A Bacillus Phage From Bangladeshi Soil, Phage APU1: Genomic Characterisation and Comparative Genomic Analysis

Abstract

Bacillus species are environmentally resilient bacteria associated with soil, food, industrial settings and opportunistic infections, yet their bacteriophages remain incompletely characterised, particularly from underexplored environmental sources. We isolated and characterised phage APU1, a dsDNA phage from agricultural soil in Bangladesh. Partial 16S rRNA gene sequencing identified the enrichment host conservatively as Bacillus sp. APU1 has a 153,847 bp genome that encodes 236 predicted proteins, including 84 shorter than 100 amino acids. CheckV classified the genome as high-quality, with an estimated completeness of 99.91% and no detectable host-gene contamination. Functional annotation identified genes associated with DNA replication, structural assembly, packaging and host lysis. PhaBOX classified APU1 as virulent, with PhaTYP and CHERRY prediction scores of 1.0. CARD/VFDB screening did not detect CARD-listed antimicrobial resistance genes or VFDB-listed virulence factor genes. Comparative genomic analyses using VICTOR, VIRIDIC and VIPTree placed APU1 within a group of related Bacillus phages. APU1 shared 89.7%–89.8% intergenomic similarity with its closest relatives, supporting its classification as a genomically distinct phage within this group. This study expands the genomic catalogue of Bacillus-associated phages from Bangladeshi soil and provides a foundation for future studies on phage diversity, host range, morphology and biological properties.