Metagenomic analysis of microbial composition and antibiotic resistance gene associations in Duroc × Landrace × Yorkshire pigs’ intestinal microbiota across different growth stages

Background With the rapid development of intensive pig farming and widespread antibiotic use, intestinal microbial communities and antibiotic resistance genes (ARGs) in pigs have attracted increasing attention due to their relevance to animal health and environmental safety. Characterizing stage-associated differences in gut microbiota and ARG profiles is essential for understanding the potential environmental loading of ARGs from livestock feces and for informing evidence-based management strategies in commercial pig production. Methods This study investigated Duroc × Landrace × Yorkshire (DLY) crossbred pigs at different growth stages from intensive farms, including piglet group (n=13), finishing pig group (n=19), and sow group (n=7). Fecal samples were collected and analyzed using metagenomic sequencing combined with bioinformatics approaches to examine the structure, function, and host attribution of intestinal microbial composition and resistance genes across growth stages. Results Finishing pigs exhibited significantly higher gene counts and species richness compared to piglets and sows ( P < 0.05). Firmicutes and Bacteroidetes were the dominant phyla in the piglet and finishing pig groups, respectively, while the sow group showed significantly increased Proteobacteria and decreased Bacteroidetes abundance ( P < 0.05). Beta diversity analysis confirmed statistically significant structural differentiation among groups (PERMANOVA, Adonis R² = 0.165, P = 0.008). ARGs exhibited the highest abundance in the finishing pig group, with tetQ and tetO as the predominant resistance genes in the piglet and finishing pig groups, respectively, and tetO abundance was significantly higher than in other groups ( P < 0.05). ARGs were primarily attributed to Firmicutes , Bacteroidetes , and Proteobacteria , with Prevotella representing a major annotated genus among ARG-associated sequences. Correlation analysis revealed positive associations between most ARGs ( tetQ , sul1 , and floR ) and Proteobacteria and Bacteroidetes taxa, while the tetL resistance gene showed a highly specific positive correlation with Streptococcus , showing a specific positive correlation ( P < 0.001), suggesting putative taxon-ARG associations between different resistance genes and specific microbial taxa. Conclusions This cross-sectional study characterized the composition and co-abundance associations between fecal microbiota and ARGs in DLY pigs at three representative production stages, providing baseline data for understanding stage-specific fecal ARG output and informing targeted management strategies to reduce environmental ARG dissemination from intensive pig operations.