title: High throughput genomic sequencing of bioaerosols in broiler chicken production facilities.
abstract: Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64-67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.
authors.affiliation: Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA.
authors.forename: Kate M
authors.initials: KM
authors.lastname: O'Brien
authors.affiliation: Iowa Institute of Human Genetics, Bioinformatics Division, University of Iowa, Iowa City, IA, USA.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Chimenti
authors.affiliation: Mississippi State University Extension Service, Mississippi State, MS, USA.
authors.forename: Morgan
authors.initials: M
authors.lastname: Farnell
authors.affiliation: Mississippi State University Extension Service, Mississippi State, MS, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Tabler
authors.affiliation: Iowa Institute of Human Genetics, Bioinformatics Division, University of Iowa, Iowa City, IA, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Bair
authors.affiliation: Department of Agriculture, Stephen F. Austin State University, Nacogdoches, TX, USA.
authors.forename: Joey L
authors.initials: JL
authors.lastname: Bray
authors.affiliation: Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA. matthew-nonnenmann@uiowa.edu.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Nonnenmann
mesh_terms: D000336:Aerosols; D000391:Air Microbiology; D000822:Animal Husbandry; D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D058448:Biota; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D004391:Dust; D005658:Fungi / Q000145:classification / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014780:Viruses / Q000145:classification / Q000235:genetics
chemical_list: D000336:Aerosols; D004391:Dust