“I Contain Multitudes”: Microbiomes, Ecology, a Book Review, and Speculation

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Perfect with a negroni.

What is the measure of a good science writer?

Both my boyfriend and I – one of us a scientist, the other not – adore reading Ed Yong’s columns in The Atlantic. That might be a pretty good measure, and it is one that Yong passes with flying colors: both the experts in fields he writes about, as well as nearly everyone else, are happy when he puts words on the internet.

(His Valentines tweets are no exception. I’m trying not to get sidetracked, but it’s hard, and that link is worth clicking, I promise.)

Nevertheless, when Yong’s first book, I Contain Multitudes, was released, I wasn’t that thrilled.

It’s about the microbiome, and I just wasn’t that excited to read about the microbiome. It seemed very of-the-moment, very bandwagon-y. As an ecologist I was kind of sick of hearing about the microbiome, and of people asking me whether my study organism’s microbiome might explain X or Y thing I had found about it.

Like, I’m studying all these complicated non-microbial things about my organism’s ecology, and I’m supposed to somehow have all the skills, techniques, and equipment to also understand its microbiome? Please go away. That’s so too much to ask.

Anyway, this month I finally read the book, and boy was I wrong.

The book was great.

And the microbiome is fascinating.

It was a delightful read, and among the reasons is that Yong describes perfectly some fundamental things about being an ecologist. Take this passage, for example:

“Here is a strange but critical sentiment to introduce in a book about the benefits of living with microbes: there is no such thing as a ‘good microbe’ or a ‘bad microbe’. These terms belong in children’s stories. They are ill-suited for describing the messy, fractious, contextual relationships of the natural world…. All of this means that labels like mutualist, commensal, pathogen, or parasite don’t quite work as badges of fixed identity. These terms are more like states of being, like hungry or awake or alive…”

For any scientist who has found a result, then explored seemingly the same situation over again and got a completely different result, this passage will spark a laugh or sigh of recognition.

It can seem like everything in ecology is context-dependent. Sometimes we can demonstrate what context matters and how the mechanism operates; other times it’s just a nice way of saying, we have no idea what’s going on.

Anyway, through Yong’s typically-excellent storytelling and the way I could identify with the scientists he profiled – men and women, young and old, at universities and zoos and NGO’s and research institutes around the world – I became immersed in tales about microbes.

As Yong points out, microbes were everywhere when multicellular life evolved. So we multicellular beings evolved with them. They made our lives easier, in some ways; and we helped them get ahead. Sometimes the relationship is good for everyone, sometimes not. But with microbes all around us for millions upon millions of years, the relationship is inevitable.

And so we have incredible interactions.

Of course, there are all the microbes in our guts: the gut microbiome, which is discussed all the time, it seems. Ours are worse than they used to be, worse than hunter-gatherer societies, worse if we eat more highly-processed food. This influences our health in so many ways.

But there are also more seemingly-fantastical things.

Microbes that help squids glow, canceling out the shadow that predators might see from below against the night sky, and thus protecting them from death! That makes a brilliantly intelligent cephalopod which just happens to be bioluminescent.

Mice that have gut microbes that help them eat creosote without any ill effects! Cute little fairy tail creatures that can eat a poison pill and just keep on going.

Another charming example? Having a pet, and a dog in particular, is one of the best ways to have a healthy, robust, microbiome. The pet brings microbes into the house from its travels outdoors, and those microbes become your microbes. I’m tallying up all the possible justifications for why we should get a dog, and this is a great one to add to the list! We need a dog because, science.

(Also on the list is that a dog can help you decide author order on papers. I mean, there are other ways, but let’s get a dog.)

Some stories are discouraging, like how a microbes help mountain pine beetles process and disarm the chemical defenses of trees, and thus to kill vast swathes of forest in North America. I thought I knew a fair bit about pine beetle devastation, but this was new to me.

Others stories are hopeful, however.

One of my favorites was a story about researchers trying to combat dengue fever. They raise mosquitos with a bacteria living inside them which makes them resistant to the dengue virus. And now they are letting those mosquitoes loose: they started in Australia, and went door to door to convince neighborhood residents to foster the new mosquitoes, even though most people would say “no way” if you asked whether you could drop some extra mosquito larvae next to their house. Bzzzzzz.

Just by carrying a bacteria, mosquitoes as a vector of this particular disease might be a thing of the past, at least in some places.

Yong also highlighted the work of Dr. Jessica Green, who was a new-ish professor in my department at University of Oregon back when I worked as a technician there.

Green studies the microbiome of buildings. It’s fascinating stuff, and even more interesting when you get to hospitals: leaving the window open to let natural microbes in might help fight off the bad microbes that give so many hospitalized people infections.

