When Antony van Leeuwenhoek, the late 17th-century drape maker turned amateur scientist, first described microbes, people thought he was crazy.
He focused his homemade microscopes on water from a pond outside his house, and on the dental plaque from his neighbors in Delft, the Netherlands. And he became the very first person to see a teeming world of life previously inaccessible to the human eye.
We’d later learn that this vast system of bacteria, fungi, archaea, and other microbes is vital to life on Earth, and that we've actually evolved from and with these organisms. But people at the time didn’t know what to make of Leeuwenhoek’s wild descriptions — the "little animals" that were "a-swimming more nimbly than any I had ever seen" — which would ultimately lay the groundwork for microbiology.
Three and a half centuries later, science journalist Ed Yong channels Leeuwenhoek’s wonder at microorganisms in his lovely and insightful new book, I Contain Multitudes.
Yong charts out how this abundant, invisible world shaped who we, and other animals in the animal kingdom, are. With the rise of microbiome science — focused on the ecosystem of microbes that lives in us and on us — he points out that we’ve begun to move past the war with bacteria.
But we’re only really just beginning to learn how to live with them.
I talked to Yong about that evolution in understanding, how the microbiome went from being a fringe science to being in the spotlight, and how he separates the real scientific promise in this area from the hype.
We evolved from microbes
Julia Belluz
How do microbes enable not just human evolution but also our continued existence? In what ways do we not appreciate them?
Ed Yong
If we look at the animal kingdom as a whole, we see that microbes have opened up the most astonishing evolutionary opportunities for animals. They are in many ways the foundations of our success.
So sap-sucking insects, of which there are some 80,000-plus species, can drink the sap of plants because they have microbes in their cells that supplement nutrients that are missing from those meals.
Animals like cows and sheep and most plant-eating mammals rely on microbes to digest the food they eat. A lot of other creatures, from some beetles to rats to koalas, rely on microbes to detoxify the poisons in the meals they eat.
When I visit zoos, when I watch nature documentaries, when I read books that enchanted me as a kid, I see this hidden layer to all that biology that we can see with our naked eyes — you know, it’s driven by all these organisms that we can’t see.
[As for humans,] we know that microbes have a really important role to play in our lives. We know they train and build our immune systems. We know they sculpt some of our organs and that different parts of our body don’t grow correctly unless we have a thriving community of microbes inside us. We know that maybe they influence our behavior, that they create communities that block out organisms that might cause disease.
Things we think of as the province of individuals really come through partnership between us and a lot of other organisms. The traditional view of the immune system, for example, is that it’s a defense force that blocks out anything that’s not self, that finds microbes and destroys them.
Actually, we see that microbes influence the development of the immune system in the first place and that the immune system tolerates a lot of microbes. It’s there to keep them in the right places and to ensure that the right species are living within us.
Julia Belluz
We only discovered microbes about 350 years ago — but they’ve been around for much, much longer.
Ed Yong
The Earth is about 4.5 billion years old, and for most of the time life has been around, for a few billion years, it’s been largely microbial.
So if we condense all of Earth’s history into a single calendar year, then life emerged around about March, and multicellular life, all the organisms that we are familiar with, really only came up in October or so. And humans emerged very, very recently indeed.
So we’re just sort of the icing on life’s cake, and for the majority of its history it’s been ruled and dominated by microbes. And to a large extent, it still is.
Julia Belluz
You have a beautiful line: "...microbes are not the enemies of animals, but the foundations upon which our animal kingdom is built." It makes this co-evolution so clear — and also shows how much we’ve misperceived microbes for so long.
Ed Yong
That’s right. So our view of microbes dates back to the time of people like [pioneering microbiologists] Robert Koch and [Louis] Pasteur — people who showed that germs, that microbes, could cause disease. And that’s how we thought of them for many, many decades. We thought of them as causes of pestilence and signs of filth. We wanted to destroy them and repel them.
So I think we neglected them for a long while and then we feared them for a very long time. And I think now we’re starting to appreciate them.
Microbial nukes: antibiotics
Julia Belluz
We’re more aware now of the importance of microbial life, that it’s not something we should strive to kill off. But we also have to confront the fact that we’ve overused antibiotics, and contend with the rise of superbugs.
Ed Yong
It is undeniable that antibiotics have been a tremendous health good, maybe one of the greatest health goods of all time. They have brought so many infectious diseases to heel and saved so many lives.
