Genomic Characterization of Four Novel Probiotic Strains with Enzymatic Activity and Their Effects on Carp (Cyprinus...

The shift toward plant-based feeds in aquaculture necessitates a search for probiotics to improve the digestibility of such feeds and fish growth. This study characterizes four Bacillus strains for their probiotic potential in carp (Cyprinus carpio). Strains isolated from river sediments underwent in vitro screening for proteolytic/amylolytic activity, antibiotic sensitivity, and biofilm formation. Whole-genome sequencing was performed and functional annotation identified probiotic-related genes. All strains were identified as Bacillus velezensis and harbored genes providing thermal, osmotic, and oxidative stress resistance, alongside enzymes and bioactive metabolite synthesis pathways. Two non-antagonistic strain pairs were solid-phase cultivated on soybeans and incorporated into carp feed (0.1% w/w) for a 76-day trial, and growth metrics and gene expression were analyzed in juvenile fish. Group 1 (strains MT14 + MT42) exhibited a 40.75% higher biomass increase than the control group while Group 2 (strains MT141 + MT142) exhibited a 56.62% higher biomass growth. No significant gene expression changes occurred in juveniles, though MT141 + MT142 transiently modulated fry expression profiles. Therefore, these Bacillus velezensis strains synergistically enhance growth in carp that are fed plant-rich diets, highlighting their viability as aquaculture probiotics.