Comparative Profiling of Antibiotic Resistance Genes and Microbial Communities in Pig and Cow Dung from Rural China:...

Antibiotic resistance genes (ARGs) and microbial communities in pig and cow dung from rural China were systematically profiled using high-throughput quantitative PCR arrays and 16S rDNA amplicon sequencing to assess their environmental dissemination and public health risks. The abundance and diversity of ARGs were markedly higher in pig dung than in cow dung. A total of 56 ARGs were enriched in pig dung, including β-lactamase genes (blaCMY, blaCTX-M) and macrolide resistance genes (ermB, ermF), along with several genes related to aminoglycoside and macrolide-lincosamide-streptogramin B resistance. In contrast, only eight ARGs were enriched in cow dung. Microbial community analysis revealed that cow dung was dominated by UCG-005, UCG-010, Methanocorpusculum, and Fibrobacter, taxa typically associated with ruminant digestion. In pig dung, Ignatzschineria, Lactobacillus, Pseudomonas, Streptococcus, Treponema, and conditional pathogens such as Escherichia coli and Leptospira were significantly enriched, indicating higher pathogen-related risks. Functional prediction identified 26 KEGG level-2 and 136 level-3 pathways, showing stronger xenobiotic degradation and amino acid metabolism in pig dung, whereas cow dung was enriched in energy metabolism and chemotaxis pathways. Moreover, the higher abundance of mobile genetic elements (e.g., intI1 and IS613) in pig dung suggests a greater potential for horizontal ARG transfer. Integrating ARG, microbial, and pathogen data reveals that pig dung acts as a composite source of "ARG-pathogen" contamination with enhanced transmission potential. These findings provide localized, data-driven evidence for developing safer livestock waste management practices, such as composting and biogas utilization, and contribute to antibiotic resistance mitigation strategies in rural China.