Shotgun Metagenomics Sequence Data from Skin Swabs

The skin is a relatively understudied niche due to downstream sample collection and preparation challenges. These challenges result from the relatively low bacterial biomass of skin, which complicates the extraction of sufficient DNA quantities for shotgun metagenomic sequencing. Moreover, availability of commercialised kit protocols specifically designed for skin (and other low biomass sites) are extremely limited and are very costly. For robust skin microbiota surveys there is a requirement for an end-to-end sample collection and preparation protocol that produces enough DNA, and is of high molecular weight, to allow for both short and long-read shotgun metagenomic sequencing and downstream analysis. We therefore aimed to optimise a comprehensive bacterial extraction method from skin that satisfied these key requirements.