Jonah asked Carl Zimmer:

I just read Microcosm and I particularly wondered, when you said salmonella is really e. coli, and that different e. coli strains have very different genomes- what defines e. coli as e. coli?

Carl Zimmer That's a great question. Microbiologists first defined species like E. coli long before they could look at the DNA of bacteria. So they just observed traits in bacteria, in the same way ornithologists would look at the color of bird feathers. Now scientists are realizing that strains that "look" like E. coli can be extremely different, genetically speaking. They descend from a common ancestor, but they've picked up lots of genes since then.

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