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Monday, April 15, 2013

Do you know your E. coli?

Salt roasted turnip salad, Oxheart, Houston, TX

You'll hear it quite often in the news nowadays. E. coli found in green leafy vegetables. Beware! People get all panicky about it now - and unlike issues like GMO labeling, this one does merit a little caution. What exactly is E. coli? Well, it is shorthand for Escherichia coli, perhaps one of the best studied bacteria on the planet. Maybe. We'll get back to that shortly.

E. coli is a commensal bacteria - one that coexists with humans (for the record, in the average human body, the bacterial cells outnumber the human cells roughly 10:1 - you are more a constellation of bacterial communities than a single organism). But the name is actually about a group of diverse microbes that live in humans. Some are so benign, their ancestors served as the domesticated workhorses of modern molecular biology. We splice genes into them (heck, we still E. coli as our major engine for most kinds of DNA engineering), make them produce proteins of interest, or even to build genetic networks.

But there's a dark side - some kinds of E. coli harbor the capability to make humans sick. In fact, what you probably hear in the news as E. coli is shorthand for E. coli O157:H7, the outbreak bacteria not to be confused with the benign laboratory bug. But there are others. You'll see the term STEC - that stands for shiga toxin-producing E. coli. Or EHEC - which is enterohemorrhagic E. coli - this one is nasty, causes internal bleeding. All these, and others, get called E. coli because they pass the physiological tests for E. coli - and this microbial classification lets us standardize our procedures once we know.

Except that the human need to classify, to impose order over nature, may actually be counterproductive in this case. A study of 186 E. coli genomes (yes, we've sequenced that many), reveals what we call E. coli is probably a lot of different species. In fact, a different organism called Shigella should actually be classified among the E. coli - and that the diversity is so big that we can probably name six different species out of the E. coli group. Truth is, biology, while beautiful in its unity, rarely divides neatly into the classifications that humans require. And dealing with that complexity is part of the challenge, the excitement and the exasperation of science.

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