In aquaculture, the secretions of cultured organisms contribute to the development of aquatic antibiotic resistance. However, the impacts of antibiotic treatment on fish feces remain poorly understood. This study aimed to assess the changes and restoration of the fecal microbiome in rainbow trout (Oncorhynchus mykiss) upon antibiotic treatment. Fish were orally administered diets supplemented with oxytetracycline (OTC) or sulfadiazine/trimethoprim (SDZ/TMP) for 10 consecutive days, followed by a 25-day withdrawal period. Fecal samples were collected before antibiotic treatment (day 0), and at 1, 3, 7, and 10 days post antibiotic administration (dpa), as well as 1, 3, 7, 14, and 25 days post antibiotic cessation (dpc). The fecal microbiome community was profiled using both culture-dependent and -independent methods. The relative abundance of antibiotic resistance genes (ARGs) and the class 1 integron-integrase gene (intI1) in the feces were quantified using real-time PCR. The result showed that antibiotic treatment disrupted the fecal microbial communities, and this alteration persisted even after antibiotic cessation. Moreover, OTC treatment increased the relative abundance of tet genes, while sul and dfrA genes increased in the SDZ/TMP-treated group. Notably, Flavobacterium, Pseudomonas, and Streptococcus exhibited a significant correlation with the abundance of ARGs, suggesting their potential role as carriers for ARGs. In conclusion, this study demonstrates the impact of antibiotic selection pressure on the fecal microbiome and the increase of ARGs in rainbow trout feces. These findings suggest that fish feces provide a non-invasive approach to predict changes in the fish gut microbiome and resistome.
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