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

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Protocol publication

[…] For comparative genomic analysis of the genome of KS1039 (GenBank accession number CP013114.1), the complete genome sequences of S. equorum KM1031 (NZ_CP013980.1), S. equorum C2014 (NZ_CP013714.1), S. equorum subsp. equorum Mu2 (CAJL00000000.1), S. equorum UMC-CNS-924 (AVBD00000000.1), and S. equorum G8HB1 (LAKE00000000.1) were obtained from the NCBI Microbial Genomes database. The average nucleotide identities of the conserved genes among the genomes were identified using the Basic Local Alignment Search Tool (BLAST), and the data was used for comparative analysis []. Genome sequences of the S. equorum species involved in this study were uploaded to the Rapid Annotations using Subsystems Technology (RAST) server for SEED-based automated annotation, whole-genome sequence-based comparative analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis []. Efficient Database framework for comparative Genome Analyses using BLAST score Ratios (EDGAR) was used for core genome, pan genome, and singleton analysis using S. equorum KS1039 as the reference genome []. Further comparative analyses were performed for specific regions and genes-of-interest using the BLASTN, BLASTX, and BLASTP tools. […]

Pipeline specifications

Software tools BLASTN, RAST, BLASTX, BLASTP
Databases KEGG
Application Phylogenetics
Organisms Staphylococcus equorum
Chemicals Acetoin, Amino Acids, Fatty Acids, Histamine, Tyramine