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Here, we evaluated the utility and limitations of repurposing unmapped ddRADseq reads to examine pathogen\u2010associated and disease\u2010associated microbiome\u2010pathobiome patterns during scale drop disease (SDD) outbreaks in farmed barramundi (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Lates calcarifer<\/jats:italic>\n                    <\/jats:styled-content>\n                    ). Using fin clips ddRADseq datasets from 4593 barramundi across four commercial sea\u2010cages, 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\u2010associated signals; 76.3%\u201380.5%), frequently co\u2010occurrence with infectious spleen and kidney necrosis virus (ISKNV; 0%\u201313.4%), along with a marked microbial shift towards\n                    <jats:italic>Vibrio<\/jats:italic>\n                    \u2010dominated bacterial communities, particularly reads classified within the\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Vibrio harveyi<\/jats:italic>\n                    <\/jats:styled-content>\n                    clade. In contrast, clinically healthy post\u2010outbreak fish showed consistently low viral signals and were characterized by distinct, more diverse microbial profiles dominated by\n                    <jats:italic>Alphanudivirus<\/jats:italic>\n                    ,\n                    <jats:italic>Cyvirus<\/jats:italic>\n                    ,\n                    <jats:italic>Stenotrophomonas<\/jats:italic>\n                    and\n                    <jats:italic>Burkholderia<\/jats:italic>\n                    , 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\u2010associated signal (\n                    <jats:italic>h<\/jats:italic>\n                    <jats:sup>2<\/jats:sup>\n                    \u2009=\u20090.08), with higher cohort\u2010specific estimates (up to 0.23), consistent with strong environmental or co\u2010infection effects and complex co\u2010infection dynamics in open\u2010sea farming systems. While ddRADseq\u2010based pathogen detection is inherently biased by restriction\u2010enzyme site representation, host\u2010DNA dominance and the lack of absolute quantification, consistent patterns observed across thousands of fish tissues across multiple cohorts and outbreak stages provide biological meaningful population\u2010level insights into farm\u2010associated microbiome and pathobiome dynamics. Together, our results support that the use of unmapped ddRADseq reads as a cost\u2010effective, complementary tool for retrospective pathogen screening and hypothesis generation in aquaculture, alongside targeted surveillance and diagnostic approaches.\n                  <\/jats:p>","DOI":"10.1111\/jfd.70225","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T06:23:24Z","timestamp":1782282204000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Microbiome and Pathobiome Characterization in Farmed Barramundi (\n                    <i>Lates calcarifer<\/i>\n                    ) During and Post Scale Drop Disease Outbreaks"],"prefix":"10.1111","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0236-0221","authenticated-orcid":false,"given":"Nguyen Thanh","family":"Vu","sequence":"first","affiliation":[{"name":"Tropical Futures Institute James Cook University Singapore 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