Integrated 16S rRNA and Metagenomic Sequencing Reveals the Distribution of Key Antibiotic Resistance Genes in Duck Gut Microbiota

The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.