These extraordinary

gene possession signaling pathway differences can only arise via HGT mechanisms. HGT is defined in contrast to vertical gene transfer, which is the standard mechanism by which a mother cell replicates her entire complement of DNA and then passes along identical (or nearly so) copies of each chromosome and plasmid to each of her daughter cells during cell division. Genes and chromosomes that are acquired solely though vertical transmission can be used to construct phylogenetic relationships among bacterial strains, species, and higher taxa; however, genes that are acquired through HGT mechanisms produce mosaic chromosomes in which each part of the chromosome that was acquired horizontally has a different ancestry from every other part of the chromosome (unless there are two or more

simultaneous transformative events arising from the uptake of DNA from a single donor/competence event), which therefore makes phylogenetics at the whole chromosome level very difficult. In other words, for any set of strains containing mosaic chromosomes, each individual gene that has been horizontally transferred and then used to build a phylogenetic HM781-36B tree will produce a different tree structure from the same set of strains (Fig. 1) (Shen et al. 2005; Hall et al., 2010). Extensive HGT does not always completely obliterate the average chromosomal phylogenetic signal as has been demonstrated recently for S. pneumoniae (Donati et al., submitted); however, because of extensive HGT, strains that are phylogenetically related may have profoundly different Non-specific serine/threonine protein kinase genic compositions and thus produce very different disease phenotypes (Buchinsky et al., 2007). HGT is accomplished largely through three fundamentally different mechanisms: competence and transformation, mating or conjugation, and viral transduction. Some species of bacteria use only one of these mechanisms, whereas

others utilize two or even all three. Transformation and mating are active processes and require significant energetic expenditures by the recipient and the donor bacteria, respectively, as well as the maintenance of entire genetic regulons that encode the necessary machinery for the uptake and transfer of DNA, respectively (Mann et al., 2009). Thus, the bacteria that possess and maintain these systems must receive an evolutionary advantage in order for them to persist, particularly in the face of strong genomic deletatory mechanisms present in bacteria that are designed to minimize the genomic burden and eliminate unwanted foreign DNA – particularly that of bacteriophages (Brussow et al., 2004). Viral transduction, on the other hand, is a passive process engendered by temperate phage. The widespread possession of HGT mechanisms among pathogenic bacterial species, regardless of phylogeny and gram status, was one of the chief observational points on which the DGH was built (Ehrlich, 2001; Shen et al.