Genome sequencing of Bacillus daqingensis and Alkalicoccus luteus reveals taxonomic insights and adaptive mechanisms

This study presents the genome sequencing of Bacillus daqingensis X10-1T and Alkalicoccus luteus KCTC 33100T, and provides a comprehensive assessment of the taxonomic status, metabolic capabilities, and adaptive features of members within the genus Alkalicoccus. Functional genome analysis revealed that Bacillus daqingensis and other Alkalicoccus species possess genes for both ‘salt-in’ and ‘salt-out’ strategies, indicating robust mechanisms for osmotic regulation under saline conditions. Phylogenetic, phylogenomic, 16S rRNA gene sequence, and orthologous gene clustering (using OrthoVenn3) analyses demonstrated a close relationship between Bacillus daqingensis X10-1T and Alkalicoccus luteus KCTC 33100T. Notably, average amino acid identity values between these strains exceed the genus-level cutoff, while the average nucleotide identity value surpasses the accepted threshold for species delineation. Based on these integrative genomic and phylogenetic findings, we propose the reclassification of Bacillus daqingensis Wang et al. 2023 as Alkalicoccus daqingensis comb. nov., and further Bacillus daqingensis Wang et al. 2023 and Alkalicoccus daqingensis should be considered later heterotypic synonyms of Bacillus luteus Subhash et al. in IJSEM 64:1580–1586, 2014 and Alkalicoccus luteus (Subhash et al. 2014 and Alkalicoccus luteus (Subhash et al. 2014) Gupta et al. 2020.