Shotgun metagenomic analysis of water samples in Atlantic salmon farming
In this study, we evaluated the suitability of a field-based filtration methodology of water for capturing a range of pathogens (viruses, bacteria, and parasites) by following a single Atlantic salmon cohort from hatchery through offshore aquaculture facilities until slaughter. Additionally, shotgun metagenomic sequencing (Oxford Nanopore Technologies) was performed for microbiome analysis and to correlate microbial community dynamics with production cycle events. The purpose of this approach is intended for pathogen surveillance in water to support aquaculture companies in implementing preventive biosecurity measures when persistent pathogen presence at high concentrations is detected or when significant shifts in the microbial community indicate potential dysbiosis.