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

by Ed Yong

we see individuals, working their way through life as a bunch of cells in a single body, driven by a single brain, and operating with a single genome. This is a pleasant fiction. In fact, we are legion, each and every one of us.

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.

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.

It’s commonly said that the average person contains ten microbial cells for every human one, making us rounding errors in our own bodies.

a wild guess, based on a back-of-the-envelope calculation that became unfortunately enshrined as fact.

There are fewer than 100 species of bacteria that cause infectious diseases in humans;

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.

Islands are where you go if you want to find life at its most outlandish, gaudy, and superlative.

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.

Some species are common, but none is everywhere.

your right hand shares just a sixth of its microbial species with your left hand.

almost three-quarters of a newborn’s strains can be traced directly back to its mother.

Where is the other quarter coming from??

Our lives are heavily influenced by external forces that are actually inside us,

John Rawls, Who has

Why is Who capitalized?

I think it’s more accurate to see the immune system as a team of rangers in charge of a national park – as ecosystem managers.

Medical funding agencies saw it as irrelevant; as German puts it, “it doesn’t have anything to do with the diseases of middle-aged white men”.

Our mothers started that trend by feeding us at the start of our lives, and we carry on their work thereafter.

So...what does that mean for people raised on formula?

It took me six years of writing about his work to get him to answer my emails, so visiting his lab is a hard-won privilege.

This is why C. difficile mostly affects people who have been taking antibiotics, and why most infections happen in hospitals, nursing homes, or other healthcare settings. Some call it a man-made disease, associated with the very institutions that are meant to keep us healthy. It is the unintended consequence of an indiscriminate approach to killing microbes, akin to blitzing a weed-infested garden with pesticides and hoping that flowers will grow in their stead; often, you just get more weeds.

Until recently, most microbiome research had focused on people from WEIRD countries – that is, Western, Educated, Industralised, Rich, and Democratic.

There is a long-standing urge in biology to search for unifying causes behind complex diseases.

They reassure us that our messy, confusing world can be understood, and perhaps even manipulated. They promise to let us eff the ineffable, and control the uncontrollable.

DNA reveals which microbes are present and what they are capable of, but the other molecules tell you what they are actually doing.

It’s an insect that’s trying very hard to be a mammal.

Just by eating seaweed, the Japanese diners of centuries past booked a group of digestive genes on an incredible voyage from sea to land. The genes moved horizontally from marine microbes to gut ones, and then vertically from one gut to another.

the kind of genes that spread very easily through HGT. They are self-sufficient, and don’t need a supporting cast of other genes to do their job.

This is what medicine looks like when you understand that microbes are not the enemies of animals, but the foundations upon which our kingdom is built. Say goodbye to dated and dangerous war metaphors, in which we are soldiers hell-bent on eradicating germs at whatever cost. Say hello to a gentler and more nuanced gardening metaphor. Yes, we still have to pull out the weeds, but we also seed and feed the species that bind the soil, freshen the air, and please the eye.

The rise of Bd is a perfect example. Yes, it is virulent. Yes, it represses the immune systems of amphibians. But it’s still just a fungus, and amphibians have been dealing with fungi for some 370 million years. This isn’t their first rodeo. They are fumbling this particular ride because they have already been weakened by changing climate, introduced predators, and environmental pollutants.

The procedure works along the same principles as a probiotic, but rather than adding just one strain of bacteria, or even 17, it adds all of them. It’s an ecosystem transplant

There’s a popular saying among doctors: There’s no such thing as alternative medicine; if it works, it’s just called medicine.

You wouldn’t create something like IBD, where a donor’s bacteria would have to colonise a hostile, inflamed environment that’s already full of indigenous, well-adapted microbes.

But what if you also gave them antibiotics?

Or, they could simply load the circuits they want into a single synthetic microbe. “The hope is to have a parts list, and that this will become a plug and play system where the results will be predictable,” says Sonnenburg.

And I'm sure this won't lead to any undesirable side effects.

Jim Collins is more circumspect. Given how much we still don’t understand about the microbiome, he is unsettled by the prospect of engineering microbes that can permanently establish themselves in our bodies.

Thank you.

meandered through several wasted years, and hit many a dead end.60

And now we have another dead end footnote. I hope the hard copy of the book doesn't have these issues.

time.” the

Argh!!!!! LET ME EDIT THIS.

I want to treat the human being like an island,” he says. “But I’m literally not allowed. I put in a proposal to take some people and lock them in a space for six weeks, and the institutional review board said no.”

What do you call a dolphin’s armpit?”

patients would recover from infections more readily if she opened a window. “Always, air from the air without, and that, too, through those windows through which the air comes freshest,” she wrote. This makes perfect sense to an ecologist: fresh air brings in harmless environmental microbes that take up space and exclude pathogens.

“With this hand here, I shook hands with the women’s world squash champion yesterday. I took her microbiome and I’m giving it to you,” says Luke Leung, shaking Gilbert’s hand. “So now is my hand going to be really good at squash?” asks Gilbert. “Just the right hand,” says Leung. “If you’re a lefty, I’m sorry.”

You haven't washed your hands since yesterday?

We see what happens when those measures break: bleached reefs, inflamed guts, and obese bodies.

There's not a bit of fatphobia in this book.

have show

This is the third typo I've noticed in this book. I hope they aren't all in the print version. And if they are - GIVE ME A JOB.

This story is recounted in Beaumont’s own words (Beaumont, 1838), and in a later biography (Roberts, 1990).

This can't be accurate. Something's up with the footnotes here. I don't know who Beaumont is yet.

The flood of papers in 2011 included work by Jane Foster (Neufeld et al., 2011); Sven Petterson (Heijtz et al., 2011); Stephen Collins (Bercik et al., 2011); and John Cryan, Ted Dinan, and John Bienenstock (Bravo et al., 2011).

Yup, there's clearly a footnote missing and everything's been shifted up.

In 2013, Dunning-Hotopp showed that these short-lived unions are surprisingly common (Riley et al., 2013). She analysed hundreds of human genomes that had been sequenced from body cells – the ones from kidneys or skin or livers, none of which get passed on to offspring. She found traces of bacterial DNA in around a third of them. They were especially common in cancer cells; an intriguing result with unclear implications. It might be that tumours are especially prone to genetic intrusions, or that bacterial genes help to transform healthy cells into cancerous ones.

There is one other example of such a set-up: one bacterium has managed to find its way inside the mitochondria of ticks, where it now resides; it has been named Midichloria, after the much-maligned symbionts from the Star Wars universe that connect their owners with the Force.

Okay. Who did this?