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Background  Our previous comparative genomic analysis of  Staphylococcus equorum  KS1039 with five  S. equorum  strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cellular components and metabolic pathways involved in the degradation of macromolecules and development of sensory properties has not been obtained for  S. equorum . Therefore, in this study, we examined the general metabolism of  S. equorum  based on information obtained from published complete genome sequences of six  S. equorum  strains isolated from different niches. Additionally, the utility of strain KS1039 as a starter culture for high-salt food fermentations was examined.    Results  All six  S. equorum  strains contained genes involved in glycolysis, the tricarboxylic acid cycle, and amino acid metabolic pathways, as well as color development. Moreover, the strains had the potential to produce acetoin, butanediol, and branched chain fatty acids, all of which are important flavor compounds. None of the strains contained decarboxylase genes, which are required for histamine and tyramine production. Strain KS1039 contained bacteriocin and CRISPR/Cas gene clusters, and experimental results suggested that these genes were functional in vitro.    Conclusions  The comparative genomic analysis carried out herein provides important information on the usefulness of  S. equorum  KS1039 as a starter culture for the fermentation of high-salt foods in terms of safety, salt tolerance, bacteriocin production, and foreign plasmid restriction.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4532-1) contains supplementary material, which is available to authorized users.

Genomic insights into Staphylococcus equorum KS1039 as a potential starter culture for the fermentation of high-salt foods