ZOE Science & Nutrition - Recap: How your gut microbes could fight disease | Suzanne Devkota & Tim Spector

Episode Date: January 13, 2026

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 Devkota and Tim Spector to explore how our gut bacteria protect us from disease and what we can do to strengthen this vital partnership. 🌱 Try our new plant based wholefood supplement - Daily30+ *Naturally high in copper which contributes to normal energy yielding metabolism and the normal function of the immune system 📚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 Ferment 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  Better Breakfast Guide Have feedback or a topic you'd like us to cover? Let us know here Listen to the full episode here

Hello and welcome to Zoe Recap, where each week we find the best bits from one of our podcast episodes to help you improve your health. 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 Dipkota and Tim Specter to explore how our gut bacteria protect us from diseases and what we can do to strengthen this vital partnership. 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, you know, 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 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 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, okay, 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 an adult, but a lot of it starts very early in life. That's probably why we've got so many allergies now that we didn't have 40, 50 years ago, because rest feeding rates have gone down and diversity of baby foods has gone right down. They're now getting ultra-fitting. processed foods very early on in life. And you combine that with cesarean sections plus antibiotics. It's a recipe for all these allergies we're getting, isn't it? Because as you said, a badly trained immune system that our ancestors didn't have. They had the perfect system to train it. I'm always conscious of we listen to this, you know, having two children in my own that'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 my youngest one, the extent to which we're all sort of pushed towards these sort of pre-packaged foods

that say they're super healthy and have all these organic ingredients. But basically, you're giving the 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 children like a lot of different foods because that's what's needed to give them a lot of different bacteria. And you want to do that 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? 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

trained 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, you know, 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 like, like, you know, go crazy because that actually is giving them the exposures that they probably need to educate their immune system.

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, like, the variety of the microbes they have, the number of the ones that are correlated with better health is, like, strikingly low.

And then you're describing this link here between sort of 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? Yes. 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 linked to microbes that are also associated. 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 us 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 can have lots of inflammatory microbes and you have a good diversity, but that doesn't mean you're healthy. So this sorts that out. 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, you know, like these two good bugs. It's like there's a lot of complexity here. It's looking a bit like the genetics, people have been following the genetics revolution. 20 years ago, we thought, oh, there's just one gene per disease. We just thought in Crohn's or ulsteraclysis, you just have 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 how you would commonly assess, say, 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. At their point, you and I are comparing if we any 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. 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'll have a different microbiome, and that makes it difficult to, 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 own starting point has really had

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 the 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 is. The same is true for your microbiome. And so you really sort of just pay attention to yourself, pay attention to what works, what doesn't, what foods work and what don't. Your microbiome is yours. And 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. I'd love to hear you say that because I do that a lot.

It's one of the benefits of being 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 Bolshevich talking about 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 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, Suzanne, I'd love to start with you.

And I think also you've done a review around this recently. From our work, 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, 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 Microseta Initiative, where they looked at microbiomes around the world and really looked at metrics of, you know, diversity and associations with disease. And what they found is the diversity of plants in your diet relate to the more diverse microbiome. And they found that individuals consume 40 or more different plant sources

within their 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? Well, it's 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 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. Would you add, Tim? Two things. 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 pretty 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. And just to add to that, I'm a big fan of fermented foods. Thank you for adding that. And the additional benefit to the fermented foods that we don't talk as much about is not just microbes in them,

but all the post-posteroidic chemicals that the microbes are producing are, you know, 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. Immune soup, yeah. I love that.

I absolutely love that. I hope you found the information in this week's episode useful. If you're interested in improving your gut health, you might want to download our free gut guide. It's packed with recipes and science-backed information to help you on your journey towards better health. Go to zoe.com slash gut guide. to download it for free.

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