Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites

• Published in: BMC genomics 2024-06, Vol.25 (1), p.575-22
• Main Authors: Sosa-Fajardo, Ana, Díaz-Muñoz, Cristian, Van der Veken, David, Pradal, Inés, Verce, Marko, Weckx, Stefan, Leroy, Frédéric
• Format: Article
• Language: English
• Subjects: Antimicrobial activity; Antimicrobial peptides; Bacteria; Bacteriocin; Bacteriocins; Bacteriocins - genetics; Bacteriocins - metabolism; Chemical properties; Clusters; Competitiveness; Competitiveness factors; Ecological niches; Fermentation; Flavors; Fluidity; Gene clusters; Genetic aspects; Genetic research; Genome, Bacterial; Genomes; Genomics; Genomics - methods; Lactic acid; Lactic acid bacteria; Lactococcin 972; Meat; Meat - microbiology; Meat fermentation; Meat products; Membrane fluidity; Metabolites; Microbiota; Microorganisms; Multigene Family; Peptides; Phylogeny; Quorum sensing; Secondary Metabolism - genetics; Secondary metabolites; Skin; Staphylococcus; Staphylococcus - genetics; Staphylococcus - metabolism; Staphylococcus shinii
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10490-0

Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated. The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms. Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.