causing even more inflammation. Many of them seem to like sugar. They're like spoiled kids who only want to eat in the sweet shop. Tim, I can tell you've long time since you've had kids. That's all kids. Yeah, yeah, yeah. All right, so yes, all right.

They're like childish nuisances that are in your gut. And once they proliferate, it's very hard for your good bugs to make a comeback. because they're like bull, they're school bullies. They're elbowing out the other guys. They're pumping out all these chemicals. And the more nasty chemicals they pump out, the harder it is for the good guys to survive and flourish. And it also attracts more bad guys.

And there's even some evidence that if you've got lots of these bad guys, they even could send signals to your brain to say, give me more junk food. They've only done this in mice and rodents, but another lower index. insects, but it's a kind of cool idea that, yeah, I like this inflammatory environment. It suits my microbes. What are my microbes like to eat? Oh, lots of fat, lots of sugar, lots of nasty stuff. And what is most dangerous about this is that you don't feel to have the bad bugs,

no, because they are there, they are doing their inflammation, but it's not like they are not as bad as pathogens that they cause infectious diseases. You don't know you've got. Pathogens that are even worse than the bad bugs that we are talking about are making you seek, so you need to be treated. These micros, you don't feel that you'll have them. Yes, you may have lower energy, lower more information, things like that, but it's difficult for you to associate it with that. That's again why it's important to test, to know that you have them and be aware about that. And Nicol, I'd love to share again, I was just, I'm listening to you

and I have opened a set of results for my own microbiome test over time. And just before I I smashed my toe to smithereens, I had six bad bugs in my gut, and immediately after the antibiotics, actually, that fell to three, because it was like almost everything was wiped out. But I was looking at, interestingly, by the end of that year, my number of bad bugs had gone all the way up to 13, so I had like twice as many bad bugs. And today, that's slowly come down, and now it's back down to four. How does that tie into the story that you're describing? Your main focus should be improving your good bugs, then by growing, they will decrease the bad bucks.

I like gardening. So this is a bit like weeds, the way I'm hearing this. Like, I've got a garden. Like, there's only so much room in the garden. So if it's full of weeds, there's not room for a lot of flowers. If I have lots of flowers, actually, it's hard for the weeds to grow, right? Because they're sort of shaded underneath. But equally well, if I have lots of weeds, it's really hard for the flowers to show.

And so there's a sort of, if one grows the other shrinks. It's a balance. It's an equilibrium, yes. There is only some ecological space is called in the gut, and if you have enough of good bags, there is no space for the bad ones, yes. And so when I took the antibiotics, it sort of wiped out the garden and then suddenly I have all these weeds shoot up. I'd worked hard on my diet. I mean, this is sitting next to Tim for a long time, who's very smug about how healthy is. I'm like, no, I want to be on this path and feeling better. And then obviously I took very intense antibiotics and it sort of wiped it out. Yeah, you're set to your microbiome. And that's why it's important, it's even more important, the diet just after the antibiotics, because it's where you are regrowing your garden. The food that you're eating after antibiotics is really important

because you need to give them, you want to sort of feed the good bugs, the flowers. And starve the bad ones. Exactly. And what is the diet that the bad bugs really want? They love junk food. They love what we call pro-inflammatory foods that are high in saturated fats.

They're high in sugars and they're low in most of the traditional fibers that are hard to digest. It's easy to be bad, you know, instead that the good bugs are much more, you know, specialized in some operations. That's why you need to put effort in diversify your diet. So the bad bugs basically love all the junk food and the good bugs are like picky and you have to give them particular sorts of plants and things. Is that the sort of rather depressing message that you're sharing here? Sadly, yes.

And we used to have the perfect diet, but, you know, suddenly the Western or the sad diet, the standard American diet has taken over the Western world. And that really suits the bad microbes and doesn't suit the good guys. I'd love now to switch to really actionable advice. And I think we've talked about a lot of things you can do. But I'd like to try and make it really specific. Maybe starting actually with what you can learn if you've actually done a gut test and got the results. because I know a lot of people listening are Zoe members, you know, quite a lot of them will have

participated in their science, and they'll have been given a list of foods that are called gut boosters associated with their microbes. What makes a food gut boosting? Is it simply like it's a fermented food like we've been talking about today or something else? It's something different. These are foods that we are associating with microbes. So when we're suggesting a gut boost, it is in the belief that if you increase that particular type of food, you're going to increase some of your good microbes and reduce some of your bad ones that are specific to you. And each time we evolve these scores, this advice is going to get better and better and more specific.

And so, hopefully this be really very targeted advice, you know, within a few years' time. And so everyone could be pinning down, okay, I've got microbiome number four is really low. What combination of foods do I need to get this guy up and going? Because it has this very specific job that I want it to deal with. So this is really the start of this journey as we get these huge numbers and we can really nail this down. But it's the era of personalized nutrition very much. and personalised microbiome analysis, which is where we're all heading here, because, yes, there is general advice, but that only gets you so far.

