Behavior of antibiotic resistance genes during co-composting of swine manure with Chinese medicinal herbal residues

•Chinese medicinal herbal residues effectively many targeted ARGs (0.18–2.82logs).•Mobile genetic element abundances decreased by 0.47–3.34logs after co-composting.•Microbial community structure had important effects on the variations in ARGs.•The potential hosts of ARGs mainly belonged to Firmicutes. Swine manure is considered to be a reservoir for antibiotic resistance genes (ARGs) but little is known about the variations in ARGs during the co-composting of swine manure with Chinese medicinal herbal residues (CMHRs). Thus, this study explored the effects of CMHRs on the variations in ARGs during co-composting with swine manure. The results showed that CMHRs could reduce effectively most of the targeted ARGs (0.18–2.82logs) and mobile genetic elements (MGEs) (0.47–3.34logs). The correlations indicated that CMHRs might decrease the spread of ARGs via horizontal gene transfer. Redundancy analysis showed that the bacterial communities had more important effects on the variations in ARGs compared with environmental factors and MGEs. The results of this study demonstrate that CMHRs can decrease the abundances of ARGs and MGEs, as well as reducing the risk of ARGs spreading during the application of compost products to farmland.