The impact of florfenicol treatment on the microbial populations present in the gill, intestine, and skin of channel catfish (Ictalurus punctatus)

Abstract Background Florfenicol is a broad-spectrum antimicrobial approved in many countries for treating bacterial infections in production animals. Although florfenicol has been widely used in the US catfish industry, its impact on the native microbiota within catfish tissues remains largely unknown. Florfenicol treatment is followed by a mandatory withdrawal period to ensure drug residues fall below regulatory limits before harvest. This interval also allows for the potential recovery of the native microbiota. In particular, the skin and gill microbiota have often been overlooked in aquaculture microbiome research. Moreover, the dynamics of microbial communities and resistome profiles following drug withdrawal are still poorly understood, despite their ecological significance. Results A significant increase in intestinal microbial diversity was observed at the end of the withdrawal period. The highest alpha diversity (Shannon index) was observed in catfish intestines. This increase indicated the restoration of the normal microbiota in catfish intestine. The predominant bacterial phyla shared among catfish gill, intestine, and skin are Proteobacteria (62%), Bacteroidetes (18%), Actinobacteriota (12%), Firmicutes (3%), Patescibacteria (2%), and Verrucomicrobiota (1%). Florfenicol application can have lasting effects through the withdrawal period, particularly altering the intestinal microbial community. Conclusion The result of this study underscores the impact of florfenicol treatment on the bacterial landscape and antibiotic resistance in catfish, highlighting significant changes in microbial composition in the catfish intestine and at the end of the withdrawal period. These findings address the need for monitoring and managing antibiotic resistance in fish farming environments.