When we find a new association between a food and a microbe, we will tell our members that this is what they need to eat without necessarily waiting for that paper to go through this rather lengthy process of peer review. So it's constantly evolving, it's constantly improving, and I think this is the whole name of the game in what we're doing. And that what makes it so exciting as our data from all our members get, you know, allows it to do better and better every time. Almost the old time. One of my gut boosters was tofu. I never ate tofu in my life. But because, oh, it's supposed to be good for my microbes. I started eating it. And what do you know? After a, after a while, I'll quite like

this. It's an interesting example of something that's sort of I've added to my diet now thinking about it. Now, a lot of people listen to this won't have ever had their microbiome tested. So what should everyone be thinking about eating more of if they want to support the sort of fussy good bugs that we've been talking about? Well, the general principles are still the same. And, you know, our research is just confirming that having a rich diversity of plants in your diet is good and we still believe that hitting a target of 30 is achievable and seems to be a reasonable one to go for, 30 different plants, including different types of nuts and seeds, herbs and spices, trying to eat the rainbow, so you're getting all the different chemicals

from these polyphenols, these defence chemicals, into your diet, having regular fermented foods, which gives you your gut microbiome a bit of a boost. in ways we don't totally understand yet. And you probably need to have three little portions a day of ideally different ones to really optimize it. And Tim, you said before that none of the probiotics that we buy in the supermarket actually match up to any of the good foods. And then you're talking about fermented foods that have like these live bugs in.

Are they going to be some of the 50 good bugs or is there something different? No, they're not because there's a different. between the microbes that live normally in food and the microbes that live normally in our gut. There's only a very small overlap of a few percent of these that you find food microbes inside your gut. And in general, they're not the ones that are in most of these fermented foods. I think I'm right, Nicola, on that. So it's a different type of microbe, and we think they might have an effect on our gut through, say, stimulate our immune system, a rather different mechanism to our normal gut microbes.

And they might be working higher up. We don't know yet. But we do know from our studies that we've done our own Zoe fermented food study and other more detailed ones that having at least three portions a day can in just a few weeks really improve your immune system. And that's going to help your gut microbes as well. So, you know, everyone should try and do that and experiment with new fermented foods. the other thing we I think people should do is to what we call pivot their protein

try and have less meat and get your protein from things like legumes and beans because you get pretty much the same quality protein but you also get lots of fiber which are microbes love so a lot of people aren't really used to you know in the US and the UK having a whole range of these beans and lentils, and I think that's something we can all do. And then finally, thinking about the quality of the food you're eating, which means you want to go for whole foods, you want to go for real food, and you want to really reduce your high-risk processed foods or what's called ultra-processed foods. And actually, Nicola, I was going to ask, because that's a lot about feeding the good bugs.

What do I want to eat less off to try and push down those weeds, you know, the bad bugs that we've been talking about? But again, I don't think there is one single food that is bad for you a priori, unless you eat too much of that bad food. So, you know, little amounts of bad foods here and there is not a big problem. I think it's much more the advantage of eating a lot of healthy foods and a diversity of healthy food and pushing down the bad bugs. So this is the first thing. Of course, too much red meat, of course, is a problem, clearly. But we shouldn't feel bad in eating every now and then the food. You can have the occasional pizza, can you?

Absolutely. I have to. And Tim, you mentioned about fermented foods. I think this is something that still for a lot of us is not very familiar. What fermented foods are in your fridge? My wife says too many. You can smell that probably. She can smell them.

Yeah, from a long way away, especially if I've had been home for a while and I've been doing a bit of my own fermenting. So I've always got yogurt and I've always got kaffir, kifah, which is fermented milk. I've just made a batch of water kaffir, which I also called tibikos, which is like a quart, sort of like a fizzy drink. No kombucha? I haven't made any kombucha at the moment. I've got my blob as in the fridge, which looks disgusting to anyone who's not an officiardo like myself. I've got kimchi, I've got some kraut in there, I've got some miso paste, I've even got some garlic in honey, it's fermented in honey, which I use in salad dressings.