Thanks to microbes, there are simple interventions that might make a big difference in people’s lives. Our modern way of living and germ-phobic worldview has broken many of the relationships we used to have, but we are learning more and more about which ones we should preserve or restore. And it’s leading us to create new ones, too.

Along the way, I also began to think about a lot of things not covered in the book.

(I Contain Multitudeswas published in 2016, so a lot of science has happened since then in this rapidly-advancing field.)

For example, how might the microbiome alter human performance? The first thing that popped to mind was sleep. I have pretty much always been terrible at sleeping. I have a hard time falling asleep at night, and sometimes my sleep is restless.

In many aspects of life, sleep is vitally important. I think back to my time as an athlete: rest is one of the most important aspects of training, but if you aren’t sleeping well, you’re missing some of it. I definitely was.

Since 2016, some science has come out suggesting that lack of sleep alters your gut microbiome, and that the relationship also goes the other way, that your microbiome affects the process leading to sleep. But it’s hard to parse this research and assess its quality. I need someone like Yong to do that for me, and condense the reliable findings down into something digestible (see what I did there?).

In fact, I wondered about how the microbiome might affect athletes more generally. People doing a lot of training would benefit from all sorts of specific adaptations, including to diet and metabolism. Do microbes help in that? Does having the wrong microbiome hold you back?

Here, too, there has been a bit of research. For example, Outside wrote up a piece where they had seven elite athletes get their gut microbiomes sequenced. They found plenty of deviation from the average American, but as you can read in the piece, what did that actually mean? Hard to say. There is still so much we don’t know about microbes and which ones do what.

Another recent paper found that rugby players had increased prevalence of microbes that with functions that increased muscle turnover. This approach, looking at “metabolic phenotyping” and metabolomics rather than only the composition of the kinds of microbes, might be more informative. However, because the athletes in the study ate different diets than the non-athletes, it’s hard to totally understand the implications of such differences.

Still, I’m interested in work like this. What would it say about endurance athletes?

Something to remember, though, is that even if we figured out that the human gut microbiome could be used to get better athletic performances or to maintain a better training load, it might be hard to act on that information.

In humans, there are still few silver bullets for the microbiome. Knowing that a microbe is good isn’t enough. In many cases, a microbe can be helpful or protective in one context but harmful in another (for instance if it reaches too-high abundance).

And it’s also hard to deliver a microbe into the gut and have it take hold.

One of the first stories I heard about the microbiome was about fecal transplants, which were used with great success to reset some people’s guts and solve major, seemingly-unsolvable health problems. It was on a podcast, although I now can’t remember which one. It was a wild story.

Yong writes about this, too. But he points out something researchers have learned in the years since the first fantastic results using fecal transplants to cure people of aggressive diseases.

The reason that fecal transplants work so well with some diseases is that the native gut flora has been pretty much wiped out by the combination of the disease and the antibiotics used to treat it in its initial stages.

“This pharmacological carpet-bombing clears many of the native bacteria from their guts,” Yong writes of patients with Clostridium difficileinfections who receive fecal transplants. “When a donor’s microbes arrive in this wasteland, they find few competitors, and certainly few that are as well adapted to the gut as they are. They can easily colonise… ‘you can’t just infuse microbes into people and expect a transplant to happen’, says [gastroenterologist Alexander] Khoruts.”

So even if we knew of a silver-bullet microbe that would help you metabolize or do something else to perform better, could we get it to colonize an athlete’s gut? Unclear.

In the end, if you want a healthier microbiome, a lot of it probably just comes down to eating a healthy, diverse diet, and having healthy habits. And that’s what athletes should be doing anyway.

I wonder if the best way to have your microbiome help your athletic career is just to do a bunch of things that you already know you should do. Eat well. Sleep. Hug the people you care about.

Here’s my final take about the measure of a science writer. A good writer can make you understand things you’re already familiar with in a whole new light.

An entire research group in my department studies the aphid-Buchnerasystem.

Aphids are small insects that like to live on, for example, pea and bean plants. Buchnera are bacteria that live inside the aphids; they got there over 200 million years ago, and each strain of aphid has its own strain of Buchnera. The bacteria produce amino acids that they don’t get from their main food source, phloem. And there’s another microbe, Hamiltonella defense, that protects the aphids against parasitoid wasps, which lay their eggs in an aphid and whose larvae gradually consume them from the inside out, turning them into “mummies”. (Yeah, it’s gross.) Different Hamiltonella strains have different protective abilities and costs.

I can’t tell you how many research talks I have listened to about aphids. Usually, it has just seemed complicated and confusing – even when my friends and close colleagues are explaining it.

But when I read Yong’s description of the study system in his book, all of a sudden, the whole thing made sense to me. First of all what was going on, and secondly why it was fascinating. I will look at my colleagues’ projects differently, and with a lot more interest.

If that isn’t the measure of science writing success, I’m not sure what is.

