Phylogenomic and functional insights into Staphylococcus shinii from blueberry production environments: intra-species structure, probiotic traits and antimicrobial resistance

Staphylococcus shinii is a recently proposed staphylococcal species identified in animal-associated microbiomes and fermented foods, with promising probiotic and biotechnological applications. However, its genomic diversity, functional traits and safety profile need to be well established. Here, we report the first recovery and genome sequencing of 41 S . shinii isolates from blueberry fruit washes and surrounding air. Phylogenomic analysis, including reference genomes, revealed at least 15 well-supported intra-species lineages (genomovars) defined by phylogenetic relationship and average nucleotide identity (>99.5% within genomovars;