The World According to Microbes

17:35 minutes

In his new book I Contain Multitudes, science writer Ed Yong examines the connections between species and ecosystems from a microbial point of view. “We can compare the gut of a person with inflammatory bowel disease to a dying coral reef or a fallow field,” he says. “Their microbes might be different to ours, but the same principles govern our alliances.” Yong takes us on a tour of bacteria at work—in the gut of mosquitoes responsible for transmitting tropical diseases, to the labs of scientistific groups creating probiotic pills for humans.

Segment Guests

Ed Yong

Ed Yong is a science writer and author of An Immense World: How Animal Senses Reveal The Hidden Realms Around Us.

Segment Transcript

IRA FLATOW: This is Science Friday. I’m Ira Flatow. If you hold your hands out in front of you– everybody do that now. Not if you’re driving. They look pretty similar. They’re the same size. You clasp them together and they line up. But if you look closely at your palms, and I mean really close up. There’s a big difference. Over 80% of the bacteria on your right hand are not found on your left hand. That’s right. 80% difference in bacteria from one hand to the other.

Microbially speaking, your hands don’t have that much in common. Things aren’t always what they seem, when you take a microbial perspective of the world. You can see new connections, not only within your own body, but between species, and even systems. And the idea of the microbiome has only taken shape within the past decade. We haven’t been talking about it for that long.

That is the subject of my next guest’s new book, and it’s one of our favorite topics on Science Friday. Ed Young is the author of the new book, I Contain Multitudes: The Microbes Within Us and a Grander View of Life. He’s also science writer for The Atlantic, based in London. Welcome back, Ed.

ED YOUNG: Hi Ira, good to be here.

IRA FLATOW: Now I know you’ve been reporting on the microbiome for 10 years, so give us a little thumbnail sketch of how it’s all changed. I mean it’s really just blossomed hasn’t it? The studies of microbiome?

ED YOUNG: It’s really taken off in the last decade. I think microbes for the first time in their history have become fashionable. We’re starting to understand just how profoundly they influence the lives of not just ourselves, but the entire animal kingdom. How they sculpt our bodies, how they shape our immune systems, how they influence our evolutionary opportunities and our genomes, and how they might profoundly affect our health.

And I think all these discoveries are coming in from lots of different fields of science, from zoology, botany, immunology, neuroscience. And they’re all coalescing together to give us this grander view of life that I talk about in the book.


ED YOUNG: The idea that everything that we see is greatly influenced by things we can’t see.

IRA FLATOW: And the fact that our microbiome interacts with the microbiome in the soil, or in the oceans, and they’re all working together. It’s just amazing.

ED YOUNG: It is. Our microbes connect us to the world around us. I’m sitting in one of your studios right now bleeding microbes all over the place. Apologies to future guests. I’m also taking up microbes from the world around me, so, yeah, there’s this constant traffic that links us to the world around us. And there are so many parallels between the microbiomes of humans, and those of other animals.

IRA FLATOW: You have a favorite microbe, a favorite bacteria, that has actually been in the news about the Zika virus lately, called the wolbachia. Tell us about why that’s so important.

ED YOUNG: So wolbachia was discovered in 1924, and no one really thought much of it. It lived in the bodies of insects. And then people realized that it was actually everywhere. It was in so many different species. And in some it’s a parasite that seems to have a thing out for males. It can transform males into females or it kills males outright. In others it’s beneficial. It acts as a kind of dietary supplement.

And it’s beneficial to us too, it turns out, because if you put wolbachia some species of mosquitoes, especially those that carry diseases like Zika, or dengue, it stops them from becoming vectors. So scientists are now trying to add– trying to release wolbachia infected mosquitoes into places that are rife with these tropical diseases. Once the bacteria is there, it’s very good at spreading through natural populations.

So the idea is you release these mosquitoes. Suddenly the wild population within a few months becomes infected with wolbachia and therefore resistant to these viruses, these parasites that cause diseases in us.

IRA FLATOW: It’s almost every day we read something new about an experiment with the microbiome, and now, this new idea of fecal transplants, making a pill out of it. And so far there has not been much success in a pill version of the transplant, has there?

ED YOUNG: No, so the transplant itself, the idea of taking stool from a healthy donor to– and putting it in a sick one, I mean the idea might still seem very unorthodox and gross to some people, but it has been incredibly successful at treating infections with this bacterium called C. diff, clostridium difficile, a very weedy species that causes really severe cases of recurring diarrhea.

But actually trying to find the particular microbes in that ecosystem, pulling them out and turning them into a standardized, well-defined pill that people can take, has proven to be very challenging. So we still don’t entirely know what it is about the fecal transplant that makes it so effective. Which of the actors that are doing the job.

So I think that will happen. We’ll probably work it out, but it just shows how complex these worlds inside us can be.

IRA FLATOW: Because we take out a few dozen of the of the bacterium. We try them out. But it could be there are thousands in there, millions, right? Of bacteria, and we don’t know how they interact with one another.

