The Loom

Here's the second winning question about Microcosm, from Kevin:

E. coli is a bacteria commonly found in the intestines of some animals. What distinguishes the common and harmless strains from those that can cause illness and death?

A lot of people asked this question in the contest. But my sense is that most people think that E. coli is just a nasty germ. When I would tell people I was going to write about E. coli, they thought I was going to pen an expose of the food industry. It came as a surprise to them when I told them that they were carrying billions of E. coli inside them. [More below the fold...]

E. coli is actually a name given to a vast number of closely related strains of bacteria. They can live not just in us, but in other warm-blooded animals. Most of these strains do not cause diseases. They quickly colonize the gut of a baby (probably by contact with the skin of mothers and other adults) and feed on sugar. I've gotten estimates that 30 strains of E. coli live in a person at any moment. They live pretty quietly in the gut, making up about one in a thousand bacteria there.

There are also some strains of E. coli that you definitely don't want in your gut. The most famous is E. coli O157:H7, which is carried in hamburgers and spinach and other food. (For more on this bad actor, see my column in Slate.) It's armed to the microbial teeth with weapons of destruction--needles for inserting molecules into intestinal cells, toxins that can cause bleeding, and so on. They even talk to each other in a chemical language in order to coordinate their attacks.

But there are other strains that cause much more harm. Some strains, known as Shigella, actually invade the intestinal cells. They cause collossal suffering, killing over a million people a year. Because those deaths happen in poor countries, Shigella is not well-known in countries like the United States. And why is it called Shigella? Because it seemed so different from E. coli when it was first studied in the late 1800s that scientists assumed it was a species of its own. In fact, Shigella is several strains of E. coli, each of which has evolved the same way of life. Shigella is not a species, so much as a state of being.

Other strains of E. coli are harmless if they stay in the gut. But if they end up somewhere else they can turn into agents of disease. Some strains can cause meningitis. Others can cause painful bladder infections, and can even creep their way up to the kidneys.

The dividing line between the harmless and harmful versions of E. coli is getting hard to draw as scientists get to know their DNA better. Some strains of E. coli actually protect against infection from harmful bacteria. When scientists sequenced their genomes, they were surprised to find lots of genes associated with disease. These "good" bugs apparently are using these weapons for our benefit, instead of our harm. They may help the bacteria colonize our guts quickly and aggressively, so that they can then shut out late-arriving pathogens.

So how did this strange collage of genes and strains come to be? Look for answer #3.