Microbiome and Pathobiome Characterization in Farmed Barramundi (Lates calcarifer) During and Post Scale Drop Disease Outbreaks.

Large-scale double-digest RAD sequencing (ddRADseq) datasets generated for genotyping are increasingly available in aquaculture, yet their unmapped reads remain largely unexplored for pathogen surveillance. Here, we evaluated the utility and limitations of repurposing unmapped ddRADseq reads to examine pathogen-associated and disease-associated microbiome-pathobiome patterns during scale drop disease (SDD) outbreaks in farmed barramundi (Lates calcarifer). Using fin clips ddRADseq datasets from 4593 barramundi across four commercial sea-cages, we profiled bacterial and viral communities by taxonomic classification of unmapped reads. Fish sampled during active outbreaks consistently exhibited strong enrichment of scale drop disease virus (SDDV-associated signals; 76.3%-80.5%), frequently co-occurrence with infectious spleen and kidney necrosis virus (ISKNV; 0%-13.4%), along with a marked microbial shift towards Vibrio-dominated bacterial communities, particularly reads classified within the Vibrio harveyi clade. In contrast, clinically healthy post-outbreak fish showed consistently low viral signals and were characterized by distinct, more diverse microbial profiles dominated by Alphanudivirus, Cyvirus, Stenotrophomonas and Burkholderia, indicating a comparatively stable microbiome state in the absence of active disease outbreaks. Treating normalized pathogen read counts as proxy traits, exploratory quantitative genetic analyses indicated low overall heritability estimates for SDDV-associated signal (h