ED YOUNG: That’s right. We need to understand how that– exactly that. How they interact with each other. Are they competing, cooperating? Which work well together? How do they interact with us, their hosts, their immune system? These are the questions of ecology. These are questions that people who work in rain forests and grasslands and coral reefs ask. And now we find us asking– we find ourselves asking these questions about our own bodies.

IRA FLATOW: Our number, 844 724 8255, if you’d like to talk to Ed Young, author of I Contain Multitudes: The Microbes Within Us and a Grander View of Life. I was struck by a bit of research I read last November that drove a lot of this home. It looked at how immunotherapy, trying to tweak the body’s immune system to fight diseases, could be improved by a certain probiotic, by a certain bacteria.

ED YOUNG: Right.

IRA FLATOW: Are you familiar with that?

ED YOUNG: I am, yeah I wrote about it for The Atlantic. So these drugs are called checkpoint inhibitors and they work by unleashing the immune system onto humans. And they’ve been such a promising advance in the realm of cancer. And then amazingly we learned that the effectiveness of these drugs can depend on the microbes that we carry. So if you have mice that don’t have any microbes at all, that they’re sterile, these drugs don’t seem to work.

And it seems that certain species of bacteria are especially good at sensitizing the animals to these medicines. And I think it just goes to show that there are many cases where drugs that we use, or the medicines we use, vary in effectiveness depending on the microbes we have.

So you could imagine that in the future after a lot more work, you might be able to give people probiotics of carefully chosen bacteria that makes them more responsive to drugs. Or maybe in the nearer term, we might be able to look at a person’s microbiome and say, OK, these medicines will work on you. These ones won’t. So we’re going to tailor your treatment that way.

IRA FLATOW: Have we found a single, simple probiotic that everybody can take? I know that there was– scientists have finally developed a successful one for goats.

ED YOUNG: Yeah, that’s right.

IRA FLATOW: Is that available to us?

ED YOUNG: That’s a very specific case. It’s this community of microbes, including one in particular, that detoxifies and poisons in a particular plant called [INAUDIBLE] which allows cattle in Australia to dine on this very nutritious but otherwise toxic plants. Now that’s a very specific case where you’re trying to do one particular thing, detoxify a particular chemical, and it works. It’s pretty easy. The things that we’re asking our own probiotics to do are much harder, which is why these products, even though they’re quite good for some things like infectious diarrheas, seem to be a little underwhelming in terms of the reality versus the benefits that they’re hoped to contain.

But I think we will get to a point where we will be able to create well-chosen formulations of probiotics that do a lot of good for our health. But we’re still only at the very beginnings of understanding this wor– these worlds inside us. So, what governs which species live in which people? How to then manipulate those to actually improve our health. We’re not quite there yet, but I think we’re getting there with more work.

IRA FLATOW: Let’s go to the phones. 844 724 8255. Adrian in Phoenix, hi, welcome to Science Friday.

ADRIAN: Hi, thanks for taking my call.

IRA FLATOW: You’re welcome. Go ahead.

ADRIAN: Well yes, so I’m wondering if the microbiome or the bacteria in the microbiome act somewhat like the animals and plants in the real world. Are there predators, and are there prey bacteria, or how do those interactions happen in the microbiome?

IRA FLATOW: Good question.

ED YOUNG: Yeah, that’s a really, really good question. Yeah, I think all the interactions that you’d expect in a broader ecosystem, parasites, predation, competition, cooperation, you’ll find those in the microbiome. You’ll see species that produce nutrients that nourish each other. You’ll see those that compete against each other.

So this is called this idea of colonization resistance, that we have this diverse array of bacteria in our bodies that stop those that are likely to cause disease from taking hold. There are all the concepts of broader ecology, are applicable to us. Invasive species, you could think of bacteria that cause disease in that way.

In the wider world you get things like successions. So a new landscape will be colonized by say, lichens and then shrubs, and then trees in a very predictable way. And you see the same thing in the gut of a newborn baby. You will get waves of microbes coming in, rising to the fore, and then fading away in very predictable patterns.

IRA FLATOW: You even mention in your book that some part of the mother’s milk is not used to nourish the baby, but the developing microbiome in the baby.

ED YOUNG: Yeah, one of my favorite microbiome stories. So we see breastfeeding as obviously a way of nourishing an infant. But it turns out that about 10% of breast milk consists of these sugars that babies can’t digest, and instead they are there to nourish microbes. To nourish specific strains that are specifically evolved to really efficiently eat these sugars. And in return they feed the baby’s cells, they shore up the lining of the gut, they quench inflammation. So a mother who’s breastfeeding isn’t just nurturing her infant, she’s also creating this entire world in her baby’s body, selecting which microbes get to live with her child.

IRA FLATOW: Isn’t the baby also sucking on– by sucking on the skin, getting mom’s microbiome off the skin, also?

ED YOUNG: Yeah, that’s part of it too. So this whole– all of these factors go into sculpting this ecosystem. Like setting up this world that then sets the child up for the rest of its life.

