Viral metagenomics reveals diverse viruses and antibiotic resistance genes in fecal samples of swine from farms in Shandong province
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Abstract
Almost all research on the swine gut microbiome has focused on bacteria. However, these studies paid little attention to the swine gut virome. Here, metagenomic sequencing was employed to characterize the gut viromes and reservoir of antibiotic resistance genes (ARGs) in 16 pig farms which are distributed in 16 different prefecture-level cities in Shandong province. We identified the community composition of the gut viromes, and the top 50 viruses, and showed the patterns of the virus in 16 pig farms at the phylum, genus, and species levels. A total of 191 ARGs potentially conferring resistance to 17 classes of antibiotics were detected in the 16 pig farms. These 16 samples exhibited a superior abundance and more widespread distribution of genes associated with tetracycline, aminoglycosides, and macrolide-lincosamide-streptogramin (MLS) than other ARGs. Our research provides a universal overview of the prevalence and expression of virus and ARGs in pig gut microbiota.
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