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Hello and welcome to Zoe Recap, where each week we find the best bits from one of our podcast episodes to.
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Help you improve your health.
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Inside each of us lives a bustling community of microbes, tiny organisms that outnumber our human cells. They're there from the very moment we're born, shaping our immune system and influencing our long term health. The science of the microbiome is evolving rapidly, but one thing is clear, we need to take care of these microbes so that they can take care of us. Today I'm joined by Dr. Suzanne Dipoter and Tim Spector to explore how our gut bacteria protect us from diseases and what we can do to strengthen this vital partnership.
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The education of our immune system by our microbes starts from the moment we're born. Looking at the early life microbiome, the first year of life tells you a lot about the interactions with the immune system and the gut microbiome. There's a lot of research now on this really critical window where a baby is born essentially sterile, no microbes until they get the first bugs from their mother and immune cells. As more bacteria start to colonize the gut, so do more immune cells start to develop, and in the intestines as well. And what's really interesting is there's this weaning period, weaning meaning when you go from breast or formula onto your native diet or table foods or adult diet, and that introduction of food, you had this rapid expansion of immune cells in the infant. And a lot of that is attributed to the more diverse foods you eat, the more diverse microbes that colonize the gut. And so there's this beautiful evolutionary conserved interplay and between microbes colonizing, immune cells growing, which you want, that's a good thing. You want diverse immune cells so that when you grow up and see different foods, as Tim said, and different life exposures, you don't react and auto react. And so there's a lot of studies saying, hey, what happens when we mess that up and we give babies a lot of antibiotics early in life or something like that? And studies show that their immune system doesn't develop as well as their microbes don't also. And the hypothesis being, could that be predisposing infants, children to autoimmune conditions, airway allergies, food allergies and so on. So I think, you know, we study a lot what happens in adults, the defects that happen in adults, but a lot of it starts very early in life.
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That's probably why we've got so many allergies now. That we didn't have 40, 50 years ago. Cause breastfeeding rates have gone down and diversity of baby foods has gone right down. They're now getting ultra processed foods very early on in life. And you combine that with Caesarean sections plus antibiotics, It's a recipe for all these allergies we're getting, isn't it? Cause, as you said, a badly trained immune system that our ancestors didn't have. They had the perfect system to train it.
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I'm always conscious, as we listen to this, you know, having two children, my own, that it's really hard to, you know, go through pregnancy, have a baby, get through this and that Often this. These podcasts always feel like. And here there's yet more ways in which as a parent and often, particularly as a mother, you feel like you're failing. So I always want to feel like, I think this is a hard, you know, it can feel hard. And lots of people are trying really hard to do their best. One of the things that I'm really struck by is how much on this podcast in the last year we've been talking about ultra processed food, and much more so than when we first started, sort of Zoe, eight years ago. And thinking about, like my own experience with my youngest one, the extent to which we're all sort of pushed towards these sort of prepackaged foods that say they're super healthy and, you know, have all these organic ingredients, but basically you're giving them mush out of a packet and there's only about four types of mush. And I think, Suzanne, you're telling me you really want to be giving your, your children, like, a lot of different foods because that's what's needed to give them a lot of different bacteria. And you want. Because that's what's needed. I've never heard this before. That's what's needed to get a lot of different immune cells, which set you up well for life.
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Yeah. There are certain things you can, you know, you have to slowly introduce diversity in, but there's a window where you make choices about what you can expose a baby to. And training a diverse palate. Right. And spices and flavors and train diversity in food, you know, preferences early actually will encourage a more diverse diet going forward and then a diverse microbiome as a result. And so, yeah, trying to create as much diversity for a baby as possible. But I think you made a point that I really agree with and I always want to make sure parents don't always feel like they're doing something wrong. All of this research actually says the opposite. It's like, take it easy. If something falls on, let your kid play in the dirt. Let your kid lick stuff. Let your kid do stuff that would make you go crazy because that actually is giving them the exposures that they probably need to educate their immune system.
