The research on the identification, taxonomy, and comparative genomics analysis of nine Bacillus velezensis strains significantly contributes to microbiology, genetics, bioinformatics, and biotechnology

Two strains, BAC144 and BAC1273, exhibited high similarity to <i>B. amyloliquefaciens subsp. plantarum</i> FZB42. However, the latter strain was subsequently reclassified as <i>B. velezensis</i>. The division pattern observed during identification was confirmed in the phylogenomic analysis, where BAC144 and BAC1273 clustered with <i>Bacillus amyloliquefaciens subsp. plantarum</i>, while the other strains clustered with <i>B. velezensis</i> NRRL B-41580, forming a clade with high genetic similarity, with a bootstrap value of 100%. Furthermore, a synteny analysis demonstrated greater conservation among the strains from this study compared to the reference strain, with the formation of distinct collinear groups. The pangenome analysis revealed an open pangenome, highlighting the genetic diversity within the species. Based on this analysis, a functional annotation was performed to compare exclusive gene repertoires across groups, uncovering distinct adaptations and functional profiles. The identification of bacterial strains belonging to this species is of great importance due to their high applicability. The strains identified in this study underscore the need for more robust taxonomic technologies to accurately classify prokaryotes, which are subject to constant evolutionary changes, requiring the reclassification of several species within the genus Bacillus, many of which are heterotypic synonyms of <i>B. velezensis</i> like <i>Bacillus oryzicola, B. amyloliquefaciens subsp. plantarum</i> and <i>Bacillus methylotrophicus</i>.