I Contain Multitudes
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I Contain Multitudes

Ed Yong

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eBook - ePub

I Contain Multitudes

Ed Yong

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About This Book

New York Times Bestseller

New York Times Notable Book of 2016 • NPR Great Read of 2016 • Named a Best Book of 2016 by The Economist, Smithsonian, NPR's Science Friday, MPR, Minnesota Star Tribune, Kirkus Reviews, Publishers Weekly, The Guardian, Times (London)

From Pulitzer Prize winner Ed Yong, a groundbreaking, wondrously informative, and vastly entertaining examination of the most significant revolution in biology since Darwin—a "microbe's-eye view" of the world that reveals a marvelous, radically reconceived picture of life on earth.

Every animal, whether human, squid, or wasp, is home to millions of bacteria and other microbes. Pulitzer Prize-winning author Ed Yong, whose humor is as evident as his erudition, prompts us to look at ourselves and our animal companions in a new light—less as individuals and more as the interconnected, interdependent multitudes we assuredly are.

The microbes in our bodies are part of our immune systems and protect us from disease. In the deep oceans, mysterious creatures without mouths or guts depend on microbes for all their energy. Bacteria provide squid with invisibility cloaks, help beetles to bring down forests, and allow worms to cause diseases that afflict millions of people.

Many people think of microbes as germs to be eradicated, but those that live with us—the microbiome—build our bodies, protect our health, shape our identities, and grant us incredible abilities. In this astonishing book, Ed Yong takes us on a grand tour through our microbial partners, and introduces us to the scientists on the front lines of discovery. It will change both our view of nature and our sense of where we belong in it.

