BACKGROUND Animal manure is one of the significant sources of antibiotic resistance genes (ARGs) and an emerging pollutant that poses a threat to human beings. Composting is a common method of treating manure. The effect of composting on the ARGs in manure has become an active research area in recent years. In this study, three common aeration strategies were used to study the removal of ARGs and to clarify their microbial mechanism during composting, i.e. forced aeration (with three ventilation rates), turn windrow and static pile. RESULTS Results showed that the variation pattern of ARGs was highly dependent on the succession of the microbial community, and environmental factors accounted for 44% of the variation. Most ARGs (tetW/tetO/tetH, qnrS, ermB and blaTEM) could be significantly reduced after composting for 77 days, but sulfonamide resistance genes (sulI/sulII) and the integrase gene (intI) were highly enriched, particularly in forced aeration treatment. These enrichments were closely correlated with an increase in the genera belonging to Actinobacteria, Proteobacteria and Bacteroidetes and a decrease in the genera affiliated with Firmicutes. CONCLUSIONS The temporal variations in ARGs were consistent under different aeration treatments. Further study should focus on optimizing the composting conditions to reduce recalcitrant ARGs. (c) 2019 Society of Chemical Industry