Metatranscriptomic Insights into Microbial Dynamics Prior to Disease Onset in Atlantic Salmon Aquaculture

Aquaculture plays a key role in global food security, yet disease outbreaks remain a major challenge. While host transcriptomic response have been widely studied, the role of microbial community in disease risk in aquaculture remains understudied. Here, we conducted a metatranscriptomic analysis of gill microbiomes in Atlantic salmon (Salmo salar) by repurposing publicly available RNA-seq data originally generated for host transcriptomics. These poly(A)-selected RNA-seq datasets were collected prior to a disease outbreak, allowing us to examine functional microbial patterns retrospectively.

Taxonomic profiles generated by Bracken and MATAM showed strong concordance across dominant genera, confirming that host RNA-seq datasets retain sufficient microbial signal for downstream classification. In addition to tank-dependent microbial variation, our presence-absence analysis revealed survival-associated microbiome shifts. Several taxa, includingSedimentibacter,Fusarium, andDemequinawere more observed in non-survived individuals, whereasMicrococcaceae, Pseudomonas, and Burkholderiaceaewere enriched in survivors. were enriched in survivors. Functional gene analysis revealed distinct transcriptional responses within the same microbial taxa between survivors and non-survivors, particularly in metabolic adaptation, stress response, and host-microbe interactions. These results suggest that host-derived RNA-seq datasets, though not originally designed for microbial analysis, offer new opportunities to investigate early microbial signals and environmental factors associated with disease susceptibility in aquaculture.