High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Kate M O'Brien; Michael S Chimenti; Morgan Farnell; Tom Tabler; Thomas Bair; Joey L Bray; Matthew W Nonnenmann

doi:10.1111/1751-7915.12380

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High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Journal article

Open access

Peer reviewed

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Kate M O'Brien, Michael S Chimenti, Morgan Farnell, Tom Tabler, Thomas Bair, Joey L Bray and Matthew W Nonnenmann

Microbial biotechnology, Vol.9(6), pp.782-791

11/2016

DOI: 10.1111/1751-7915.12380

PMCID: PMC5072194

PMID: 27470660

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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.

Computational Biology - methods

Viruses - genetics

Fungi - classification

Soil Microbiology

Air Microbiology

Biota

Humans

Archaea - classification

Bacteria - genetics

Fungi - genetics

Sequence Analysis, DNA

Viruses - classification

Dust

Animals

Chickens

Aerosols

Animal Husbandry

Bacteria - classification

Archaea - genetics

High-Throughput Nucleotide Sequencing - methods

Details

Title: Subtitle: High throughput genomic sequencing of bioaerosols in broiler chicken production facilities
Creators: Kate M O'Brien - Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA
Michael S Chimenti - Iowa Institute of Human Genetics, Bioinformatics Division, University of Iowa, Iowa City, IA, USA
Morgan Farnell - Mississippi State University Extension Service, Mississippi State, MS, USA
Tom Tabler - Mississippi State University Extension Service, Mississippi State, MS, USA
Thomas Bair - Iowa Institute of Human Genetics, Bioinformatics Division, University of Iowa, Iowa City, IA, USA
Joey L Bray - Department of Agriculture, Stephen F. Austin State University, Nacogdoches, TX, USA
Matthew W Nonnenmann - Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA. matthew-nonnenmann@uiowa.edu
Resource Type: Journal article
Publication Details: Microbial biotechnology, Vol.9(6), pp.782-791
DOI: 10.1111/1751-7915.12380
PMID: 27470660
PMCID: PMC5072194
NLM abbreviation: Microb Biotechnol
ISSN: 1751-7915
eISSN: 1751-7915
Publisher: United States
Grant note: P30 ES005605 / NIEHS NIH HHS
Language: English
Date published: 11/2016
Academic Unit: Occupational and Environmental Health; Internal Medicine; Iowa Institute of Human Genetics
Record Identifier: 9983997314402771

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