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By Root 1209 0

known as A0 34/86, shields its hosts from invasions of diarrhea-causing bacteria. Doctors sometimes administer it to premature babies to protect their underdeveloped intestines from attack. In 2005, scientists published the genome of A0 34/86. They found genes for cell-killing factors, bloodletting proteins, and other weapons used by O157:H7 and other lethal strains. A0 34/86 uses these dark powers for our good, by aggressively establishing colonies in the guts of babies, thereby preventing disease-causing strains from finding a place to settle. We may try to draw sharp lines through nature’s diversity, to split E. coli up between its killers and its protectors. But evolution does not deal in sharp lines. It blurs.

ONE LIFE, MANY MASTERS

Another blurred line is the one that divides E. coli from its viruses. It may seem sharp if you are looking at E. coli ripped open by viruses streaming out to infect a new host. These seem like two different beasts. But E. coli has many different kinds of relationships with its viruses. Prophages can, at least for a time, seamlessly blend themselves into their host genomes. They do not necessarily surrender their sense of identity, though. They can sense when their host begins to suffer and at that point they turn back into familiar, host-killing viruses again. And then there are the viruses that lug around bundles of genes that can be very helpful to a microbe but offer no immediate benefit to themselves. When they slip into the genome of E. coli, it becomes much harder to say where the virus leaves off and the host begins. The viruses may then become trapped for good inside E. coli’s genome, thanks to mutations that destroy their ability to make new copies. Over time, new mutations may chop out much of the virus’s original DNA, leaving behind only those genes that are useful to the host. They are viral genes in name and origin only.

To make sense of this confusing relationship between E. coli and its viruses, it helps to set aside the “us versus them” view of life and to think of life as a braiding stream of genes. The genes carried by a virus at any moment form a coalition of evolutionary partners that have more success working together than any one of them could have on its own. Some coalitions thrive simply by invading a host and using it to replicate more copies of themselves. But in other cases, the interests of the virus’s genes and E. coli align. They may enjoy more reproductive success if they spare their host rather than kill it. Some viruses end up as itinerant Samaritans, bringing with them many genes that benefit their host—and, by extension, themselves. They are constantly trying out new combinations of genes as they travel, and the combinations that bring the most success to their hosts are the ones that survive.

These relationships can get complicated, as most relationships do. A virus can be simultaneously benign and malignant toward its E. coli host. E. coli O157:H7, for example, carries the genes of a virus that include the toxin gene. It’s possible that the bacteria benefit from making the toxin, perhaps because it keeps predators at bay; but for the individual microbes that actually produce it, the experience is not so pleasant. The virus forces the microbe to make both toxin molecules and new copies of itself until it bursts.

The decision to make the toxin lies with the virus, not with E. coli. It produces the toxin in times of stress—which is one reason why doctors generally don’t prescribe antibiotics for an infection of E. coli O157:H7. The drugs trigger the viruses to escape their hosts, turning what might have been an unpleasant bout of bloody diarrhea into a potentially lethal case of organ failure. The virus’s habit of killing its E. coli O157:H7 host is almost enough to inspire pity for the microbe. It is as much a victim of the virus as we are. Even after the viruses have killed their original host, they continue to make things worse for E. coli. They infect the harmless strains of E. coli in our gut, transforming them into factories that turn out