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, including Sedimentibacter , Fusarium , and Demequina were more observed in non-survived individuals, whereas Micrococcaceae, Pseudomonas, and Burkholderiaceae were 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.