, 2005), which posits that bacterial biofilms associated with chronic infections are composed of multiple strains of a single species (as well as often being polymicrobial or polykingdom communities) and that real-time HGT among the component strains (and species) leads to the continuous generation of a cloud of new strains with a novel combinations

of genes, thereby providing the bacterial community with a means to thwart the adaptive immune response of the host. Bacterial HGT is defined as the movement of genes (almost always in a unidirectional manner) between two, often unrelated, bacterial GSK3235025 nmr cells. It is important to understand that the donor cell from which the horizontally transferred DNA arose does not have to be viable at the time of HGT, and in fact, is definitely not the case in two of the three major HGT mechanisms used by bacterial species. HGT mechanisms usually result in the IWR-1 nmr transfer of one or more relatively small blocks of donor DNA into the recipient cell and thus provide for only the partial replacement of the receiving bacterium’s chromosome. The mean sizes of horizontally acquired gene blocks for those species such as Haemophilus influenzae, Streptococcus pneumoniae, and Staphylococcus aureus that have been studied extensively are usually only between 1 and 2 kb (Hiller et al., 2007; Hogg et al., 2007; Hall et al., 2010), but larger horizontally

acquired regions of 50–100 kb in size are not uncommon. Detailed comparative whole chromosomal analyses among large numbers of strains of H. influenzae (Hogg et al., 2007) and S. pneumoniae (Table 1) have revealed that, on average, each strain contains between 200 and 400 insertions/deletions

(indels) throughout their chromosome relative to other strains of the species. Thus, each chromosome is highly mosaic with respect to the origin of its own component genes, and further, each strain’s chromosome is highly unique with respect to its gene possession oxyclozanide complement. In fact, gene possession differences among the strains of a species account for the vast majority of the genetic heterogeneity within a species and dwarf the number of allelic differences observed within genes (Hall et al., 2009). Exhaustive pair-wise comparisons among all of the genomically sequenced strains for each of the species H. influenzae, S. pneumoniae, S. aureus, and Gardnerella vaginalis reveal that there are 385, 407, 246, and 608 gene possession differences, respectively, on average between every pair of strains that has been sequenced within these species (Hiller et al., 2007; Hogg et al., 2007). The 12-strain G. vaginalis supragenome (pangenome) contains 2248 genes, of which only 719 are core, with the remaining 1529 genes being distributed (noncore) among the 12 strains. Thus, more than two-thirds of the species’ genes are found in only a subset of strains.