Certain viruses slip into E. coli through one of the many kinds of channels in its membrane. In a colony of genetically identical bacteria, some may be covered with these channels like pincushions. Others have none at all. The viruses will kill the vulnerable clones, while the other clones live on.

E. coli’s quirks can be a matter of life and death for us, as well. Some strains cause infections in the gut, the bladder, the blood and even the brain. In many cases, doctors try to kill the bacteria with antibiotics, which jam up the normal workings of their genes and proteins. In a susceptible colony of E. coli, a strong antibiotic will kill most of the bacteria, but not all of them. Some will survive.

The survivors escape death because they are trapped in a strange twilight existence called persistence. They make hardly any new proteins and grow barely, if at all. Antibiotics can’t kill persisters because there’s nothing in them to attack. The difference between normal cells and persisters cannot be found in their DNA. After persister cells survive an attack of antibiotics, some of their offspring switch back to normal growth and rebuild the colony. Most of their descendants will be normal E. coli. But some will be persisters. The colony remains the same motley crew of clones.

Image Even among simple forms of life, like the common bacterium E. coli, genetics only partly determines what any one organism is like. E. coli expresses its individuality in many ways. All the bacilli above are genetically identical, but the shades show differences in the production of proteins that digest lactose. Credit... Dr. Michael Elowitz

The key to understanding E. coli’s fingerprints is to recognize that the bacteria are not simple machines. Unlike wires and transistors, E. coli’s molecules are floppy, twitchy and unpredictable. In an electronic device, like a computer or a radio, electrons stream in a steady flow through the machine’s circuits, but the molecules in E. coli jostle and wander. When E. coli begins using a gene to make a protein, it does not produce a smoothly increasing supply. It spurts out the proteins in fits and starts. One clone may produce half a dozen copies of a protein in an hour, while a clone right next to it produces none.

Michael Elowitz, a physicist at Caltech, put these bursts on display in an elegant experiment. He and his colleagues incited E. coli to produce its proteins for feeding on lactose. Dr. Elowitz and his colleagues added extra genes to the bacteria so that when they made lactose-digesting proteins, they also released light.

The bacteria, Dr. Elowitz found, did not produce a uniform glow. They flickered, sometimes brightly, sometimes dimly. And when Dr. Elowitz took a snapshot of the colony, it was not a uniform sea of light. Some microbes were dark at that moment while others shone at full strength.