Bacterial and fungal aerosols in poultry houses: PM2.5 metagenomics via single-molecule real-time sequencing

Microbial aerosol contamination is a common problem in poultry farms, posing potential health risks to poultry and their caretakers. Exploring the distribution and diversity of the microbial community in poultry farm aerosols is crucial for effective mitigation strategies. The composition of bacterial and fungal aerosols is poorly understood, particularly the prevalence of potential pathogenic microorganisms in fine particulate matter (PM_2.5) in various types of poultry houses. In this study, 27 PM_2.5 samples were collected from 5 chicken houses and 4 duck houses in Shandong Province, China. Species-level diversity of bacterial and fungal components in PM_2.5 samples was determined using advanced single-molecule real-time sequencing (SMRT) technology, based on the 16S and internal transcribed spacer 1 (ITS) ribosomal genes. Microbial diversity and community composition varied significantly across the different poultry house. Notably, duck houses had higher concentrations (p < 0.01) of PM_2.5 (92.8-143.1 μg/m³) than chicken houses (42.0-56.4 μg/m³). Furthermore, microbial variation in PM_2.5 samples was associated with the type of poultry facility. The predominant pathogenic microorganisms included Aspergillus sydowii, Penicillium sp., Aspergillus insolitus, Cladosporium sp., Aspergillus sp., Aspergillus pseudoglaucus, Cladosporium sp. C4092-2-PD1, and Colletotrichum sp., all of which were classified as second category of pathogens. Aspergillus sydowii and Penicillium sp. were the dominant species in chicken houses, while Cladosporium sp., Aspergillus sp., and Aspergillus pseudoglaucus were the dominant species identified in duck houses. To our knowledge, this study is the first to investigate bacterial and fungal diversity in PM_2.5 samples collected from various types of poultry houses. These findings advance our understanding of poultry environmental microbiology and have important implications for safeguarding the health of both poultry and their caretakers.