Amoebic Gill Disease ( <scp>AGD</scp> ) in Atlantic Salmon Investigated Through a Holo‐Omic Lens

Interactions between host genetics and the resident microbiota are complex. Understanding these interactions offers interesting alternatives for addressing gill health and disease resistance in salmonids. Amoebic gill disease (AGD), caused by <i>Neoparamoeba perurans</i>, remains a threat to Atlantic salmon, particularly in aquaculture where prevention and treatment options are scant. Selective breeding or genetic engineering towards AGD resilience presents viable prevention strategies. While several studies have addressed AGD resistance in Atlantic salmon using transcriptomic and quantitative genetic approaches, the influence of the gill microbiota as a genotypic encoded phenotype for AGD resilience remains underexplored. Addressing this, we leveraged a holo-omic approach using 16S rRNA profiling and quantitative genetics, treating the microbiota as an extended resistance trait. In this small-scale exploratory work, we investigated the microbiota of AGD-challenged Atlantic salmon in terms of two common resistance indicator traits: gill score and amoebic load. We then performed a GWAS using the traditional indicator traits and traits of the microbiota. We found that the gill microbiota of the AGD-affected salmon was dominated by two bacterial families, <i>Simkaniaceae</i> and <i>Arcobacteraceae</i>. Additionally microbial diversity and the relative abundance of <i>Simkaniaceae</i>, potentially derived from the amoeba, showed moderate variation with indicator traits. We identified several genomic regions that showed suggestive association with gill score and traits of the microbiota, and explored genes in these regions in relation to AGD resistance. Although the underlying mechanisms shaping gill microbiota dynamics in gill disease remain unknown, this study highlights the potential of addressing AGD through an integrative approach that considers the interplay between host genetics, the microbiota, and their roles in disease resistance.