Computational protocol: Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species

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Protocol publication

[…] The genus Staphylococcus contains important members of the human skin microbiome (). The major members are commensal under normal circumstances but can also be pathogenic. Staphylococcus aureus is so far the main species of interest, as it is a major source of nosocomial infections and can afflict numerous organs (). Other examples include Staphylococcus haemolyticus (causing infective endocarditis []) and Staphylococcus saprophyticus (causing urinary tract infections []). Staphylococcus epidermidis, on the other hand, is of critical importance, as it is the most common source of medical device-associated infections (), but at the same time, it is capable of inhibiting S. aureus colonization in human nasal cavities (). Given this important clinical relevance, infection models are established in mice but are so far limited to human S. aureus isolates (). Understanding the interaction and coevolutionary history between mice and their native bacterial species has attracted recent attention (), although native Staphylococcus strains remain unexplored. Furthermore, we recently discovered Staphylococcus to contain important members of the native mouse skin microbiota influencing susceptibility to autoimmune skin blistering ().In order to provide insight into the native species of Staphylococcus inhabiting mice, we isolated Staphylococcus spp. from 11 wild mice representing five species and subspecies (Mus musculus musculus, M. musculus domesticus, M. musculus castaneus, M. musculus spicilegus, and Apodemus uralensis), which were captured from the wild and maintained in conventional animal facilities at the Max Planck Institute for Evolutionary Biology, Ploen, Germany. The majority of isolates belonged to S. epidermidis, and we subsequently selected 11 strains for genome sequencing. The sequencing libraries were prepared using the Illumina Nextera XT kit and run on the MiSeq platform with paired-end reads of 250 bp, with a minimum coverage of 31× and a maximum of 61×. The reads were assembled de novo using Velvet () with parameters optimized by VelvetOptimiser (http://www.vicbioinformatics.com/software.velvetoptimiser.shtml). The contigs were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.0 ().For the 11 strains, we obtained a minimum of 91 and maximum of 277 contigs, and the total number of assembled nucleotides ranged from 2,458,755 to 2,762,809 per strain. The average G+C contents ranged from 31.7% to 32.0%, which is close to those of the available reference strains (32.1% for S. epidermidis ATCC 12228 and 32.2% for S. epidermidis RP62A). A range of 2,259 to 2,541 proteins were predicted and annotated using the NCBI PGAP, with 83.6% to 92.2% of the proteins having homologs in the S. epidermidis ATCC 12228 (NCBI accession no. NC_004461) () and/or RP62A genomes (NCBI accession no. NC_002976) () (BLASTp [] with an E value of 1E-20 and similarity threshold of 0.8). Thirteen to 70 tRNA genes and 3 to 24 rRNA genes are predicted for each strain. Further analyses of the genomic content may reveal important aspects of the interaction and coevolution of S. epidermidis and mouse hosts. […]

Pipeline specifications

Software tools Velvet, VelvetOptimiser, PGAP, PGAP, BLASTP
Applications Genome annotation, WGS analysis
Organisms Mus musculus, Homo sapiens, Staphylococcus epidermidis
Diseases Staphylococcal Infections