Whole-genome sequencing and comparative genomic analysis of a novel Bacillus subtilis strain YE16 isolated from yak dung

In this study, genomic and functional characterization of the previously identified lignocellulolytic Bacillus sp. strain YE16 from an underrepresented ecological niche (yak dung) in the Sikkim Himalayas was performed-thus making it the first report of such a study of a strain from this region. Whole genome sequencing resolved the ambiguity regarding its taxonomic placement where it showed 98.63% ANI and 89.4% dDDH with the reference genome Bacillus subtilis subsp. subtilis 168, definitively assigning YE16 to B. subtilis. This was further confirmed by core-pangenome SNP based phylogenetic analysis, where the YE16 strain forms a separate branch on the phylogenetic tree, with a core-genome SNP distance of 33,807 relative to strain 168, indicating substantial strain-level genomic differentiation. YE16 encodes 43 strain specific genes with nutrient transportation, metabolism and defense mechanisms as the primary functional groups. The isolate possessed a total of 95 GHs, 83 GTs, 38 CBMs, consistent with the previously demonstrated lignocellulolytic phenotype. 18 biosynthetic gene clusters were identified with expanded lipopeptide-related NRPS clusters, of which 4 showed low similarity (< 50%). A single intact prophage related to Brevibacillus phage Osiris was also detected, augmenting its genomic variability. Preliminary biosafety assessment identified no major virulence-associated determinants or evidence of acquired multidrug resistance within the scope of the study. Based on its distinct phylogenetic position, strain-specific gene content, diverse CAZyme and Biosynthetic Gene Cluster (BGC) repertoires, and isolation from an underrepresented niche, YE16 represents a genomically distinct strain of Bacillus subtilis.