Microbiome Collapse in the Ornamental Fish Trade: A Hidden Driver of Post-Purchase Mortality

Prophylactic antibiotic use in high-density ornamental aquaculture aims to mitigate infections, yet it is hypothesized to induce severe gut microbiome dysbiosis, contributing to high post-purchase mortality of goldfish purchased from retail stores by end consumers. This study utilized 16S rRNA gene amplicon sequencing, a rapid and high-resolution tool to characterize gut bacterial communities in six goldfish (Carassius auratus) sourced from antibiotic-intensive retail market in Hong Kong SAR, China. Diversity metrics were compared to unexposed reference controls and experimentally antibiotic-exposed cyprinid groups from published datasets. Market-sourced goldfish showed a profound collapse in alpha diversity (mean Shannon index 0.107 ± 0.141), far lower than controls (typically 2.0–4.5) and experimental groups (1.06–4.34). The microbiota exhibited extreme oligodominance by Cetobacterium and Vibrio, with near-total loss of beneficial commensal taxa. Principal coordinates analysis (PCoA) revealed distinct clustering, indicating fundamental and likely irreversible microbial restructuring. These findings show that chronic antibiotic exposure in ornamental supply chains induces a depauperate microbiome state, compromising host resilience and physiological homeostasis during environmental transitions. This dysbiosis provides a microbiological explanation for widespread post-purchase die-off, highlighting a major animal welfare and biosecurity concern. High-throughput sequencing offers quick, in-depth microbiome health assessment, essential for developing interventions to improve husbandry and reduce antimicrobial reliance in the global ornamental fish trade.