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The Earth is 4.54 billion years old. A span of time that big is too mind-boggling to comprehend, so let’s collapse the planet’s entire history into a single calendar year.1 Right now, as you’re reading this page, it is 31st December, just before the stroke of midnight. (Thankfully, fireworks were invented nine seconds ago.) Humans have only existed for the 30 minutes or fewer. The dinosaurs ruled the world until the evening of 26th December, when an asteroid hit the planet and wiped them out (except for the birds). Flowers and mammals evolved earlier in December. In November, plants invaded the land and most of the major animal groups appeared in the seas. Plants and animals are all made up of many cells, and similar multicellular organisms had certainly evolved by the start of October. They may have appeared before that – the fossils are ambiguous and open to interpretation – but they would have been rare. Before October, almost every living thing on the planet consisted of single cells. They would have been invisible to the naked eye, had eyes existed. They had been that way ever since life first emerged, some time in March.
Let me stress: all the visible organisms that we’re familiar with, everything that springs to mind when we think of “nature”, are latecomers to life’s story. They are part of the coda. For most of the tale, microbes were the only living things on Earth. From March to October in our imaginary calendar, they had the sole run of the planet.
During that time, they changed it irrevocably. Bacteria enrich soils and break down pollutants. They drive planetary cycles of carbon, nitrogen, sulphur and phosphorus, by converting these elements into compounds that can be used by animals and plants and then returning them to the world by decomposing organic bodies. They were the first organisms to make their own food, by harnessing the sun’s energy in a process called photosynthesis. They released oxygen as a waste product, pumping out so much of the gas that they permanently changed the atmosphere of our planet. It is thanks to them that we live in an oxygenated world. Even now, the photosynthetic bacteria in the oceans produce the oxygen in half the breaths you take, and they lock away an equal amount of carbon dioxide.2 It is said that we are now in the Anthropocene: a new geological period characterised by the enormous impact that humans have had on the planet. You could equally argue that we are still living in the Microbiocene: a period that started at the dawn of life itself and will continue to its very end.
Indeed, microbes are everywhere. They live in the water of the deepest oceanic trenches and in the rocks below. They persist in belching hydrothermal vents, boiling springs, and Antarctic ice. They can even be found in clouds, where they act as seeds for rain and snow. They exist in astronomical numbers. Actually, they far exceed astronomical numbers: there are more bacteria in your gut than there are stars in our galaxy.3
This is the world in which animals originated, one smothered in and transformed by microbes. As palaeontologist Andrew Knoll once said, “Animals might be evolution’s icing, but bacteria are really the cake.”4 They have always been part of our ecology. We evolved among them. Also, we evolved from them. Animals belong to a group of organisms called eukaryotes, which also includes every plant, fungus and alga. Despite our obvious variety, all eukaryotes are built from cells that share the same basic architecture, which distinguishes them from other forms of life. They pack almost all their DNA into a central nucleus, a structure that gives the group its name – “eukaryote” comes from the Greek for “true nut”. They have an internal “skeleton” that provides structural support and shuttles molecules from place to place. And they have mitochondriabean-shaped power stations that supply cells with energy.
All eukaryotes share these traits because we all evolved from a single ancestor, around two billion years ago. Before that point, life on Earth could be divided into two camps or domains: the bacteria, which we already know about, and the archaea, which are less familiar and have a fondness for colonising inhospitable and extreme environments. These two groups both consisted of single cells that lack the sophistication of eukaryotes. They had no internal skeleton. They lacked a nucleus. They had no energy-providing mitochondria, for reasons that will soon become abundantly clear. They also looked superficially similar, which is why scientists originally believed that archaea were bacteria. But appearances are deceptive; archaea are as different from bacteria in biochemistry as PCs are from Macs in operating systems.
For roughly the first 2.5 billion years of life on Earth, bacteria and archaea charted largely separate evolutionary courses. Then, on one fateful occasion, a bacterium somehow merged with an archaeon, losing its free-living existence and becoming entrapped forever within its new host. That is how many scientists believe eukaryotes came to be. It’s our creation story: two great domains of life merging to create a third, in the greatest symbiosis of all time. The archaeon provided the chassis of the eukaryotic cell while the bacterium eventually transformed into the mitochondria.5
