Whole-genome sequencing and comparative genomic analysis of a novel Bacillus subtilis strain YE16 isolated from yak dung
Year: 2026
Type: article
Abstract: 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.
Source: Scientific Reports
Authors: Dixita Chettri, Anil Kumar Verma
Institution: Sikkim University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,690
Funder: University Grants Commission
Award: G5548239280
OpenAlex ID: W7166593152