Isolation, Genomic Taxonomy, and Genome Characterization of Streptomyces fradiae SS162, Which has Antibacterial Activity Against Vibrio parahaemolyticus

Abstract

Biocontrol of Vibrio parahaemolyticus, a pathogen responsible for acute hepatopancreatic necrosis disease (AHPND) in shrimp, has gained attention as an alternative to antibiotics in aquaculture. In this study, a bacterial strain isolated from a coral sample was preliminarily identified as Streptomyces sp. SS162 through 16S rRNA analysis exhibiting potent antibacterial activity with a high selectivity index against V. parahaemolyticus. This activity remained stable under high temperatures, various pH conditions, UV exposure, and proteinase K treatment. Furthermore, SS162 effectively inhibited biofilm formation by V. parahaemolyticus. Strain SS162 maintained the antibacterial activity over ten consecutive generations. For genomic taxonomy and characterization, a high-quality draft genome of 6,778,597 bp for the SS162 strain was obtained using next-generation sequencing with Nanopore technology. This genome had a GC content of 74.5% and contained 5,761 protein-coding genes. The genome of Streptomyces sp. SS162 possessed 23 subsystems belonging to 24 categories revealed by the RAST system. Comparative genomic analysis using Orthovenn3 indicated that SS162 shared the highest number of gene clusters with Streptomyces fradiae ATCC 10475. The genome phylogeny and relatedness analyses suggested that Streptomyces sp. SS162 was a strain within the Streptomyces fradiae species. Importantly, AntiSMASH analysis identified 28 biosynthetic gene clusters (BGCs), many of which were predicted to produce novel secondary metabolites. The remarkable in vitro activity against V. parahaemolyticus prompted further studies employing S. fradiae SS162 for AHPND management, whereas its taxonomic characterization and BGC identification confirmed the identity and uncovered the biotechnological potential in this strain.