But it’s also clear that they have negative effects on our microbiome. So they are indiscriminate weapons. They kill the microbes that we depend upon and that are good for us as well as the ones that are causing disease and causing us harm. They’re like nukes, rather than precision weapons.
So we’re in a difficult situation now, where on the one hand we’re running out of antibiotics, and the rise of antibiotic-resistant bacteria is a huge public health threat. But at the same time we’re aware of the need to preserve the microbiome.
A lot of claims around antibiotics and the microbiome are very exaggerated. We see that [antibiotics] do have an effect, but certainly in adults, and even to an extent in kids, we see that antibiotics change the microbiome and then the microbiome bounces back. So they are resilient.
So to what extent antibiotics are negatively affecting the microbiome is an open question. There’s a lot of talk about [antibiotics] increasing obesity or allergies or asthma because they’re changing the microbiomes of kids. But some of those claims are based on animal studies where the effects are quite small. If you look at humans, the epidemiology is quite mixed.
Julia Belluz
In light of that, how should we view antibiotics?
Ed Yong
It was already clear that we needed to cut back on the indiscriminate and unnecessary use of antibiotics. It’s clear that people are getting prescribed antibiotics for diseases where these drugs are not going to do any good, viral diseases or even bacterial diseases where the bugs are already resistant. And that kids are getting far more doses of antibiotics than they necessarily should be getting.
If we use them more judiciously, we’re going to forestall the rise of antibiotic-resistant bacteria. And we’re going to be helping out the microbes we depend upon. But we also need to not demonize antibiotics. We’re not to say, "Oh, you should never take them." I think that’s the risk of hype, of making parents think that if their child takes antibiotics, something really bad is going to happen.
How changes in our microbiome might make us sicker or healthier
Julia Belluz
In your book, you point to this absurdly long list of illnesses that are now linked to troubles with the microbiome (the collection of microbes that lives in and on us). They include Crohn’s disease, Type 1 diabetes, stroke, even psoriasis.
Ed Yong
The microbiome has been linked to so many different diseases and disorders that it almost invites parody. And a lot of those I think will just turn out to be correlations.
Julia Belluz
Right — you note that even when the evidence hints at a causal link between, say, allergies and changes in the microbiome, there are still ultimately more questions than answers.
Ed Yong
I think there is some evidence of the microbiome having a strong influence on our health. There are certainly studies in animals showing that if you transplant a microbiome from a sick to a healthy individual, then some of the traits of the disorders go with it. And that includes things like heart disease and colorectal cancer, obesity and malnutrition, and inflammatory bowel disease.
But I think that sort of leaves the question of, even if the microbes are influencing those conditions, are they initiating them or just exacerbating them? And if they are having an influence, then how great it is? How strong is the effect, and how does it compare to all the other things that increase the risk of these diseases?
Julia Belluz
What do you think are the most promising opportunities to alter the microbiome for health?
Ed Yong
I’m quite excited about some work in malnutrition. There are some really good researchers, like Jeff Gordon and David Mills, who are looking at kids in places like Malawi and Bangladesh and showing that their microbiomes don’t mature correctly, at the usual rate, when they’re very young. So they end up with a microbiological age that lags behind their biological age, and that seems to correlate with signs of malnutrition.
And it might help to explain why [malnutrition] is very difficult to treat through seemingly obvious means. Just giving them rich food doesn’t seem to quite work, and maybe it’s because they’re caught in this vicious cycle where they’ve got immune problems, microbiome problems, problems with their gut that are all feeding into each other.
Julia Belluz
One area that has been the subject of so much hype is the link between obesity and our microbiome. Obesity is such a massive, crushing problem, and it seems like over a decade ago that we started to learn that our microbes might be implicated. But there haven’t been many breakthroughs on that science since. What do you make of that?
Ed Yong
There’s been probably more research done on this health problem and the microbiome than any other.
About 10 years ago, studies came out showing that the microbiomes of obese and lean people and rodents were different. They showed that if you take the microbes of, say, an obese mouse and put them into a germ-free mouse, that rodent will then put on more weight than if you’d loaded it with a lean microbiome. So that suggests there is at least some degree of causal influence.
