In the past decade, significant advancements in high-throughput sequencing have greatly enhanced our understanding of the impact of microbial communities on various aspects, such as human health and the environment. These advancements have unveiled intricate relationships between bacteria and the host organism. Consequently, there has been a growing interest in uncovering the underlying processes that govern microbial diversity, stability, and evolution. The concept of Hologenomic evolution seeks to explain this relationship by exploring how the host organism coevolves in conjunction with microorganisms, by investigating how the host genome selects for beneficial microorganisms. However, environmental studies have demonstrated the immense impact viruses have on the microbial community ecology. In the marine environment, viruses infect 10^23 microbes every second, affecting biogeochemical cycles and shaping the microbial community composition and evolution through top-down control and impacting the genetic abilities through temperate infections. Acknowledging the influence from host-controlled environments and complex interactions with the microbiota, the role viruses play in shaping the microbiome within these environments is vastly unknown. Studies in humans have investigated patterns of viral community changes depending on disease states and viral dynamics through different life stages. In other metazoans, mainly the eukaryotic virus community has been studied, leaving significant knowledge gaps in understanding how phages interact and shape the host-associated microbiome in a host controlled environment. In this study, we aim to address this knowledge gap by using Atlantic salmon as a model organism. Atlantic salmon is a fascinating species, not only due to its importance in aquaculture or role as a keystone species in the wild, but also because salmonids have been found to have an intriguingly simple microbiome compared to terrestrial vertebrate microbiomes. In healthy and wild Salmonella, one genus of intracellular bacteria dominates their gastrointestinal tract, whereas sick or stressed fish have a diverse microbiome. This makes them ideal candidates to investigate how the viral community ecology is shaped in an organism that shows evidence of codivergence with its microbiome. We conducted a study to investigate the diverse viral community and its potential interactions with the host organism's microbiota. We utilized metagenomic and metaviromic datasets and employed bioinformatic tools to uncover the composition and diversity of the viruses present. Specifically, we examined distal gut samples from both farmed Norwegian Atlantic salmon with different phenotypes (sick or healthy) and wild adult Norwegian salmon. In a pilot study focused on these farmed salmon samples, we observed significant correlations between the viral population and the dysbiotic microbiome community in sick fish, while there was minimal correlation in the healthy microbiota. These findings enhance the mystery surrounding the role of the viral community in healthy and wild salmon.