Dataset Information

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.

SUBMITTER: O'Brien KM

PROVIDER: S-EPMC5072194 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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High throughput genomic sequencing of bioaerosols in broiler chicken production facilities.

O'Brien Kate M KM Chimenti Michael S MS Farnell Morgan M Tabler Tom T Bair Thomas T Bray Joey L JL Nonnenmann Matthew W MW

Microbial biotechnology 20160728 6

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-synt ...[more]

PMID: 27470660

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Project description:BackgroundAs one of "γδ-high" species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using high-throughput sequencing.MethodsIn this study, we first obtained the detailed genomic organization of the TCRγ locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCRγ repertoire in the thymus of four chickens by using 5' Rapid Amplification of cDNA Ends (5' RACE) along with high-throughput sequencing (HTS).ResultsThe chicken TCRγ locus contains a single Cγ gene, three functional Jγ segments and 44 Vγ segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken TCRγ locus against itself showed that almost all the entire zone containing Vγ segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 Vγ gene segments, has tandemly duplicated for four times. For the analysis of chicken TCRγ repertoire, more than 100,000 unique Vγ-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline Vγ and Jγ segments identified above, we found that the four chickens had similar repertoire profile of TCRγ. In brief, four Vγ segments (including Vγ3.7, Vγ2.13, Vγ1.6 and Vγ1.3) and six Vγ-Jγ pairs (including Vγ3.7-Jγ3, Vγ2.13-Jγ1, Vγ2.13-Jγ3, Vγ1.6-Jγ3, Vγ3.7-Jγ1 and Vγ1.6-Jγ1) were preferentially utilized by all four individuals, and vast majority of the unique CDR3γ sequences encoded 4 to 22 amino acids with mean 12.90 amino acids, which exhibits a wider length distribution and/or a longer mean length than CDR3γ of human, mice and other animal species.ConclusionsIn this study, we present the first in-depth characterization of the TCRγ repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.

Project description:Although efforts to improve antimicrobial stewardship should include the collection of antimicrobial use data, most antimicrobial datasets collected at the national level consist of antimicrobial sales data which cannot inform stewardship. These data lack context, such as information regarding target species, disease indication, and regimen specifics like dose, route and duration. Therefore, the goal of this study was to develop a system for collecting data on the use of antimicrobials in the U.S. broiler chicken industry. This study utilized a public-private partnership to enable collection and protection of sensitive data from an extremely large industry while releasing deidentified and aggregated information regarding the details of antimicrobial use on U.S. broiler chicken farms over time. Participation was voluntary. Data were collected for the period 2013 through 2021 and are reported on a calendar year basis. Using production statistics from USDA:NASS as a denominator, the data supplied by participating companies represented approximately 82.1% of broiler chicken production in the U.S. in 2013, approximately 88.6% in 2017, and approximately 85.0% in 2021. The data that were submitted for 2021 are based on approximately 7,826,121,178 chickens slaughtered and 50,550,817,859 pounds liveweight produced. Granular flock-level treatment records were available for 75-90% of the birds represented in the 2018-2021 dataset. There was no use of antimicrobials in the hatchery for the years 2020 and 2021. Medically important in-feed antimicrobial use decreased substantially, with all in-feed tetracycline use being eliminated by 2020, and the use of virginiamycin being reduced by more than 97% since 2013. Medically important water-soluble antimicrobials are used for the treatment of disease in broiler production. Use decreased substantially for most water-soluble antimicrobials. The most important diseases necessitating treatment were necrotic enteritis and gangrenous dermatitis as well as E. coli-related disease. A focus on reducing the incidence of these diseases would reduce the need for antimicrobial therapy but will require an investment in research to find efficacious and cost-effective interventions for these diseases.

Dataset Information

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities.

Publications

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities.

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