Standard metabolic rate (SMR) influences growth, behavior, and energy use in fish, yet its relationship with gut microbiota remains unclear. Here, we combined physiological measurements with 16S rRNA sequencing of foregut and hindgut tissue to test whether gut microbial communities differ with metabolic phenotype in juvenile Atlantic salmon. High-SMR fish showed greater growth efficiency and lower body water content than low-SMR fish, indicating higher fat levels. In contrast, microbial differences were most evident in the foregut, where low-SMR fish exhibited significantly higher alpha diversity. Microbial beta-diversity analyses revealed clear segregation among metabolic groups, and distance-based redundancy analysis showed that both SMR and body mass strongly explained variation in foregut microbial composition. Correlation analysis identified a negative association between SMR and members of the Rhodobacteraceae family, which were consistently more abundant in the foregut of low-SMR fish. Together, indicate that the metabolic phenotype is associated with distinct patterns of energy utilisation and gut microbiota composition, suggesting that foregut microbial communities may contribute to individual differences in metabolic strategy.

The development, progression, and dissemination of antimicrobial resistance (AMR) is determined by interlinked human, animal, and environmental drivers, posing severe risks to human health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. Besides antibiotic judicious use and implementation of antibiotic stewardship programs, mitigating antibiotic resistance spread requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistant plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture. Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors developed for the SalmoSim gut system. The model system was then inoculated with an Escherichia coli strain ATCC 25922 carrying plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L fish feed media for five days prior to a washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including to gram-negative and gram-positive taxa and, crucially, continuing transfer and persistence of the plasmid once florfenicol treatment had been withdrawn. Our findings highlight the role of commensal teleost gut flora as a reservoir for AMR, and our system provides a model to study how different treatment regimes and interventions may be deployed to mitigate AMR persistence.