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It's really fascinating, I think, this link between the food we're eating, the fact that we know that the food we're eating is not as good as we had in the past, the impact on our gut bacteria. A lot of listeners to this show are Zoe members. They'll have had their gut microbiome tested as part of this, and many of them will have it also retested after going through the membership of this app and sort of guides you to what to eat. And what's striking is how many people living in the west have very poor microbiomes. So the variety of the microbes they have, the number of the ones that are correlated with better health is strikingly low. And then you're describing this link here between the immune system and what happens else. And so we've definitely got ourselves into a difficult place, haven't we, that we now need to sort of wind out of. And, Tim, I think you have a big new paper that's coming soon looking at the latest data of associations between bacteria and the source of health outcomes. Can you tell us a little bit about that and sort of sneak peek?
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Yes. Well, now the Zoe database of all the members who've given their microbiome is over hundreds of thousands of individuals. And many of these we've linked to their diet and these other factors. And so we've put a lot of this together to work out new ways of scoring what is good and bad bugs. Because up to now, we've just used this, what's called diversity, which is the number of different microbes, which I think Suzanne agrees is a rather crude tool that doesn't really sort of help in a number of situations because you get good and bad ones lumped together. And what we've found is by getting all these outcomes, including things like visceral fat and body mass index and heart problems and blood cholesterol and blood pressure, everything bad about you link that to foods that are associated with that and link to microbes that are also associated with, we've come up with this cool way of finding what are the good and bad microbes that predict these outcomes. So this is a paper that's coming, but that first paper is mainly to give us a new way of looking at gut Health through these really big, massive samples that finally are going to tell people how they can assess their own gut health compared to others in a way that doesn't get messed up like it used to in the past by you could have lots of inflammatory microbes and you have a good diversity, but that doesn't mean you're healthy.
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Right.
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So this sorts that out.
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It feels like the longer we've gone on, the larger the number of bugs that we're identifying that are both associated with health and poor health. And therefore the way that we're scoring this as you go through and do this test is like sort of taking into account more and more of these bacteria. So it's not as simple as there's like this one bad bug and there's like these two good bugs. It's like there's a lot of complexity here.
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It's looking a bit like the genetics. People have been following the genetics revolution. Twenty years ago we thought, oh, it was just one gene per disease. You know, we just thought in Crohn's or ulcerative colitis, you just got one gene and then you measure everyone again. Human biology is much more complex and so we also know that unlike genetics, all of us are much more unique in our gut microbes. So we need very big databases to work out what the, you know, how you would commonly assess, say that even the three of us to say who's healthier in terms of gut microbes, because we've got to have the same group that are common between us in order to compare them. No point you and I comparing if we only share on average 20% of them. So, yeah, it's really complicated. But the good news is we're making progress really fast because now, thanks to all the Zoe members, we're getting this vast database that is doing things that no one else can.
C
It's really valuable information and I think the inter individual differences in the microbiome are sort of the big wrench. In all of our studies, any person you encounter, you have a different microbiome and that makes it difficult to prescribe. That's why one size doesn't fit all for anything really. But you're your best comparison ultimately. So being able, if you have the opportunity to sample yourself over time, you can see what's changing within yourself. We often use this word, dysbiosis in the microbiome field, which means essentially a weird microbiome that's not normal. But what is that for every. There's no, there's no normal for everyone. And there's no abnormal for everyone. And so I always press, you know, define dysbiosis compared to what is it to your, your own starting point is really the best way to define it. And then you can start to understand like, just like with. You see many individuals with diabetes who walk around with a blood glucose of 200 and they're not passing out, they're just fine. Their set point is a little bit different than everyone else's. The same is true for your microbiome. And, and so you really sort of just pay attention to yourself, pay attention to what works, what doesn't, what foods work and what, what don't. Your microbiome is yours. And you, maybe you can compare to individuals within your household. You're more likely to share microbes with them versus others. But I think frequent sampling within an individual is very valuable.
