Given the general difficulty in defining bacterial species and th

Given the EPZ5676 General difficulty in defining bacterial species and the ready availability of genome sequence data,

we sought to evaluate a range of novel genotypic and genome-based metrics for species delineation. In light of discussed obstacles and the on-going public health concern, we believe that genus Acinetobacter provides a timely test case to evaluate the validity and robustness of these sequence-based approaches. In pursuit of this goal, we generated a diverse and informative set of thirteen new draft genome sequences, representing ten species, and we analyzed the whole-genome sequences from a total of 38 strains BI 2536 nmr belonging to the genus. Results and discussion General genome characteristics The genomes of thirteen Acinetobacter strains, including seven type strains, were sequenced to draft quality using 454 sequencing (Table 1). The A. bereziniae strain was found to have the largest genome size within the genus (~ 5 Mb), while the strain with the smallest genome (~2.9 Mb) belonged to the species A. parvus, which is known to have a reduced metabolic repertoire compared to see more other Acinetobacter species [39]. These thirteen genomes were considered

alongside twenty-five other publicly available genome sequences from the genus Acinetobacter (see Additional file 1). Table 1 Genome sizes, sequencing statistics, G+C content, number of CDSs in the thirteen sequenced Acinetobacter isolates   Species   Strain Genome size (Mb) Peak coverage No. of contigs G+C content (%) No. of predicted good quality CDSs† GenBank accession number A. parvus DSM 16617 (T) 2.88 24x 257 41.6 2681 AIEB00000000

A. radioresistens DSM 6976 (T) 3.35 13x 354 41.4 2964 AIDZ00000000 A. lwoffii NCTC 5866 (T) 3.35 14x 260 43.0 3005 AIEL00000000 A. ursingii DSM 16037 (T) 3.57 21x 158 40.0 3252 AIEA00000000 A. pittii* DSM 21653 (T) 3.75 8x 468 38.8 3252 AIEK00000000 A. calcoaceticus DSM 30006 (T) 3.89 10x 373 38.6 3377 AIEC00000000 A. baumannii W6976 3.91 8x 537 39.0 3252 Cyclin-dependent kinase 3 AIEG00000000 A. baumannii W7282 3.95 14x 140 39.0 3466 AIEH00000000 A. baumannii NCTC 7422 3.99 22x 179 41.3 3626 AIED00000000 A. pittii* DSM 9306 4.03 11x 339 38.8 3553 AIEF00000000 A. nosocomialis* NCTC 8102 4.12 10x 283 38.7 3596 AIEJ00000000 A. nosocomialis* NCTC 10304 4.16 10x 387 39.1 3501 AIEE00000000 A. bereziniae LMG 1003 (T) 4.98 12x 392 38.1 4480 AIEI00000000 * Species names as proposed by Nemec et al.[39]. † Definition of good quality CDS is length ≥ 50 codons, of which less than 2% are stop codons. (T) = Type strain. A. ursingii DSM 16037 genome characteristics The species A. ursingii was first described by Nemec et al. in 2001 [40]. We have genome sequenced the type strain DSM 16037, which was isolated from a blood culture taken from an inpatient in Prague, Czech Republic in 1993 [40].

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