Draft Genome Sequences of Four Commensal Strains of Staphylococcus and Pseudomonas Isolated from Healthy Human Skin

Staphylococcus spp. and Pseudomonas spp. are widely distributed bacteria in the environment and are found in association with animals and humans. Here, we present the draft genome sequence data of the healthy human skin commensal strains Staphylococcus aureus MFP03, Staphylococcus epidermidis MFP04, Staphylococcus capitis MFP08, and Pseudomonas fluorescens MFP05.

S taphylococcus and Pseudomonas are among the most abundant genera of Firmicutes and Proteobacteria, respectively, which are major phyla of the skin microbiota (1)(2)(3). Although Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus capitis are species that reside abundantly on the skin (4), they are described mainly as pathogens. Therefore, it seems relevant to sequence skin commensal strains of these species. Moreover, no sequences of Pseudomonas fluorescens cutaneous commensal isolates had been reported yet.
In healthy individuals, skin microbiota bacteria are harmless to the host and play a central role in skin homeostasis (5); therefore, they should possess few virulence factors. Nevertheless, exoenzymes, often considered virulence factors in pathogens (6), are also secreted by commensals contributing to host innate defense mechanisms (7). Here, we report the draft genome sequences of four skin commensal bacterial strains previously isolated from healthy volunteers (8), i.e., Staphylococcus aureus MFP03, Staphylococcus epidermidis MFP04, Staphylococcus capitis MFP08, and Pseudomonas fluorescens MFP05. A particular focus was given to virulence and exoenzyme genes.
Cryo-frozen isolates were grown 24 h in LB medium at 180 rpm and 37°C for Staphylococcus strains or at 28°C for the Pseudomonas fluorescens MFP05 strain. Genomic DNA was extracted using the GeneJET genomic DNA purification kit (Thermo Fisher Scientific, USA), following the manufacturer's instructions, directly on the Pseudomonas fluorescens pellet or after a 60-min treatment of Staphylococcus strain pellets with lysis solution (400 mg/ml lysostaphin, 20 mg/ml lysozyme, 20 mM Tris-HCl [pH 8.0], 2 mM EDTA, and 1.2% Triton X-100). The quality and concentration of DNA were determined on a Nanodrop spectrophotometer and a Qubit 4.0 fluorometer (Thermo Fisher Scientific). Libraries were prepared using the Illumina Nextera XT or the Nextera Flex DNA library prep kits (Table 1) and sequenced on the MiSeq platform (Illumina) according to the manufacturer's protocol, with the MiSeq reagent cartridge V3 (600 cycles, 250-bp or 300-bp dual-index paired-end reads).
These draft annotated genome sequences of human skin isolates will improve the understanding of genetic diversity and enzymatic activities as well as the mechanisms involved in microbiota-human skin interactions.
Data availability. MiSeq sequencing reads and draft genome assemblies and annotations have been deposited in the Sequence Read Archive (SRA) and GenBank, respectively, under the accession numbers listed in Table 1. The abricate custom databases used in this study are available from the corresponding authors upon request.