Several forces shape the evolution of bacterial genomes: the steady accumulation of point mutations or small insertions/deletions (indels), potentially giving rise to a tree-like phylogeny; the influence of homologous recombination in some lineages, obscuring such diversification; and the key role of gene gain/loss, particularly the pervasive

influence of horizontal gene transfer, which, if substantial, could obliterate phylogenetic signals. These forces act with different strength on different parts of the genome and on different bacterial lineages. For example, sequences from a single gene such as the 16S rRNA gene have been shown to fail to capture the true genome-wide divergence between two strains [19–21]. Additionally, it may GANT61 purchase be expected that the various novel sequence-based metrics would be affected differently by different evolutionary forces.

This raises potential problems with the consistency of classification (results may or may not be consistent across the metrics) and backwards compatibility (classification may or may not correspond to already named species within a genus). In this work, we wished to explore these issues on a well-characterized and important bacterial genus, Acinetobacter. The genus Acinetobacter was first proposed by Brisou and Prévot in 1954 [22]; however, it was not until Baumann et al.[23] published their comprehensive study based on nutritional and biochemical properties that this designation became more widely accepted. In 1974 the genus was listed in Bergey’s Manual of Systematic Bacteriology with the description of a single species, Bucladesine research buy A. Casein kinase 1 calcoaceticus. To date, there are 27 species described in the genus (http://www.bacterio.cict.fr/a/acinetobacter.html). To fall within genus Acinetobacter, isolates must be Gram-negative, strictly aerobic, non-fermenting, non-fastidious, non-motile, catalase-positive, oxidase-negative and have a DNA G+C content of 38-47% [24]. Some isolates within the genus are naturally competent resulting in intra-species recombination [25–27]. Environmental isolates, such as A. calcoaceticus PHEA-2 and Acinetobacter oleivorans DR1, have attracted interest because they

are able to metabolize a diverse range of compounds [28–30]. However, most research on the genus has focused on clinical isolates, particularly from the species A. baumannii. This species has shown an astonishing ability to acquire antibiotic resistance genes and some strains are now close to being untreatable [31, 32]. Worryingly, the incidence of serious infections caused by other Acinetobacter species is also increasing [33]. Genotypic approaches have suggested that A. baumannii forms a complex—the A. baumannii/calcoaceticus or ACB complex—with three other species A. calcoaceticus, A. EPZ015938 datasheet nosocomialis and A. pittii. However, it remains very difficult, if not impossible, for a conventional reference laboratory to distinguish these species on phenotypic grounds alone [34].