Metagenomics reveals the diversity and taxonomy of antibiotic resistance genes in sufu bacterial communities

Consumption of fermented food increases the risk of dissemination of microbial antibiotic resistance genes (ARGs) in the human intestinal tract. However, the diversity and taxonomic origin of ARGs in fermented foods are not well understood. In this study, genome-centered metagenomics was used to identify distribution patterns of ARGs in major bacterial species in sufu. In total, 13 high-quality metagenome-assembled genomes (MAGs) (with average completeness of 88.24% and contamination of 2.08%) were recruited from a combined metagenome of 25 sufu samples, which were assigned to eight genera. The number of ARGs in MAGs differed in various phylogenetic positions; MAGs associated with the genera Enterococcus and Kurthia, and family Flavobacteriaceae, harbored more ARGs than those associated with the genera Lactobacillus and Weissella. Among the twelve detected ARG types, glycopeptide resistance genes were present in all MAGs, and genes conferring resistance to oxazolidinone, beta-lactam, macrolide-lincosamide-streptogramin, and tetracycline were identified in 84.6%, 76.9%, 76.9%, and 76.9% of the MAGs, respectively. The number and diversity of ARGs in MAGs differed in taxonomic lineages, reflecting antibiotic resistance in different sufu bacterial species. Thus, owing to an abundance of species with diverse ARGs, stringent quantity control involving microbial species, especially those carrying abundant ARGs, is critical to reduce the risk of ARG uptake through the consumption of fermented foods.