Skin transcriptome and microbiome profiling are associated with Atlantic salmon resistance/susceptibility to sea lice infestation.

Salmon aquaculture is continually threatened by sea lice infestations, which impact fish health, welfare, and productivity. Thus, breeding programs enable the selection of phenotypes to improve productive performance. This study uses a controlled, repeated lice infestation model to analyze the skin transcriptome and microbiome of Atlantic salmon concerning their resistance or susceptibility to sea lice infestation. The transcriptomic profile of skin from three phenotypes-resistant (R), susceptible (S), and one salmon family presumably associated with acquired resistance to sea lice (ALR)-was analyzed through RNA sequencing. Additionally, full-length 16S rRNA sequencing with Oxford Nanopore was utilized to characterize the skin microbiota of each phenotype. Transcriptome data were mapped to the Atlantic salmon genome, and the chromosome genome expression (CGE) index was applied, revealing differences in chromosome modulation among the phenotypes. Interestingly, among the chromosomes with significant differences among the three phenotypes, Gene Ontology (GO) terms associated with heme binding, ion binding, extracellular region, and collagen trimmer were identified. Additionally, the R and ALR families demonstrated up-regulation of immune genes in comparison to the S family. Notably, beta diversity analysis revealed significant differences among the bacteria associated with each salmon phenotype. After the third infestation, the S, R, and ALR phenotypes displayed a high abundance of Gammaproteobacteria, Enterobacteriaceae, and Flavobacteriaceae, respectively. This study indicates that Atlantic salmon's resistance to sea lice is linked not only to family genotype but also to their microbiome signatures. Overall, there is molecular evidence that after repeated lice infestations, certain fish families develop the resistant phenotype during sea lice infections.