I've got usually a whole range of smelly cheeses, lots of different ones. And I also got my sourdough mother, and I've just made some sourdough yesterday, actually. So that's on the go. So I've got a full range, and so, yeah, I'm never short of fermented food. So I always try and get my three portions in. Amazing. And might you have a new fermented recipe, a simple one, that someone listening to this could follow? Oh, it depends what you've got, but it's a very practical one. So often I find I have to go away on trips. I've left my fridge with vegetables in the bottom shelf that are probably going to go off if I don't do something with them. So I call this my fridge raid ferment. And whatever's in that lower compartment, except ovigines, which go horribly soggy. So things, whether it's carrots, sweet potato, cauliflower,

broccoli, onions, tomatoes, garlic, doesn't really matter, a bit of cabbage, and even it's, you know, a quarter of it, you chop it up into small chunks, half an inch thick, try and get it fairly even, stick them in a bowl, weigh them, then do some maths and calculate 2% of that weight and you put that as salt and you throw salt on it, massage it in a bit until it's really worked into the veg, stuff it in a jar, which has a lid and ideally a little valve. So you've either got to burp it every day or the valve will do the trick for you and leave it for five days while you're away. You leave it out in room temperature and that will be bubbling away and fermenting. And you should, when you come

back, have beautifully preserved, fermented fridge veg. And it's, yeah, that's an easy way to start and very good for the planet. That sounds great, Tim. And I think that that is actually a recipe that is coming from your brand new book. Am I right? That's right. Yeah, this is a sneak preview, which you can pre-order. And there are, you know, many other recipes that are really useful and practical in this book. If you want to learn more about your ferment, well, we will share the recipe in the show notes. And we'll also share a link to your new book. Tim, I know that you like to spend months and months hiding in your room writing these books. So I always think it's an immense amount of work, but I appreciate the amount of effort you go into to then

allow us to understand like the latest science and how that ties into our health. You're very welcome, Jonathan. Thank you both. Thank you so much, Nicola, for flying in to take us through this amazing new paper. We're trying to do a quick summary. I think I'm going to start with the thing that is brand new for me and I love, which is I am a coral reef, which is a brilliant idea that somehow I have all these bacteria sort of living in me and I'm sort of coexisting with them. On a more serious note, you're both clearly very excited. You feel like this is a really major breakthrough. Tim, you gave this great analogy that being published in nature is sort of like winning the Oscars for scientists.

And the key point I think I've taken away is this is like 34 times bigger than the previous biggest study. And that scale is allowing scientists to unlock really the links between food and bacteria and the links between individual bacteria and health in a way that hasn't been possible before. And I think, you know, I would definitely like to thank everyone listening to this who's actually contributed to the research, which I know is a lot of the listeners. you have, which is amazing. I know you're very excited because you're already working on the next stage of this, you know, with hundreds of thousands of samples. So thank you, everybody. And the key

thing that this enables us to do is to really take a snapshot of our gut microbiome today and understand its health, not in some vague way, but really literally, yes, there are specifically good bugs and bad bugs, and you can look at the amount between them. And that then you can track it over time in the way that, you know, I've been able to do since, since my antibiotics and really see, you know, that you're making progress, which I find incredibly reassuring. Like, it's a big part of my motivation to continue is to see the progress, while also maybe a little frustrated that I haven't got all the way that I want to, because I can be a perfectionist, but that's my own issue. I think the other big thing I took away is that the good bugs are pickier than the bad

bugs. The bad bugs, they love junk food. And they really, you know, they then create all the these chemicals that are damaging your gut and causing inflammation, but they're very happy with just eating, you know, whatever the junk is that surrounds you, the good bugs are pickier, and it's not all right to just feed like one good bug, actually you really want to have all 50 of these good bugs, and so you need to be trying to feed them all of these different things. We know they like plants, but they like different plants. And so that is really where, you know, Tim, you often talk about this idea of diversity, and I think it sounds like the science is helping to understand more of this, which is, you know,

they actually respond differently. And Nicola, you predicted that I had this particular bug, and you were right, which I wrote down, 4964 needs a better name, because we now know it really likes nuts and seeds. And if you feed it, then you're going to have that. And I think the final thing that I took away is the food that we eat and the sort of pre-biotic, as you describe it, is the most important thing, because, you know, we've all been told about these probiotics with like living bugs that you can take. But actually we now know that none of those are actually the same as these 50 good bugs that you want. And even fermented food that you're talking

about, which has really great positive impact, isn't going to replace the 50 good bugs. So I can't just say, oh, I'm getting fermented food and then eat my junk food. Like the most important thing is like these foods that actually are going to feed my bugs. And if I can do that right, a bit like in my garden, like I have more of these flowers, less of the weeds. And that brings us right back to the beginning of saying, genuinely, this is linked to better health and reducing my risk of heart disease and diabetes and all of these things. You got a fantastic summary. Now, if you listen to the show regularly, you already believe that changing how you eat

can transform your health, but you can only do so much with general advice from a weekly podcast. If you want to feel much better now and be on the path to live many more healthy years, you need something more. And that's why more than 100,000 members trust Zoe each day to help them make the smartest food choices. Combining our world-leading science with your Zoe test results, Zoe's your daily companion to better health for life. So how does it work? Zoe membership starts with at-home testing to understand your unique body.

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