High-throughput sequencing comparative analyses of bacterial communities and human pathogens during the mesophilic anaerobic fermentation of swine feces

Abstract

Manure as a resource is a major issue in the agricultural sector. Mesophilic anaerobic fermentation is the most common treatment modality for livestock manure, but it cannot completely eliminate human pathogens. Recently several reports characterized bacteria and human pathogens after manure treatment by mesophilic anaerobic fermentation. In this study, we used high-throughput sequencing to analyze bacterial and pathogen composition and diversity in fecal samples and digestates using three mesophilic anaerobic fermentation methods. The three methods altered composition and diversity, with the traditional fermentation method having the least effect on composition and diversity. In contrast, mesophilic anaerobic treatments plus extra bacteria displayed the greatest effects. We established a large-scale primary screening method for human pathogens at the genus level based on the mesophilic anaerobic fermentation system, and investigated pathogen survival rates at the species level. We provide a method for the preliminary evaluation and treatment of manure and we provide insights on the rational use of manure. • A large-scale primary screening method for human pathogens in the harmless treatment of livestock manure was established in this study. • Mesophilic anaerobic fermentation is difficult to control the abundance of Acinetobacter , Corynebacterium , Enterococcus , Pseudomonas and Streptococcus in fecal samples. • A method of traditional mesophilic anaerobic fermentation with extra bacteria was best to control potential human pathogen.