Thursday, May 11, 2006

Your personalized bacteria   posted by JP @ 5/11/2006 09:44:00 AM

A new paper in PNAS shows how the power of cheap(er) sequencing is changing how a lot of people approach questions.

Here, the question is this: once a person is infected with a bacteria, obviously the bacteria population doesn't stay static; your body and whatever you put into it are a different environment, and the bacteria are likely to be under selective pressures. But by what mechanisms does the bacteria evolve over the course of an infection?

To answer this, researchers isolated P. aeruginosa, an opportinistic bacterial pathogen, from a cystic fibrosis patient at various points over the course of 8 years. Then, they took the first and last isolates and-- hell, why not-- just sequenced them. Your average whole genome shotgun.

Their results are convincing-- you're not an easy environment to live in. There was selection all over the genome, particularly against virulence factors and for drug resistance, as you might expect. They then looked at some of the mutated genes in other patients (apparently full genome sequencing is still a little too expensive to be completely routine) and found, in those genes, 5 synonymous mutations and 103 nonsynonymous mutations. That gives a ratio of a hell of a lot (keep in mind as well that there are more synonymous than nonsynonymous sites).

However, outside of those few genes selected in most other patients, the genes mutated in the original patient were rarely mutated in the others. There could be any number of explanations for this, and the authors don't really speculate. However, in my mind the most chilling (or reassuring) possibility is that, after 8 years, a bacteria isn't adapted to just any human body, it's adapted to you.