Flow of bacterial genes in the environment analyzed

January 2012

PROBLEM

The human body is a complex biological network that relies on microbes to help with metabolism and other essential functions. The microbes living in humans outnumber human cells 10 to 1. Their interaction with microbes in the environment often leads to horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, an important feature of bacterial evolution. In particular, HGT provides bacteria with rapid access to genetic innovations, allowing traits such as virulence and antibiotic resistance to spread through the human microbiome. Recent studies — like the one in 2010 that identified the so-called sushi gene, which had been transferred from a marine microbe to a bacteria living in the human gut — provide snapshots of active gene flow. These studies, along with growing concern that antibiotic resistance is being transferred from bacteria in livestock to bacteria in humans, highlight the need to determine the frequency of such transfers and the forces that govern them.

APPROACH

Using computational biology to determine the evolutionary ancestry of the genes in 2,235 complete bacteria genomes, Professor Eric Alm and graduate students Chris Smillie<