Computational protocol: Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA 19 (DSM 43852T)

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Protocol publication

[…] The genus Oerskovia was first characterized in 1970 by Prauser et al. (), and members are described as Gram-positive bacteria that show extensively branching vegetative hyphae, growing on and into the agar. In addition, a very variable cell shape was observed (). The species O. enterophila was first described as Promicromonospora enterophila due to microscopic structures erroneously identified as spores and the supposed close relationship to the type strain Promicromonospora citrae (). Subsequent phylogenetic analysis revealed P. enterophila as a member of the genus Oerskovia. Moreover, the type strain of O. turbata shows 99.6% 16S rRNA gene sequence similarity with the type strain of P. enterophila, and thus both are close phylogenetic neighbors ().For genome sequencing of O. enterophila DFA-19, the strain was received from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) and was inoculated in 5 ml trypticase soy-yeast extract medium (medium 92; DSMZ) and incubated overnight at 30°C. Whole-genomic DNA was isolated using the MasterPure Gram-positive DNA purification kit (Epicentre, Madison, WI, USA). Isolated DNA was used to generate Illumina shotgun sequencing libraries. Sequencing was performed by employing a MiSeq system using a MiSeq reagent kit version 3 (600 cycles), as recommended by the manufacturer (Illumina, San Diego, CA, USA). Sequencing resulted in 2,498,636 paired-end reads that were trimmed using Trimmomatic version 0.32 (). De novo assembly performed with the SPAdes genome assembler software version 3.8.0 () yielded 114 contigs (>500 bp) with an average coverage of 90.5-fold. The genome of O. enterophila DFA-19 (DSM 43852T) consists of a circular chromosome of 4.65 Mb with an overall G+C content of 72.28%. Gene prediction and annotation were performed using the Prokka rapid prokaryotic genome annotation tool (). The genome harbored three rRNA genes, 58 tRNA genes, 2,820 protein-encoding genes with predicted functions, and 1,224 genes coding for hypothetical proteins.Analysis of the genome revealed that O. enterophila DFA-19 has several genes encoding enzymes involved in the degradation of plant polymers that are ubiquitously available in soils, such as cellulose, starch, or chitin (). Accordingly, O. enterophila DFA-19 was first isolated from millipede feces and described as a soil bacterium (). Potential genes encoding two endoglucanases and one cellulose 1,4-beta-cellobiosidase are present in the O. enterophila DFA-19 genome. Furthermore, putative genes encoding amylases for the conversion of starch or glycogen to dextrin were identified. Additionally, genes encoding chitinases, chitin-binding proteins, and a chitobiose phosphorylase were also present in the genome. […]

Pipeline specifications

Software tools Trimmomatic, SPAdes, Prokka
Applications Phylogenetics, WGS analysis