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

TL;DR

This study explores the genetic diversity and functional traits of Staphylococcus shinii from blueberry environments, revealing its potential as a probiotic while highlighting antimicrobial resistance and safety concerns.

Contribution

First genome sequencing of S. shinii isolates from blueberry environments, revealing intra-species genomic structure and functional traits.

Findings

S. shinii has at least 15 genomovars with distinct phylogenetic and genomic identities.

Core genome functions include carbohydrate metabolism and probiotic-related traits, but antimicrobial resistance genes vary across genomovars.

Putative pathogenicity-related genes and ARGs suggest caution in clinical use despite potential agri-food applications.

Abstract

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; <99.5% between them). Pangenome analysis showed a highly conserved core genome comprising 83.3% of genes, alongside diverse accessory genes across genomovars. Core functions in S. shinii included carbohydrate metabolism, vitamin biosynthesis and short-chain fatty acid production, traits potentially linked to probiotic properties. Biosynthetic gene clusters for bioactive compounds were broadly conserved, although genes encoding ribosomally synthesized and post-translationally modified peptides varied among genomovars. About 10–18 antimicrobial resistance genes (ARGs) were identified per S. shinii genome, several of which were located on the chromosome. Phenotypic testing confirmed susceptibility to ciprofloxacin, gentamicin and ampicillin, while resistance to other antimicrobials varied and was often plasmid-associated. Resistance patterns differed across genomovars, emphasizing the need for intra-species resolution in risk assessment. Although major virulence factors listed in the Virulence Factor Database were absent, putative pathogenicity-related genes were found in the core genome using the Pathogen–Host Interaction Database. Their presence, along with ARGs, underscores the need for caution in clinical contexts. Nonetheless, the absence of major virulence determinants and the presence of beneficial traits in some S. shinii isolates support their potential use in the agri-food system or environmental biotechnology, pending strain-specific safety evaluation.

Figures