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I love to hear you say that because I do that a lot. It's one of the benefits. I've been the co founder here, so I've been taking my microbiome frequently and there's a podcast that I recorded with Tim and with Will Bolcevich talking sort of what to do when taking antibiotics, because having sampled this regularly, I had to take some pretty heavy duty antibiotics at the beginning of last year and it basically smashed my microbiome and took a very long time to start to come back. And I think only with that comparison do I also sort of know I've still got further to go, which I find quite, quite motivating. Now, all of that said, I'm going to be in a lot of trouble if I don't switch to actionable advice. So I think people are listening to this. They're saying, wow, there's this link between the microbiome, my belly fat, that's important. I want to do something about it. I'd love to talk about what we can eat that might be able to make a difference. And we had Tim talk about this a lot. So actually, Suzanne, I'd love to start with you and I think also you've done a review around this recently from our work.
C
You know, in studying translocation, it really starts in the gut, you know, and healing the gut and maintaining a healthy gut barrier. And so foods that help support the integrity of the gut is really where it's at. And so then how do you do that? In my view, it is having you need a lot of functional redundancy. What that means is you need a lot of diversity, which is a crude measure, but many different kinds of bacteria, their presence Means that you have a lot of functions that can be carried out. And if you do something inadvertently to your microbiome and one drops out, you have others there to carry out those functions. And so how do you create diversity? We kind of touched on it earlier, but that is really a diversity of your diet. There's been some interesting research from the Microsetta initiative where they looked at microbiomes around the world and really looked at metrics of, you know, diversity and associations with, with disease. And what they found is the diversity of plants in your diet relate to the more diverse microbiome. And they sample, they found that individuals consume 40 or more different plant sources diet in a given week had a more diverse robust microbiome and plant sources come in all forms. And so what does that do to us? Probably the fiber content of the diet. And fiber is really the key. It's not sexy, it sounds boring, but it is critically important. And there's a lot of deep research on what fiber does to certain microbes, what those microbes do with the fiber and, and they relate to everything from educating the immune system, which we talked about earlier, to maintaining an anaerobic environment, a low oxygen environment in the gut, which is key for maintaining a gut barrier. So it's all cyclical, but it really starts with the diet. And feeding your good microbes through fiber, in my opinion, is you can't get around that.
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What would you add, Tim?
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Two things really. I think fermented food has been shown thanks to a study from Stanford to have anti inflammatory effects, which means we get this boost of extra microbes that are in food and the probiotics in food, if you have them regularly, and we're talking at least probably three times a day, you're getting a sample of it can dampen down inflammation, keep your immune system in much better shape, less likely to cause these problems which that visceral fat we think thrives off. So I think the idea is to keep that inflammation down. And the other thing, in addition to what Suzanne said, is avoiding ultra processed foods as much as possible. It's probably impossible to cut them out completely, but get it down to less than 10% of your diet so that you're getting many whole foods because we know that there's a pro inflammatory reaction when you're having a lot of these foods and that causes problems for your gut microbes as well as depriving them of fiber and normal nutrients. So that's what everybody should be aiming at is to shift more towards real food, less fake foods in their diet, plus getting more different fermented foods in their diet.
C
And just to add to that, I'm a big fan of fermented foods. Thank you for adding that in. The additional benefit to the fermented foods that we don't talk as much about is not just microbes in them, but all the postbiotic the chemicals that the microbes are producing. Fermented foods are like a living food and so you're getting not just live bacteria, but you're getting this sort of soup of all these beneficial products the microbes are making. And then when you consume it, you get the benefit of those chemicals as well. So there's multiple benefits to immune soup.
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Immune soup, yeah, I love that. I absolutely love that.
