Metagenomic characterization of microbial communities and antimicrobial resistance in Bulgarian aquaculture systems
This project investigates microbial communities in freshwater aquaculture systems, with a primary focus on flow-through fish farms in which surface water is diverted into interconnected cascade-style basins and subsequently discharged back into the receiving water body. The sampling design therefore emphasizes paired inlet and outlet water samples in order to characterize the microbial and functional profiles associated with water entering and leaving these aquaculture facilities. Shotgun metagenomic sequencing is combined with taxonomic profiling, metagenomic assembly, recovery of metagenome-assembled genomes (MAGs), and phylogenomic analyses to describe the microbial diversity and the genomic composition. Recovered genomes and metagenomic datasets are further examined for antimicrobial resistance genes, virulence-associated genes, plasmids, and other mobile genetic elements. The dataset also includes two samples representing additional aquaculture-associated contexts outside the predominant flow-through farm design.