BackgroundLivestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting.ResultsThe absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments.ConclusionAmong the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.