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As you can imagine hosting this podcast, running Zoe, juggling family life, it all keeps me pretty busy. So I try as best I can to stay energized and show up well in all those parts of my life by fueling my body with the right food, by exercising, and by adding a scoop of daily 30 to my meals every day. If you haven't heard of Daily 30 yet, it's the gut supplement designed by our gut health scientists here at Zoe. It's made of over 30 high quality hand picked plants, including seaweed, fungi and different types of fiber. Better yet, it contains ingredients that support gut health, digestion and energy, which is ideal for packed calendars and busy lives. Simply add one scoop a day to any meal for an extra boost of fibre and plant diversity. And because it tastes delicious on just about anything and adds a satisfying crunch, it quite quickly slots into your life, becoming a daily healthy habit you'll always have time for. By the way, whenever we talk about Daily 30 as a good source of fiber, we're required to say that it contains 4 grams of total fat per serving. Obviously, that's all amazing healthy fats from plants, so order yours today@zoe.com daily30. Thanks for listening and see you next time.
Podcast: ZOE Science & Nutrition
Episode: Recap: How your gut microbes could fight disease
Date: January 13, 2026
Host: Jonathan Wolf (ZOE)
Guests: Dr. Suzanne Devkota, Tim Spector
This episode explores the fundamental role of the gut microbiome in immune system development and disease prevention, translating the latest research into actionable steps for improving gut health. Jonathan Wolf, Dr. Suzanne Devkota, and Tim Spector discuss how early life exposures and dietary diversity support a healthy microbiome, make sense of the newest science, and give practical tips for everyday life.
Importance of Early Microbiome Development
"The more diverse foods you eat, the more diverse microbes that colonize the gut... You want diverse immune cells so that when you grow up and see different foods ... you don't react and auto react." (01:45)
Modern Lifestyle Risks
"Breastfeeding rates have gone down and diversity of baby foods has gone right down ... It's a recipe for all these allergies we're getting, isn't it?... Our ancestors had the perfect system to train [the immune system]." (02:45)
"Let your kid play in the dirt. Let your kid lick stuff. Let your kid do stuff that would make you go crazy because that actually is giving them the exposures that they probably need to educate their immune system." (04:44)
Large datasets (hundreds of thousands) allow better scoring of "good" and "bad" microbes.
"Getting all these outcomes, including things like visceral fat and body mass index ... link that to foods ... and link to microbes ... we've come up with this cool way of finding what are the good and bad microbes that predict these outcomes." (06:46)
Microbial scoring is now more nuanced, considering the complexity and inter-individual uniqueness of each person's microbiome (08:00–09:19).
"There's no normal for everyone ... your own starting point is really the best way to define it." (09:43)
Dietary Diversity Is Key
"What they found is the diversity of plants in your diet relate[s] to the more diverse microbiome... Fiber is really the key. It's not sexy, it sounds boring, but it is critically important." (12:23)
Fermented Foods & Inflammation
"Fermented food ... has anti inflammatory effects ... keep your immune system in much better shape." (13:48)
Avoid Ultra-Processed Foods
"Everybody should be aiming at ... shift more towards real food, less fake foods... plus getting more different fermented foods in their diet." (14:22)
Postbiotics in Fermented Foods
"[Fermented foods are] not just live bacteria, but you're getting this sort of soup of all these beneficial products the microbes are making. And then when you consume it, you get the benefit of those chemicals as well." (15:02)
On the importance of natural exposures for children:
"Let your kid play in the dirt… because that actually is giving them the exposures that they probably need to educate their immune system."
—Suzanne Devkota (04:44)
On new microbiome science:
"Getting all these outcomes… we've come up with this cool way of finding what are the good and bad microbes that predict these outcomes."
—Tim Spector (06:46)
On personalizing gut health:
"There's no normal for everyone…your own starting point is really the best way to define it."
—Suzanne Devkota (09:43)
On plant diversity and fiber:
"Fiber is really the key. It's not sexy, it sounds boring, but it is critically important."
—Suzanne Devkota (12:44)
On the idea of “immune soup”:
"[Fermented foods are] a living food… you're getting this sort of soup of all these beneficial products the microbes are making."
—Suzanne Devkota (15:02)
This recap translates cutting-edge science into practical habits—all with the encouragement that gut health is a lifelong, dynamic process unique to each of us.