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fragments in E. coli’s relative Salmonella enterica. Many scientists assumed that E. coli’s entire genome would follow this pattern. They thought E. coli’s evolutionary history was tidy. An ancestral microbe had given rise to many lineages, some of which evolved into today’s strains. Mutations cropped up in each lineage, a few of which were favored by natural selection, driving their cousins to extinction. Horizontal gene transfer might have imported a few genes from other species, but many scientists assumed that had been a rare event, Lederberg’s and Watanabe’s work notwithstanding.

But when scientists were finally able to compare the genomes of K-12 and O157:H7, that’s not what they found. Vast amounts of DNA in each strain had no obvious counterpart in the other. E. coli O157:H7 has 5.5 million base pairs of DNA, while K-12 has only 4.6 million. About 1.34 million base pairs in O157:H7 cannot be found in K-12, and more than half a million base pairs in K-12 have no counterpart in O157:H7. A map of the genes in each genome offered a similar picture. K-12 has 4,405 genes, 528 with no counterpart in O157:H7. Some 1,387 genes in O157:H7 cannot be found in K-12.

Each genome is like a circle in a Venn diagram. The overlap between K-12 and O157:H7 represents a core of shared genes, inherited from a common ancestor. After the two lineages diverged, they acquired new genes from other microbes—not just genes for resistance to antibiotics, but hundreds of other genes that came to make up a quarter of their genomes.

A year after the publication of O157:H7’s genome, scientists published the genome of a third strain. Known as CFT073, it lives harmlessly in the intestines, but if it gets into the bladder it can cause painful infections. The scientists discovered that its genome formed a third overlapping circle on the E. coli Venn diagram. CFT073 shares some genes with K-12 that it doesn’t share with O157:H7. And it shares some genes with O157:H7 that it doesn’t share with K-12. But scientists could not find any counterpart for 1,623 of its genes in the other two strains. At the center of the new Venn diagram was the new core of E. coli genes. Of all the E. coli genes scientists had now identified, only 40 percent could be found in all three strains. The core was shrinking.

As I write this, scientists have sequenced more than thirty E. coli genomes; a vast number of other strains are left to examine. With every new strain, scientists continue to discover dozens, even hundreds of genes found in no other E. coli strain. Each strain also carries hundreds of genes that it shares with some other strains. The list of genes shared by every E. coli is getting shorter, while the list of genes found in at least one strain is getting longer. Scientists call this total set of E. coli genes the pangenome. It’s up to 11,000 genes now, and at the current rate it will probably become larger than the 18,000 or so genes in the human genome.

The discovery of the E. coli pangenome called for a radical rethinking of how the microbe evolved. Tidy is precisely the wrong word to describe the history of E. coli over the past 30 million years. From the earliest days of its existence, a steady surge of new DNA has entered its genomes. Some of those genes moved from one strain of E. coli to another, while some of them came from other species.

Foreign DNA has taken several routes into E. coli’s genome. Plasmids, those tiny ringlets of DNA, brought some. Viruses that infect E. coli brought more. In some cases, viruses have brought only one or two genes. In other cases, they have brought dozens. These gene cassettes, as they’re sometimes called, are not random collections of DNA. They often contain all the instructions necessary to build a complex structure, such as a syringe for injecting toxins. Once these genes become part of the genome of a strain of E. coli, the microbes pass them down to their descendants. Ordinary natural selection can fine-tune the genes for the microbe’s particular way of life. Sometimes the genes slip away to a new host.

Viruses