Identification of Size-segregated Bioaerosol Community and Pathogenic Bacteria in a Tunnel-ventilated Layer House: Effect of Manure Removal

Bioaerosols in commercial livestock barns threaten the health of animals and humans. To better understand microbial dynamics in the layer house, we characterized and compared the size-segregated bacterial community of the manure cleaning process in a typical commercial laying hen house equipped with an H-type manure removal belt and negative pressure tunnel ventilation system in Ningbo, China by using full-length 16S rRNA gene sequences. The third-generation single-molecule real-time sequencing (SMRT Cell) based on the Pacific BioSciences (PacBio) RS II platform was performed for capturing sequence information of the microbial aerosol samples. The results showed that the concentrations of total airborne bacteria in the layer house were in the range of 0.35 × 103 CFU/m3 to 0.70 × 103 CFU/m3, 2.76 × 103 CFU/m3 to 2.88 × 103 CFU/m3, and 2.10 × 103 CFU/m3 to 2.54 × 103 CFU/m3 before, during, and after manure removal, respectively. The airborne bacteria concentrations were significantly increased by the manure removal process. According to LEfSe analysis results, g_Escherichia_Shigella, s_Escherichia_coli, o_Enterobacteriales, f_Enterobacteriaceae could be suggested as biomarkers during manure removal. The dominant bacterial phyla in the layer house monitored were Proteobacteria, Bacteroidetes, Firmicutes, and genera were Pseudomonas, Escherichia-Shigella, Comamonas. The predominant potential pathogenic bacteria in the layer house were Pseudomonas, Escherichia, Enterobacter, and Acinetobacter.