Bacterial geneology: not dead yet

The importance of horizontal gene transfer (HGT) in bacterial evolution has led many bacteriologists to question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic and metagenomic studies suggest, how could bacterial species survive such genomic fluidity? Indeed, some go so far as to propose the metagenome as the appropriate unit of evolutionary distinction. The coherence and continuity of the metagenome remains, for us, an open question. Whatever the ultimate fate of metagenome-based phylogenetic reconstructions, we contend that genetic information in the bacterial world still comes in discrete, discernible and discontinuous packages that retain their integrity over evolutionary time. Despite the many fascinating instances of horizontal gene transfer that have been documented, the genetic coherence of bacterial species has not devolved into a continuous smear of promiscuously shared genetic information. The distinctions that we see and name in the microbial world are not arbitrary slicings of a continuous distribution, but natural breakpoints and boundaries that reflect the operation of time, history and selection on bacterial populations.