Exploring the prevalence and distribution patterns of antibiotic resistance genes in bovine gut microbiota using a metagenomic approach

Background: Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear. Methods: 30 of the fecal samples were obtained from bovine and were immediately frozen in liquid nitrogen. Total metagenomic DNA was extracted by cetyltrimethylammonium bromide (CTAB) method and sequenced by Illumina HiSeq X Ten platform. After quality control and assembled, the sequence were annotated by NR, CARD and ISfinder. Statistical analysis was performed using SPSS 19.0. Results: A total of 42 ARG types were detected by annotating the metagenomic sequencing data from the Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle. The results of heat map and single-nucleotide polymorphism (SNP) clustering suggest that ARGs from dairy and beef cattle are more similar, while those from yaks cluster separately. Conclusion: The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions and integrations were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.