Mucosal immunity and microbiota change in the rainbow trout (Oncorhynchus mykiss) gills after being challenged with infectious hematopoietic necrosis virus

Nanopore‐Enabled Microbiome Analysis: Investigating Environmental and Host‐Associated Samples in Rainbow Trout Aquaculture

“…In particular, the opportunity to monitor a large number of microbes at the same time is naturally appealing in agriculture and the food production chain, and as expected, the fish farming industry has recently joined in the collective interest towards microbiome investigation as well (Llewellyn et al., 2014). In fact, shifts in the host and/or surrounding environment microbial communities’ compositions have been related to exposure of fish to antibiotics (Almeida et al., 2021) or experimental phage therapy (Donati et al., 2022), pollutants (Bellec et al., 2022; Hano et al., 2021), diet variations (Serra et al., 2021) and prebiotics administration (Menanteau‐Ledouble et al., 2022), hypoxia conditions (Gatesoupe et al., 2016), early‐life stress (Uren Webster et al., 2021), and to deteriorating health status (Bozzi et al., 2021; Brown et al., 2021; Tongsri et al., 2023; Vasemägi et al., 2017), with compelling possibilities for disease prevention, management, and informed decision making in the fish farm industries. The vast majority of the current literature on the subject was generated based on short reads (Illumina sequencing platform) up to 600 bp.…”