Genomic Analysis and Metabolite Profiling of Three Probiotic Bacillus Strains for Potential Application in Aquaculture.

In this study, we investigated the genomic characteristics and bioactive metabolite profiles of three novel Bacillus strains that were isolated from the intestinal tracts of healthy carp (Cyprinus carpio). Strain identification and whole-genome sequencing were performed before analysis. Among the three novel strains, R1 and R4 were classified as Bacillus subtilis, and strain R5 was classified as Bacillus velezensis. Genome mining revealed a repertoire of secondary metabolites, including bacillaene, bacillibactin, bacilysin, difficidin, and fengycin, which likely contribute to the probiotic potential of these strains. The metabolite profiles were further characterized using matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry, with fengycins and bacillibactin specifically isolated and identified. Additionally, the presence of genetic markers associated with antimicrobial resistance was assessed, and these gene profiles were reconstructed. These Bacillus strains represent promising candidates for the development of novel feed additives for aquaculture.