Temporal dynamics of the gut microbiome during smoltification in Atlantic salmon (Salmo salar)

Smoltification enables seawater adaptation in Atlantic salmon, yet gut microbiome temporal dynamics remain poorly understood. Gut communities from n = 162 fish across smoltification were profiled by 16S rRNA sequencing (DADA2/Phyloseq). Alpha diversity varied significantly among weeks; beta diversity (Bray–Curtis PERMANOVA) showed temporal differentiation consistent with ecological succession. Bacillota and Pseudomonadota may serve as indicators of seawater adaptation. Microbiome composition is a complex quantitative trait shaped by development and environment, with implications for salmon health at sea.