Thirdly, our approach is faster and cheaper than traditional taxonomic methods, as well as being easily replicable and transferable among research institutions. Finally a method that combines phylogeny and pragmatism falls in line with Darwin’s vision of classification, as stated in the conclusion of Origin of Species: “Our classification will come Selleckchem INCB018424 to be, as far as they can be so made, genealogies…” [2]. Methods Strain selection and growth conditions Details of Acinetobacter strains used in this study are listed

in Additional file 1. Acinetobacter baumannii W6976 and W7282 were provided by Drs. Mike Hornsey and David Wareham at Barts and The London NHS Trust, whilst the remaining strains were obtained from the UK, German and Belgium culture collections. Selleckchem S3I-201 sequenced isolates were cultured in Nutrient broth or Tryptic soy medium at 25°C or 30°C. DNA was extracted from single buy LY3009104 colony cultures using Qiagen 100/G Genomic-tips and quantified using Quant-iT PicoGreen dsDNA kits (Invitrogen). DNA was stored at 4°C. Genomic sequencing and annotation DNA from thirteen isolates

was sequenced by 454 GS FLX pyrosequencing (Roche, Branford, CT, USA) according to the standard protocol for whole-genome shotgun sequencing, producing an average of 450bp fragment reads. Draft genomes were assembled from flowgram data using Newbler 2.5 (Roche). The resulting contigs were annotated using the automated annotation pipeline on the xBASE server [61]. The genome sequences of the thirteen newly sequenced strains have been deposited in GenBank as whole genome shotgun projects (Table 1). Ortholog computation We computed the set of all orthologs within the 38 strains Digestive enzyme in our study with OrthoMCL [62] which performs a bidirectional best hit search in the amino-acid space, followed by a subsequent clustering step (percentMatchCutoff = 70, evalueCutoff = 1e-05, I = 1.5). Predicted are 7,334 clusters

of orthologous groups (COGs) containing 124,870 coding sequences (CDSs), which represents 95.7% of all good-quality CDSs (length at least 50 codons of which less than 2% are stop codons). Core genome phylogenetic tree construction Using the orthologs data, we extracted the genus core genome, i.e. the set of COGs which are present in each of the 38 strains (911 COGs). We filtered this set to exclude COGs containing paralogs and obtained a set of 827 single-copy COGs. The nucleotide gene sequences of each single-copy COG were aligned using MUSCLE 3.8.31 [63] with default parameters and the alignments were trimmed for quality, leading and trailing blocks using GBlocks 0.91b [64] with default parameters. After excluding 8 COGs with trimmed length < 50 bp, we screened the remaining 819 COGs for possible evidence of recombination using the PHI [65], MaxChi [66] and Neighbour similarity score [67] tests implemented in PhiPack (http://​www.​maths.​otago.​ac.​nz/​~dbryant/​software/​PhiPack.