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Our bacteria, ourselves: appreciating E. coli

By Anthony Doerr
August 17, 2008
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Microcosm: E. coli and the New Science of Life
By Carl Zimmer
Pantheon, 243 pp., illustrated, $25.95

At birth, a baby's digestive system is a sterile, undiscovered continent. Then the world gets hold of it. Within minutes, microbes have started pouring in from every direction. They come from the birth canal, from the mother's breast milk, from the fingertips of nurses and the lips of happy relatives.

Within a few days, millions of competing microorganisms will have colonized a newborn's intestines. Soon an immense bacterial ecosystem will have taken up residence in her gut, hundreds of different species competing for food in a dark, bubbling wilderness teeming with as many as 100 trillion microbes.

If that doesn't make you feel a bit bloated, think about this: An adult human will have about 30 feet of intestine coiled inside her. To a microbe, that's something like 7 million body lengths. For a 6-foot man, 7 million body lengths is around the distance between Boston and Myanmar.

Lurking down in that vast digestive backcountry inside each of us are as many as 30 strains of a bacterium known as Escherichia coli. E. coli is a humble germ, thousands of times smaller than a human cell. It's shaped like a Cheeto and smells like a toilet. It also happens to be the organism scientists most frequently use to explore the molecular foundations of life.

"Aside from ourselves," contends acclaimed science writer Carl Zimmer in his superb new book, "Microcosm: E. coli and the New Science of Life," "we have chronicled no other species so thoroughly."

E. coli, Zimmer reminds us, is a diverse species. There are the benign, sugar-eating colonizers of the guts of newborns. There are strains that shield us from dangerous pathogens. And there are strains that make us terribly sick, like O157:H7, the bacteria that periodically show up in undercooked fast-food hamburgers or on cable news shows. E. coli caused Pembroke residents last week to boil their water.

There are also innumerable colonies of E. coli in biotechnology and microbiology labs around the world. Every day pharmaceutical companies manipulate E. coli to produce human-growth hormone, insulin, vitamins, and even the rennet used to make cheese. Biologists use E. coli to map metabolic pathways. Geneticists use E. coli to investigate why genetically identical organisms sometimes behave in radically different ways. Scientists are even using E. coli to try to understand why we age and die. In many ways "Microcosm" is a sort of correction, an appreciation, an attempt to demonstrate just how indispensable a humble bacterium has been to human life in 2008. It is, in a sense, a paean to a microbe.

E. coli, Zimmer shows us, have sex, make chemical weapons, wage wars, get old, deceive one another, and even "build microbial cities." They can make heat-shock proteins to protect their colonies when they get too warm; they can maintain a sense of direction; they can communicate with other members of their species. What we think of as infinitesimal and primitive, Zimmer reminds us, is often totally remarkable and complicated.

One of the book's fundamental assertions is that life on earth, despite its apparent diversity, is actually quite uniform. "E. coli and elephants both encode genes with DNA," writes Zimmer, "both use RNA to carry that information to ribosomes, and both use the same genetic code to translate it into proteins." To put it more rudely, we are all - dolphins, sea cucumbers, bacteria, and people - membranes stretched around some proteins and some DNA. We've known this much for about 40 years.

But Zimmer's research is also extremely contemporary, and it's in his ability to synthesize the latest findings in microbiology that "Microcosm" becomes a quietly revolutionary book.

As scientists study the genes of more and more strains of E. coli, they're finding that foreign DNA has been steadily pouring into the genome. Not only is E. coli mutating within itself, it's also claiming new genes from elsewhere.

A major source of this input is viruses. As Zimmer notes, "Viruses are quickly losing their reputation as insignificant parasites." Viruses, we now know, pick up genes from one host and plug them like cassette tapes into the genome of a new host. This sort of gene-leapfrogging is called horizontal gene transfer, and it's not limited to bacteria and viruses. We've already identified around 100,000 viruses in the human genome, and the vestiges of 150,000 more.

What findings like this, and writers as capable as Zimmer, force us to ask is: What does it mean to be a human being? Are the barriers between species really as distinct and inviolable as we think they are? If human beings were nothing at all like bacteria, why would pharmaceutical companies be able to successfully plug human genes into microbes like E. coli?

Humans are, in Zimmer's words, "a complex cloud of genes, traits, environmental influences, and cultural forces." At a time when we can grow insulin inside the bodies of bacteria, or tiny, perfectly operable human kidneys inside mice, when practically every hand soap on supermarket shelves is marketed as "antibacterial," when more and more microbes are evolving resistances to antibiotics, when synthetic biologists are trying to create a kind of E. coli that can transform solar energy into fuel, we're learning more and more that we are inextricably linked to our ancestors and neighbors, all the way down to our genome, even to the microscopic bacteria and viruses that swim in our guts.

Anthony Doerr is the author of "The Shell Collector," "About Grace," and "Four Seasons in Rome."

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