I Contain Multitudes: The Microbes Within Us and a Grander View of Life

by Ed Yong

Even when we are alone, we are never alone. We exist in symbiosis

Through microbes, we find unity with our fellow creatures, despite our incredibly different lives. None of those lives is lived in isolation; they always exist in a microbial context, and involve constant negotiations between species big and small.

we are legion, each and every one of us. Always a “we” and never a “me”. Forget Orson Welles, and heed Walt Whitman: “I am large, I contain multitudes.”5 1.

Each of us has our own distinctive microbiome, sculpted by the genes we inherited, the places we’ve lived in, the drugs we’ve taken, the food we’ve eaten, the years we’ve lived, the hands we’ve shaken. Microbially, we are similar but different. When microbiologists first started cataloguing the human microbiome in its entirety they hoped to discover a “core” microbiome: a group of species that everyone shares. It’s now debatable if that core exists.

different (and our viromes even more so). Perhaps it is less that I contain multitudes and more that I am multitudes.

that Woese craved. By 1976, he had profiled 16S rRNA from around 30 different microbes. And in June of that year he started work on the species that would change his life – and biology as we know it.

“When you look from really close, a new world is revealed to you, more beautiful and spectacular than you would ever have imagined,” the words say. “Welcome to Micropia.”

“The germ-free animal is, by and large, a miserable creature, seeming at nearly every point to require an artificial substitute for the germs he lacks,” wrote Theodor Rosebury. “He is as a child might be if we could keep him under glass, entirely protected against the buffets of the outside world.”5

Why? Why have animals effectively outsourced parts of their development to other species? Why not just do everything in-house? “I think it’s unavoidable,” says John Rawls, who has worked with germ-free mice and squid. “Microbes are a necessary part of animal life. There’s no getting rid of them.” Remember that animals emerged in a world that had already been teeming with microbes for billions of years. They were the rulers of the planet long before we arrived. And when we did arrive, of course we evolved ways of interacting with the microbes around us. It would be absurd not to, like moving into a new city wearing a blindfold, earplugs, and a muzzle.

All modern animals are multicellular creatures that begin life as a hollow ball of cells and eat other things for sustenance, so it’s reasonable to think that our common ancestor shared the same traits.12 These rosettes, then, are modern representations of what the first animals may have looked like. And the process that creates them, where a single cell divides into a cohesive colony, recapitulates the kind of evolutionary transition that gave rise to those proto-animals, and eventually to squirrels, pigeons, ducks, children and every other beast in the park where King and I are talking.

At some point, the larvae settle down. They abandon their youthful wanderlust and remodel their bodies into sedentary adult shapes. This process – metamorphosis – is the most important moment in their lives. Scientists once suspected that it happened randomly, with the larvae settling in arbitrary places and surviving if they were lucky enough to hit a good location. In fact, they are purposeful and selective. They follow clues like chemical trails, temperature gradients, and even sounds, to find the best spots for metamorphosis.

our bodies are continuously built and reshaped by the bacteria inside us. Our relationship with them isn’t a one-off exchange but a continuous negotiation.

that the microbes are at least partly responsible for these behaviours. “I don’t think anyone would ever claim that you can reproduce autism in a mouse model,”

any kind of stress – starvation, sleeplessness, being separated from one’s mother, the sudden arrival of an aggressive individual, uncomfortable temperatures, overcrowding, even loud noises – can change a mouse’s gut microbiome. The opposite is also true: the microbiome can affect a host’s behaviour, including its social attitudes and its ability to deal with stress.40

swapping the bacteria in the animals’ guts, he had also swapped part of their personalities.

Drinking lots of alcohol makes the gut leakier, allowing microbes to more readily influence the brain – could that help to explain why alcoholics often experience depression or anxiety? Our diet reshapes the microbes in our gut – could those changes ripple out to affect our minds?47 The gut microbiome becomes less stable in old age – could that contribute to the rise of brain diseases in the elderly? And could our microbes manipulate our food cravings in the first place? If you reach for a burger or a chocolate bar, what exactly is pushing that hand forward?

When you choose your meals, you are also choosing which bacteria get fed, and which get an advantage over their peers. But they don’t have to sit there and graciously await your decision. As we have seen, bacteria have ways of hacking into the nervous system. If they released dopamine, a chemical involved in feelings of pleasure and reward, when you ate the ‘right’ things, could they potentially train you to choose certain foods over others? Do they get a say in your menu picks?48

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.6 In reality, bacteria exist along a continuum of lifestyles, between “bad” parasites and “good” mutualists.