Abstract

The microbiota plays functional roles in almost all living organisms, influencing metabolism, defense, and nutrition. Conventionally, parasitism is defined as a bipartite interaction between host and parasites, where both organisms display molecular responses mainly associated with the immune system. However, the microbial community is another relevant factor that can interact during the parasite infection in fish farming. Therefore, this study aimed to characterize the Atlantic salmon microbiota's dynamics, correlation, and functional potential in skin and gut tissues during the sea louse Caligus rogercresseyi parasitism. The findings showed that the parasitism reduced the alpha and beta diversity in infested salmon's microbiota. This reduction favored the tissuespecific occurrence of opportunistic bacterial pathogens. Notably, Photobacterium was identified primarily on the skin, and Vibrio was predominant in the gut microbiota of infested individuals. Cluster analysis of full-length 16S rRNA sequencing suggested that C. rogercresseyi could be a vector for transmitting Tenacibaculum and Vibrio species. Network analysis evidenced that parasitism also perturbs the correlation of the skin and gut microbiota, revealing fewer associations in infested individuals. Finally, a contrasting effect on the functional potential of the skin and gut microbiome was found. Herein, the parasitism increased the biosynthetic processes and reduced degradation pathways in the skin; meanwhile, the opposite trend was observed in the gut microbiome. Overall, our results evidenced that sea lice parasitism induces tissue-specific functional dysbiosis and provides novel evidence about the harmful effects of sea lice in salmon aquaculture.