Global salmon aquaculture is facing a significant threat from pathogens that affect the health and welfare of fish. One of the most common pathogens in the industry is sea lice, and the primary control method is the use of pesticides. Current strategies for improving fish resistance include in-feed additives and genetic selection. However, the immune response to ectoparasites involves interplay with the host’s microbiota community during infestation. To develop sustainable strategies in fish aquaculture, it is essential to use the hologenomics approach to uncover the molecular interactions among the host, parasites, and their microbiome. This study aimed to report new sea lice vaccines using the hologenome approach. Here, we challenged Atlantic salmons against sea lice and analyzed them after different immunization strategies using inactivated and live vaccines delivered orally or intraperitoneally. The investigation obtained transcriptional information of skin tissue through RNA Illumina and nanopore sequencing. Additionally, we analyzed the skin’s microbiome through full-length 16S RNA nanopore sequencing and functional analysis. The hologenomics approach revealed that the microbiome of Atlantic salmon is a key component in the immune response to pathogens and a novel research field for developing novel fish vaccines.
Acknowledgments: This study was funded by FONDAP grant #1522A0004, FONDECYT #11220307.