Computational protocol: Genome Sequences of Two Enterobacter pulveris Strains, 601/05T (=LMG 24057T =DSM 19144T) and 1160/04 (=LMG 24058 =DSM 19146), Isolated from Fruit Powder

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Protocol publication

[…] Stephan et al. () reported the isolation of six strains from fruit powder and from infant formula and its production environment, which were presumptively identified as Enterobacter sakazakii, now in the genus Cronobacter, through the use of differential chromogenic media. Additionally, these isolates displayed the yellow pigmentation on tryptone soy agar plates that is typical of Cronobacter (). Using a typical polyphasic taxonomic scheme, Stephan et al. () classified these strains as belonging to the novel species Enterobacter pulveris.Recently, Brady et al. () proposed that E. pulveris be recognized as a new Cronobacter species, and subsequently, Masood et al. () published a first draft genome sequence for E. pulveris strain E441 (=LMG24059). Because the taxonomic position remains unclear, we sequenced two strains of E. pulveris, the type strain 601/05 (=LMG24057 =DSM19144) and strain 1160/04 (=LMG24058 =DSM19146), which were originally described by Stephan et al. (). The libraries were constructed using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA), and whole-genome sequencing was performed on a MiSeq sequencer (Illumina, San Diego, CA), utilizing 500-cycle paired-end version 2 chemistry. Paired-end FASTQ datasets were trimmed and assembled using the CLC Genomics Workbench, version 6.5 (CLC bio, Aarhus, Denmark). A draft genome of 4,708,624 bp, contained on 252 contigs (>500 bp in size), was obtained for strain 601/05T, while that of strain 1160/04 was 4,811,103 bp on 137 contigs (>500 bp in size). The genomic contigs were annotated using the RAST server () to identify RNAs and protein-coding genes. The draft genomes of strains 601/05T and 1160/04 are predicted to contain 4,440 and 4,570 coding sequences (CDSs), respectively.The two E. pulveris genomes share an average nucleotide identity of 98.98%. Both genomes possess a number of noteworthy features, namely, operons for the catabolism of protocatechuate, xylose, β-xyloside, sucrose, pentose sugar alcohol, l-rhamnose, d-galactarate, d-galactonate, d-serine, fructoselysine, sialic acid, 5-keto-d-gluconate, and l-idonic acid, as well as the presence of three type 1, one P, and one sigma chaperone-usher fimbria clusters, curli fimbriae, a pga biofilm operon, a CRISPR element, and the lsr autoinducer-2 operon. Additionally, each genome contains the uptake of hexose phosphates (uhp) system and a number of PTS- and ABC-type transporters of unidentified substrates.There are also a number of genes and features that are unique to each genome, such as prophages and prophage-like elements and type VI secretion system cluster genes. Additionally, the genome of the type strain 601/05 harbors an α-xyloside and a β-linked disaccharide utilization operon, as well as two additional type 1 fimbria clusters. Conversely, the genome of strain 1160/04 contains a melibiose catabolism operon, a Tn7-like transposon harboring cobalt, cadmium, zinc, and mercury resistance, and an IncF class conjugative (tra) plasmid. […]

Pipeline specifications

Software tools CLC Genomics Workbench, RAST
Application WGS analysis