Hatchery type influences the gill microbiome of Atlantic farmed salmon (Salmo salar) after transfer to sea

We showed hatchery system, loch, FT or RAS, significantly impacted the gill microbiome. On transfer to sea, the microbiomes changed and became more similar. After transfer, the individual sites to which the fish were transferred has a significant influence on microbiome composition, but interesting some clustering by hatchery system remained. Future gill disease mitigation methods that target enhancing the gill microbiome may be most effective in the freshwater stage, as there were more shared ASVs between water and gill at hatchery, compared to at sea.