Genomic Characterization and Biotechnological Potential of a Skatole-Degrading Bacillus pumilus Strain hhy901 Isolated from Bovine Manure

Abstract

Skatole (3-methylindole) is a primary malodorous compound emitted from livestock manure, posing significant challenges for odor control in intensive animal production. In this study, a skatole-degrading bacterial strain, designated hhy901, was isolated from fresh cattle manure and identified as Bacillus pumilus through polyphasic taxonomy, including 16S rRNA and gyrB gene phylogeny, morphological characterization, biochemical profiling, and whole-cell fatty acid analysis. Under an initial skatole concentration of 100 mg/L in Bacillus liquid medium, strain hhy901 removed 87.2% of skatole within 96 h, as determined by high-performance liquid chromatography (HPLC). Whole-genome sequencing revealed a genome of approximately 3.60 Mb with a GC content of 41.91%, encoding 3564 predicted protein-coding genes. Functional genomic annotation identified 39 genes associated with xenobiotic biodegradation and metabolism, including putative catechol dioxygenase, aldehyde dehydrogenase, and cytochrome P450 genes, which together suggest a potential skatole catabolic pathway. Furthermore, the genome harbored a broad repertoire of genes associated with resistance to heavy metals, disinfectants, and multiple antibiotic classes, indicating a potential for environmental stress adaptation. Virulence factor profiling predominantly identified genes related to nutrient acquisition and microbial competition, with only a single invasion-associated factor detected, suggesting a relatively low invasive pathogenic potential. However, the presence of multiple antimicrobial resistance determinants warrants cautious interpretation, and phenotypic validation of both degradation function and biosafety is required before environmental application. These results establish B. pumilus hhy901 as a promising microbial candidate for further development of bio-deodorization strategies in livestock production, pending functional and safety validation.