# Amoebic Gill Disease (AGD) in Atlantic Salmon Investigated Through a Holo‐Omic Lens

## TL;DR

This study explores how Atlantic salmon's gill microbiota and genetics interact to influence resistance to amoebic gill disease, using a combined genetic and microbial approach.

## Contribution

The study introduces the gill microbiota as an extended resistance trait in AGD research, integrating 16S rRNA profiling with quantitative genetics.

## Key findings

- The gill microbiota of AGD-affected salmon is dominated by Simkaniaceae and Arcobacteraceae.
- Microbial diversity and Simkaniaceae abundance show moderate associations with resistance indicators like gill score and amoebic load.
- Genome-wide associations suggest several genomic regions linked to resistance traits and microbiota characteristics.

## Abstract

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 Neoparamoeba perurans, 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, Simkaniaceae and Arcobacteraceae. Additionally microbial diversity and the relative abundance of Simkaniaceae, 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.

In this exploratory study, we integrated 16S rRNA profiling with quantitative genetics to examine the gill microbiota of Atlantic salmon during infection with Neoparamoeba perurans, the causative agent of amoebic gill disease (AGD), treating the microbiota as an extended resistance trait. Microbial communities were dominated by Simkaniaceae and Arcobacteraceae, and microbial diversity and the relative abundance of key taxa showed moderate associations with resistance indicators, gill score and amoebic load. Genome‐wide association analyses using both disease traits and microbial traits indicated several genomic regions with suggestive associations, providing a preliminary basis for the future implementation of microbiota data in AGD resistance studies.