IRA FLATOW: It’s fascinating. Let’s go to the phones, back to– let’s go to Brian in Orem, Utah. Hi, Brian.

BRIAN: Hi, yeah. This is my favorite part of each Friday.

IRA FLATOW: Thank you.

BRIAN: I’ve learned a lot about microbiomes through this show. And last time I had a whole antibiotic system, one antibiotic. It made me wonder, how does that affect the microbiome?

IRA FLATOW: Good question. Yeah, we wonder about that too. When we’re sick and want to get an antibiotic, are we upsetting our microbiome?

ED YOUNG: Yeah, there’s loads of studies now showing that antibiotics, because they do kill bacteria, do have some negative effects on the microbiome. They seem to change it, as you would expect. They have very broad brush weapons. They’re kind of like nukes, rather than sniper rifles. So you get a lot of collateral damage in the gut.

Now the big question is, does that lead to long term problems? We see that the microbiome shifts upon antibiotic assaults, but it does also bounce back. It’s an ecosystem. It has resilience to it. And maybe it takes a lot of things in order to really throw it off course. So that’s something that’s being investigated now.

I think the critical thing to note with antibiotics is that they have been a massive health good. They have brought a lot of infectious disease under heel, and they have saved countless lives. The thing to note is that we should be using them carefully and judiciously. And that will not only spare the microbes that we rely upon, but it was also delay the rise of drug resistant infections that are so problematic right now.

IRA FLATOW: This is Science Friday from PRI, Public Radio International. I’m Ira Flatow talking with Ed Young about the microbiome. He’s author of I Contain Multitudes: The Microbes Within Us and the Grander View of Life.

Ed, we live with pets. They become another family member. Are we sharing microbiomes, their microbiomes on us, we on them?

ED YOUNG: Yeah, I think it’s almost certainly the case that we do. There are flows of microbes from the creatures in the world around us. And there have been studies showing that homes with dogs in particular, have this extra microbial richness. The rest of us live in these quite sanitized homes that are like microbial deserts. And you put a dog in the mix, and suddenly the diversity goes up.

And that might be good for us. That might give us a wider range of microbes that calibrates our immune system and gets a better balance between reacting, between dealing with infectious threats, and then not overreacting, so not just going berserk when we sense harmless things in the world around us.

IRA FLATOW: You know there was a study out this week that compared asthma rates between Amish and Hutterite communities. And they found a big difference between the two, just because they lived with farm animals differently.

ED YOUNG: Yes, so the idea there is that because Amish kids play in these barns, they get exposed to dust which is really rich in microbes. They better– they are better– their immune systems are better trained from an early age for all the exposures that you get in the wider world. So they get that balance between reaction and overreaction. And that might explain why they have low rates of things like asthma.

This fits with this general idea that early exposures to microbes are a good thing. They help to build and to calibrate the immune system correctly. That’s part of this view of microbes not just as germs, as agents of disease, but as important influences in our lives. And the immune system, not just as this militaristic defense force that kills microbes, and senses and destroys them, but as the rangers of a national park whose job it is to manage this ecosystem of lots of different species, chuck out invasive ones, and it’s more about control, rather than destruction.

IRA FLATOW: How can we control our– what do we need to feed it? What do we need to feed our microbiome to keep it healthy? And are there certain foods does it like to eat more than anything else?

ED YOUNG: So fiber is a good thing. So fiber consists of a wide range of complex carbohydrates from plants, and that nourishes an equally diverse range of microbes in the gut. And fiber has many other benefits in the microbiome too, so that’s one piece of solid advice. And many, many animals rely on their microbiome in order to break down these chemicals in plants. Humans do, to an extent, something like a cow, something so familiar to us, gets like 70% of its energy from microbial metabolism. The animal would not be able to survive if it didn’t have microbes as partners in digestion.

IRA FLATOW: Give me the answer where I started at, why do I have 80% different bacteria on one hand than the other?

ED YOUNG: Yeah, that’s a really good question. I think the answer is, kind of we don’t know. We are still starting to get to grips about, what is it that shapes these ecosystems. So we know that like, take my body, my forearm is dry like a desert, the inside of my nose or my mouth is wet and humid like a rain forest. So those physical conditions affect the microbes that get to live in that space.

But if we go broader, if we try to understand, what is it that makes this part of the body have these microbes and this one doesn’t? We’re still starting to answer those questions. And even for– my microbiome is very different to yours, which would be very different to those of our listeners. And one big study recently tried to look at the reasons behind those differences. And they could only account for something like 10% of their variation. So we’re only starting on this journey.

IRA FLATOW: Well, if you want to read the rest of the journey, it’s a great book, Ed. Ed Young is author of I Contain Multitudes: The Microbes Within Us and a Grander View of Life. You can read an excerpt of the book on our website at sciencefriday dot com slash microbe. Thank you, Ed, for taking time to be with us today.

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