All eukaryotes descend from that fateful union. It’s why our genomes contain many genes that still have an archaeal character and others that more resemble those of bacteria. It’s also is why all of us contain mitochondria in our cells. These domesticated bacteria changed everything. By providing an extra source of energy, they allowed eukaryotic cells to get bigger, to accumulate more genes, and to become more complex. This explains what biochemist Nick Lane calls the “black hole at the heart of biology”. There’s a huge void between the simpler cells of bacteria and archaea and the more complex ones of eukaryotes, and life has managed to cross that void exactly once in four billion years. Since then, the countless bacteria and archaea in the world, all evolving at breakneck speed, have never again managed to produce a eukaryote. How could that possibly be? Other complex structures, from eyes to armour to many-celled bodies, have evolved on many independent occasions but the eukaryotic cell is a one-off innovation. That’s because, as Lane and others argue, the merger that created it – the one between an archaeon and a bacterium – was so breathtakingly improbable that it has never been duplicated, or at least never with success. By forging a union, those two microbes defied the odds and enabled the existence of all plants, animals, and anything visible to the naked eye – or anything with eyes, for that matter. They’re the reason I exist to write this book and you exist to read it. In our imaginary calendar, their merger happened some time in the middle of July. This book is about what happened afterwards.
After eukaryotic cells evolved, some of them started cooperating and clustering together, giving rise to multicellular creatures, like animals and plants. For the first time, living things became big – so big that they could host huge communities of bacteria and other microbes in their bodies.6 Counting such microbes is difficult. It’s commonly said that the average person contains ten microbial cells for every human one, making us rounding errors in our own bodies. But this 10-to-1 ratio, which shows up in books, magazines, TED talks, and virtually every scientific review on this topic, is a wild guess, based on a back-of-the-envelope calculation that became unfortunately enshrined as fact.7 The latest estimates suggest that we have around 30 trillion human cells and 39 trillion microbial ones – a roughly even split. Even these numbers are inexact, but that does not really matter: by any reckoning, we contain multitudes.
If we zoomed in on our skin, we would see them: spherical beads, sausage-like rods, and comma-shaped beans, each just a few millionths of a metre across. They are so small that, despite their numbers, they collectively weigh just a few pounds in total. A dozen or more would line up cosily in the width of a human hair. A million could dance on the head of a pin.
Without access to a microscope, most of us will never directly glimpse these miniature organisms. We only notice their consequences, and especially the negative ones. We can feel the painful cramp of an inflamed gut, and hear the sound of an uncontrollable sneeze. We can’t see the bacterium Mycobacterium tuberculosis with our naked eyes, but we can see the bloody spittle of a tuberculosis patient. Yersinia pestis, another bacterium, is similarly invisible to us, but the plague epidemics that it causes are all too obvious. These disease-causing microbes – pathogens – have traumatised humans throughout history, and have left a lingering cultural scar. Most of us still see microbes as germs: unwanted bringers of pestilence that we must avoid at all costs. Newspapers regularly churn out scare stories in which everyday items, from keyboards to mobile phones to doorknobs, turn out to be – gasp! – covered in bacteria. Even more bacteria than on a toilet seat! The implication is that these microbes are contaminants, and their presence a sign of filth, squalor, and imminent disease. This stereotype is grossly unfair. Most microbes are not pathogens. They do not make us sick. There are fewer than 100 species of bacteria that cause infectious diseases in humans;8 by contrast, the thousands of species in our guts are mostly harmless. At worst, they are passengers or hitchhikers. At best, they are invaluable parts of our bodies: not takers of life but its guardians. They behave like a hidden organ, as important as a stomach or an eye but made of trillions of swarming individual cells rather than a single unified mass.
The microbiome is infinitely more versatile than any of our familiar body parts. Your cells carry between 20,000 and 25,000 genes, but it is estimated that the microbes inside you wield around 500 times more.9 This genetic wealth, combined with their rapid evolution, makes them virtuosos of biochemistry, able to adapt to any possible challenge. They help to digest our food, releasing otherwise inaccessible nutrients. They produce vitamins and minerals that are missing from our diet. They break down toxins and hazardous chemicals. They protect us from disease by crowding out more dangerous microbes or killing them directly with antimicrobial chemicals. They produce substances that affect the way we smell. They are such an inevitable presence that we have outsourced surprising aspects of our lives to them. They guide the construction of our bodies, releasing molecules and signals that steer the growth of our organs. They educate our immune system, teaching it to tell friend from foe. They affect the development of the nervous system, and perhaps even influence our behaviour. They contribute to our lives in profound and wide-ranging ways; no corner of our biology is untouched. If we ignore them, we are looking at our lives through a keyhole.
This book will open the door fully. We are going to explore the incredible universe that exists within our bodies. We’ll learn about the origins of our alliances with microbes, the counter-intuitive ways in which they sculpt our bodies and shape our everyday lives, and the tricks we use for keeping them in line and ensuring a cordial partnership. We’ll look at how we inadvertently disrupt these partnerships and, in doing so, jeopardise our health. We’ll see how we might reverse these problems by manipulating the microbiome for our benefit. And we’ll hear the stories of the gleeful, imaginative, driven scientists who have dedicated their lives to understanding the microbial world, often in the face of scorn, dismissal, and failure.
