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Over 90% of juvenile salmon migrating from freshwater into the ocean will die before returning to freshwater to spawn. Although mortality is believed to be highest during the first few months in the marine environment, the relative importance of infectious and non-infectious causes remains largely unknown. Current knowledge of infectious diseases in salmon is derived almost exclusively from observations of cultured fish (both enhancement and commercial). Consequently, we have a fair understanding of pathogens and clinical disease impacting salmon in freshwater hatcheries and sea-water net pens, but a much poorer understanding of pathogens affecting wild Pacific salmon in the ocean. Motivated by the need to fill this gap and the recognition that novel genomic approaches may provide a depth of resolution not previously available, the DFO Molecular Genetics Laboratory developed a 4-phase project with the Pacific Salmon Foundation and Genome British Columbia to describe the microbes (defined as viral, bacterial, fungal and protozoan micro-organisms) in British Columbia (BC) salmon, and identify those that may influence productivity and performance of BC’s wild, hatchery and farmed salmon populations. The Project focuses principally on microbes that are recognized globally to cause clinical disease (or related to opportunistic infections of immune compromised fish) in salmonids, and utilizes genomic methods to identify and verify which microbes are presently detectable in wild and cultured (federal hatcheries and salmon farms) fishes in BC, Canada. Later phases of the project will develop challenge studies on top ranking …