Gut microbial dysbiosis in antibiotic treated Mystus cavasius using a combined culture-dependent and shotgun metagenomic approach

Antibiotics in aquaculture feed disrupt the gut microbiome, promote antibiotic resistance, and pose risks to fish, nontarget organisms, and human health. This study investigated gut microbial dysbiosis in oxytetracycline-treated Mystus cavasius using a combined culture-dependent and shotgun metagenomic approach. Culture-dependent enumeration revealed a significant 2–3-fold reduction in total viable bacterial count (TVBC) in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic analysis revealed a clear shift in the gut microbiota, characterized by a decline in Proteobacteria and Bacteroidetes, an increase in Firmicutes, and the enrichment of antibiotic-tolerant taxa. Metagenomic profiling identified over 1,400 bacterial species, with notable taxonomic shifts: the control groups were enriched in beneficial genera (Lactiplantibacillus, Arthrospira), whereas the treated fish were dominated by opportunistic or resistant taxa (Plesiomonas, Staphylococcus, Acinetobacter). The more even alpha diversity indices in treated samples indicated a restructuring of the microbial hierarchy after OTC exposure, while beta diversity analysis revealed moderate separation between control and treated groups. Collectively, these findings demonstrate that OTC exposure induces gut microbial dysbiosis characterized by a decreased bacterial load, altered community composition, increased antibiotic resistance, and increased evenness. This study represents the health implications of antibiotic use in freshwater aquaculture and provides foundational insights for microbiome-informed management of M. cavasius.