ZOE Science & Nutrition
Recap: How your gut microbes could fight disease | Suzanne Devkota & Tim Spector
13 Jan 2026
Chapter 1: What role do gut microbes play in our health?
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 Spector 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 a microbe 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 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 on to 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 we study a lot what happens in adults, the defects that happen in adults, 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 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 cesarean sections. Right. 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.
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Chapter 2: How does the early life microbiome influence immune development?
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 exposure 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 guide you to what to eat. And what's striking is, you know, 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. Well, now the ZOE database of all the members who've given their microbiomes 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 Susanna 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 and everything bad about you, link that to foods that are associated with that and link to microbes that are also associated.
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Chapter 3: What impact do antibiotics have on infant immune systems?
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 on
where they looked at microbiomes around the world and really looked at metrics of 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 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 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.
What 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 3%.
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... 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 it 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 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...
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