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

Anna K. Harding,

Célian Diblasi, Domniki Manousi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Abstract Aquaculture plays a key role in global food security, yet disease outbreaks remain major challenge. While host transcriptomic response have been widely studied, the of microbial community risk aquaculture remains understudied. Here, we conducted metatranscriptomic analysis gill microbiomes Atlantic salmon ( Salmo salar ) by repurposing publicly available RNA-seq data originally generated for transcriptomics. These poly(A)-selected datasets were collected prior to outbreak, allowing us examine functional patterns retrospectively. Taxonomic profiles Bracken and MATAM showed strong concordance across dominant genera, confirming that retain sufficient signal downstream classification. In addition tank-dependent variation, our presence-absence revealed survival-associated microbiome shifts. Several taxa, including Sedimentibacter , Fusarium Demequina more observed non-survived individuals, whereas Micrococcaceae, Pseudomonas, Burkholderiaceae enriched survivors. Functional gene distinct transcriptional responses within same taxa between survivors non-survivors, particularly metabolic adaptation, stress response, host-microbe interactions. results suggest host-derived datasets, though not designed analysis, offer new opportunities investigate early signals environmental factors associated with susceptibility aquaculture. Short Summary This study shows can be repurposed reveal changes shifts outcomes

Language: Английский

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

Anna K. Harding,

Célian Diblasi, Domniki Manousi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Abstract Aquaculture plays a key role in global food security, yet disease outbreaks remain major challenge. While host transcriptomic response have been widely studied, the of microbial community risk aquaculture remains understudied. Here, we conducted metatranscriptomic analysis gill microbiomes Atlantic salmon ( Salmo salar ) by repurposing publicly available RNA-seq data originally generated for transcriptomics. These poly(A)-selected datasets were collected prior to outbreak, allowing us examine functional patterns retrospectively. Taxonomic profiles Bracken and MATAM showed strong concordance across dominant genera, confirming that retain sufficient signal downstream classification. In addition tank-dependent variation, our presence-absence revealed survival-associated microbiome shifts. Several taxa, including Sedimentibacter , Fusarium Demequina more observed non-survived individuals, whereas Micrococcaceae, Pseudomonas, Burkholderiaceae enriched survivors. Functional gene distinct transcriptional responses within same taxa between survivors non-survivors, particularly metabolic adaptation, stress response, host-microbe interactions. results suggest host-derived datasets, though not designed analysis, offer new opportunities investigate early signals environmental factors associated with susceptibility aquaculture. Short Summary This study shows can be repurposed reveal changes shifts outcomes

Language: Английский

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