Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.
Keywords: Antibiotic resistance ontology; Gut microbiota; Micropterus salmoides; Shotgun metagenomic analysis; Untargeted metabolomics.
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