You can purchase I Contain Multitudes at Powell’s or your favorite independent bookseller.

Book Review: Spying On Whales by Nick Pyenson

My aunt sends us books for Christmas every year, a.k.a. the best kind of holiday presents. In this year’s box was Spying on Whales by Nick Pyenson, and I sat down to start reading it that very night.

In some ways, I’m the perfect audience for this book. I’m interested in nature, natural history, and evolution, but I actually didn’t know much of anything about whales.

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Whale territory. You just can’t see them because they are under the water – as Pyenson discusses, this is one of the things that make these giant animals so mysterious and compelling.

In November I had gone on a whale-watching boat ride in northern Norway, and more or less everything I knew came from the Ukrainian guide on the boat. It wasn’t much, but before and after the trip, I thought whales were cool, when I thought about them at all.

If you are already a little obsessed with whales, then I think you’ll like the book too. All the facts are there for you to nerd out on.

9780735224568But Pyenson writes impressively well, and the book is never bogged down in this nerdery. Instead, it’s fun and adventurous. Chapters sometimes end in cliffhangers – I certainly couldn’t stop reading. And at times, it’s quite a moving read.

In the prologue, Pyenson describes how the Voyager 1 and Voyager 2 spacecraft are carrying whalesong into the outer reaches of the solar system. We may not understand what whales are saying, but we intuitively feel that they are intelligent and powerful – and that their communication is not only beautiful but probably important.

“They’re so compelling that we imagine aliens might find them interesting,” Pyenson writes of whales.

And yet, he continues, we know very little about whales, either the ones that live in our oceans today or the whales of the past.

I’ll admit: I didn’t actually really realize that.

Pyenson fills in details that I never knew I didn’t know, and certainly didn’t realize were so recently discovered. He discusses what things we still don’t know, and what mysteries will be exciting to solve. This book is filled with behavior, anatomy, and evolutionary history, as well as discussions of how all three connect to make a modern whale.

“Nothing in biology makes sense except in the light of evolution”, foundational biologist Theodosius Dobzhansky wrote as the title of one of his essays.

In my fields – ecology and evolutionary biology – this is tossed back and forth. “Nothing in ecology makes sense except in the light of evolution,” an evolutionary biologist will say, scoffing at ecology as boring (yes, this has happened to me, in person).

“Well, nothing in evolution makes sense except in the light of ecology,” a ecologist might retort.

Pyenson’s book is a great demonstration that both are true. In trying to piece together – literally, based on fossil fragments – how whales went from living on dry land to being the biggest animals in the oceans and indeed on the planet, ever, both ecology and evolution are needed. The two are woven together throughout the book as Pyenson describes working with one collaborator after another.

“The trip was an opportunity to push at the questions sitting on the edges of our disciplines, at the intersection of Ari’s understanding of behavior and local ecology, Jeremy’s grasp of physiology and biomechanics, and my background in paleontology and Earth history,” Pyenson writes at one point. “The basic questions about how whales do that they do require all these fields of understanding, and I’ve always thought the best way to answer them was through this Venn diagram of disciplines and personalities.”

Now that’s a scientific approach I admire, and he demonstrates that it’s fun, too. Minus the part at the whale slaughterhouse.

How does this approach deliver answers? Here’s an example question. If whales have gradually evolved to be bigger and bigger, why aren’t they even bigger still? That evolutionary question has an ecological answer.

The first two-thirds of the book are about the past and the present of whales. But my favorite part was the last third, about the future of whales, and of us. Whales live a very long time, sometimes two hundred years. There is a beautiful description of all that a 200-year-old whale has seen in its lifetime.

And then, a description of what today’s whales might see in the future, things that you and I will not live to see.

“Any bowheads living today do so in a liminal gap between a familiar past and a potentially unrecognizable future,” Pyenson writes of climate change in the Arctic. “A bowhead calf born today will live in an Arctic that, by the next century, will be a different world than that experienced by all of its ancestors.”

Maybe that sounds trivial – like, duh, climate change is happening fast – but after reading a hundred pages about all of the different environments that whales have encountered through their long evolutionary history, it is powerful when you reach this point.

And that is one of the things that kept me reading this book. It is peppered with fun facts – large baleen whales grow at a rate of a hundred pounds a day before reaching maturity, dang, that seems impossible! – but also with profound observations and good writing.

Finally, as a field ecologist, I really enjoyed Pyenson’s descriptions of fieldwork trips. He takes us to Chile, Panama, Iceland, and Antarctica, as well as more familiar-to-Americans spots like California and North Carolina. All of his descriptions of the challenges and successes of fieldwork, the camaraderie between colleagues, and even that one wonderful-but-definitely-weirdo collaborator (we all have at least one), feel authentic.

If you like science and nature writing, and compelling nonfiction in general, I think you’ll like this book. I did. Thanks Lizzie!