But over time, bigger studies and meta-analyses have shown that some of those early results aren’t reproducible. So we’re in a really weird position now where in any one study you can detect a clear difference between obese and lean people, but those differences don’t reliably duplicate across studies.
It certainly makes a lot of sense that the microbes in our gut could affect the way we process energy and the way we deal with the nutrients that we bring in. But I think it’s still an open question of what does that mean and how might we exploit that to improve people’s health.
Why the microbiome suddenly rose to prominence in science — and science hype
Julia Belluz
In the book, you note that the study of the microbiome was once a very peripheral field of science that was actually quite marginalized — and yet more recently, it’s become a very hot topic and an area of focus. What accounts for the rise of the microbiome in science?
Ed Yong
I think it’s actually a symbiosis of researchers that has led to this. It’s people that are working in these very disparate pockets that suddenly realize they were seeing similar trends.
And then you’ve got the technological advances: the sequencing approaches that let us characterize and study microbes that show just the true diversity of the microbiome.
And then some really important experiments showing the influence on our health about 10 years ago — on obesity and inflammatory bowel disease.
Julia Belluz
Consumers now get a lot of messages about "friendly bacteria" in things like yogurts or probiotics. But of course many of those claims have jumped way ahead of the science.
Ed Yong
Probiotics are very overhyped. There’s so many claims about what they can or can’t do, but a lot of the evidence is pretty underwhelming. They seem to be good for infectious diarrhea and a few other things, but they’re linked to so many things and there’s so much exaggeration around the benefits.
Julia Belluz
What do you do for your microbiome? I guess you don’t take probiotics.
Ed Yong
I do not. I’ve really not changed my lifestyle very much, if at all, because of anything I’ve read about the microbiome. I still think [the field is] in such an early stage. There are some strong results. For example, we know that fiber is a great way of nourishing a wide diversity of microbes.
One thing I found really interesting is the idea that your microbiome waxes and wanes, and some species are more common in some parts of the day than others. Jet lag, for some reason, throws off this cycle, because when we fly to different places, we start eating meals at random times.
This is one of the few microbiome studies I’ve actually taken to heart in terms of my own behavior. So now if I fly back from DC to London, I’ll try to start eating meals as if I was in London at the time. I don’t know whether really that’s made a difference to how jet-lagged I am.
Breast milk doesn’t only feed babies — it feeds babies’ microbes
Julia Belluz
One of the most spectacular bits of evidence of our co-evolution with microbes you uncovered was the wild research about breast milk.
Ed Yong
About 10 percent of breast milk consists of these sugars that babies can’t actually digest. They’re there to nourish microbes in the baby’s gut. So when a mother is breastfeeding, she’s nourishing not only her child but also her child’s first microbes. And she’s specifically nourishing some strains [that have] evolved to digest those particular sugars.
So milk not only nourishes the microbes, but it selects for the right ones — the ones that have co-evolved with those infants, the ones that will protect the baby’s health and create an ecosystem which is resilient to other more dangerous species.
Julia Belluz
What does that mean for whether women need to breastfeed?
Ed Yong
The obvious message is that breast milk is good. It has benefits, and those benefits extend to the microbiome as well as to babies and mothers. But if you’re not breastfeeding, you’re not screwing up your baby’s microbiome.
One of the things I noticed when I was researching the book is that these pathways are very resilient. The development of the microbiome can go down lots of different paths, and they may absorb certain knocks while still retaining the ability to bounce back. And maybe it’s just a multitude of knocks; maybe it takes a lot of disruptions to the microbiome to really set it down the wrong course.
And I think that’s one thing that we still don’t really understand: What does it really take to disrupt the normal development of a child’s microbiome?
Julia Belluz
There’s a lot of fear right now, I think, about what it means for your microbiome if you weren’t breastfed, or if you were born through a c-section, or if you were given a lot of antibiotics. So your message about the microbiome being resilient is comforting.
Ed Yong
I guess it is and it isn’t in some ways. I think there are bigger questions about what effects those have in the long run and whether they compound each other.
We know that all these things are influencing the microbiome, but what I think we don't understand is whether they matter. How strong are the effects?
So it’s a bit of a tricky time, because we’re seeing these things, but I think it’s hard to give people health advice that they can act upon.
Learn more
The 7 biggest problems facing science, according to 270 scientists
What research on English dukes can teach us about why the rich live longer
This new research rewrites the history of HIV in America