We won’t focus only on humans, either.10 We’ll see how microbes have bestowed on animals extraordinary powers, evolutionary opportunities, and even their own genes. The hoopoe, a bird with a pickaxe profile and a tiger’s colours, paints its eggs with a bacteria-rich fluid that it secretes from a gland beneath its tail; the bacteria release antibiotics that stop more dangerous microbes from infiltrating the eggs and harming the chicks. Leafcutter ants also carry antibiotic-producing microbes on their bodies, and use these to disinfect the fungi that they cultivate in underground gardens. The spiky, expandable pufferfish uses bacteria to make tetrodotoxin – an exceptionally lethal substance which poisons any predator that tries to eat it. The Colorado potato beetle, a major pest, uses bacteria in its saliva to suppress the defences of the plants that it eats. The zebra-striped cardinalfish houses luminous bacteria, which it uses to attract its prey. The ant lion, a predatory insect with fearsome jaws, paralyses its victims with toxins produced by the bacteria in its saliva. Some nematode worms kill insects by vomiting toxic glowing bacteria into their bodies;11 others burrow into plant cells, and cause vast agricultural losses, using genes stolen from microbes.
Our alliances with microbes have repeatedly changed the course of animal evolution and transformed the world around us. It is easiest to appreciate how important these partnerships are by considering what would happen if they broke. Imagine if all microbes on the planet suddenly disappeared. On the upside, infectious diseases would be a thing of the past, and many pest insects would be unable to eke out a living. But that’s where the good news ends. Grazing mammals, like cows, sheep, antelope, and deer would starve since they are utterly dependent on their gut microbes to break down the tough fibres in the plants they eat. The great herds of Africa’s grasslands would vanish. Termites are similarly dependent on the digestive services of microbes, so they would also disappear, as would the larger animals that depend on them for food, or on their mounds for shelter. Aphids, cicadas, and other sap-sucking bugs would perish without bacteria to supplement the nutrients that are missing from their diets. In the deep oceans, many worms, shellfish, and other animals rely on bacteria for all of their energy. Without microbes, they too would die, and the entire food webs of these dark, abyssal worlds would collapse. Shallower oceans would fare little better. Corals, which depend on microscopic algae and a surprisingly diverse collection of bacteria, would become weak and vulnerable. Their mighty reefs would bleach and erode, and all the life they support would suffer.
Humans, oddly, would be fine. Unlike other animals, for whom sterility would mean a quick death, we would get by for weeks, months, even years. Our health might eventually suffer, but we’d have more pressing concerns. Waste would rapidly build up, for microbes are lords of decay. Along with other grazing mammals, our livestock would perish. So would our crop plants; without microbes to provide plants with nitrogen, the Earth would experience a catastrophic de-greening. (Since this book focuses entirely on animals, I offer my sincerest apologies to enthusiasts of botany.) “We predict complete societal collapse only within a year or so, linked to catastrophic failure of the food supply chain,” wrote microbiologists Jack Gilbert and Josh Neufeld, after running through this thought experiment.12 “Most species on Earth would become extinct, and population sizes would be reduced greatly for the species that endured.”
Microbes matter. We have ignored them. We have feared and hated them. Now, it is time to appreciate them, for our grasp of our own biology is greatly impoverished if we don’t. In this book, I want to show you what the animal kingdom really looks like, and how much more wondrous it becomes when you see it as the world of partnerships that it actually is. This is a version of natural history that deepens the more familiar one, the one laid down by the greatest naturalists of the past.
In March 1854, a 31-year-old British man named Alfred Russel Wallace began an epic eight-year trek through the islands of Malaysia and Indonesia.13 He saw fiery-furred orang-utans, kangaroos that hopped in trees, resplendent birds of paradise, giant birdwing butterflies, the babirusa pig whose tusks grow up through its snout, and a frog that glides from tree to tree on parachute-like feet. Wallace netted, grabbed, and shot the wonders he saw, eventually amassing an astonishing collection of over 125,000 specimens: shells; plants; thousands of insects, pinned in trays; birds and mammals, skinned, stuffed, or preserved in spirits. But unlike many of his contemporaries, Wallace also labelled everything meticulously, noting where each specimen was collected.
That was crucial. From these details, Wallace extracted patterns. He noticed a lot of variation in the animals that live in a certain place, even among those of the same species. He saw that some islands were home to unique species. He realised that as he sailed east from Bali to Lombok – a distance of just 22 miles – the animals of Asia suddenly gave way to the very different fauna of Australasia, as if these two islands were separated by an invisible barrier (which would later be called the Wallace Line). For good reason, Wallace is today heralded as the father of biogeography – the science of where species are, and where they are not. But as David Quammen writes in The Song of the Dodo: “As practiced by thoughtful scientists, biogeography does more than ask Which species? and Where? It also asks Why? And, what is sometimes even more crucial, Why not?”14
The study of microbiomes begins in exactly this way: cataloguing the ones that are found on different animals, or on different body parts of the same animal. Which species live where? Why? And why not? We need to know their biogeography before we can gain deeper insights into their c...

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