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Genomic sequencing of vineyard-isolated Bacillus strains and comparison with closely related Bacillus species reveals a putative new lineage; distinct pan-genome architecture and secondary metabolism potential
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DOI：10.3389/fmicb.2026.1871298.png)
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Abstract
En 中文
IntroductionBacillus species are ubiquitous in nature; and they display diverse traits of biotechnological importance; including the production of various enzymes and secondary metabolites. In this study; we profiled the genomes of vineyard-derived Bacillus strains shown to inhibit Botrytis cinerea mycelial growth and spore germination through the production of cyclic lipopeptides and cell wall-degrading enzymes.MethodologyLong-reads-whole genome sequencing was conducted using PacBio Sequel II Single-Molecule Real-Time platform; followed by genome assembly; phylogenetic analysis and functional annotation using different bioinformatics pipelines.ResultsThe strains possess ~3.900; 000 bp genome size and %GC ranging between 45%–46.7%; as expected in Bacillus species. Phylogenetic analysis separated the vineyard-derived strains into two lineages. Strains B4003 and B4005 grouped with B. velezensis. Notably; three Bacillus strains (B4022; B4001; and B4023) clustered with the undescribed strains with placeholders “sp018613535”; an undescribed taxon in the genome taxonomy database; supported by the Average Nucleotide Identity (ANI) score above 96%. Putative biosynthetic gene clusters (BGCs) involved in secondary metabolite production were identified by AntiSMASH analysis among the isolates. Orthologous cluster analysis further identified 3203 genes conserved across all strains; constituting a stable core genome that supports essential cellular and metabolic functions. Comparative pan-genome analysis of the Bacillus velezensis and Bacillus spp. revealed clear species-level differentiation alongside a conserved functional backbone. Furthermore; functional annotation revealed strain-specific enrichment in metabolic and environmental response pathways; emphasizing the ecological specialization and adaptive diversification.DiscussionOverall; these findings emphasize the dynamic interplay between genomic conservation and flexibility within the Bacillus genus and support the biological control potential of these strains. Furthermore; genomic evidence strongly indicates that B4001; B4022 and B4023; represent members of a putatively novel species.
Keywords:
whole genome sequencing
secondary metabolites
biocontrol
Bacillus spp.
bunch rot
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