Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing
Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompani...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-03-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/4/721 |
| _version_ | 1797539378568888320 |
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| author | Kelly A. Mulholland Monique G. Robinson Sharon J. Keeler Timothy J. Johnson Bonnie W. Weber Calvin L. Keeler |
| author_facet | Kelly A. Mulholland Monique G. Robinson Sharon J. Keeler Timothy J. Johnson Bonnie W. Weber Calvin L. Keeler |
| author_sort | Kelly A. Mulholland |
| collection | DOAJ |
| description | Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases. |
| first_indexed | 2024-03-10T12:45:10Z |
| format | Article |
| id | doaj.art-153d63f340204287bc8adef39ba5d31f |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T12:45:10Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-153d63f340204287bc8adef39ba5d31f2023-11-21T13:33:19ZengMDPI AGMicroorganisms2076-26072021-03-019472110.3390/microorganisms9040721Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to ProcessingKelly A. Mulholland0Monique G. Robinson1Sharon J. Keeler2Timothy J. Johnson3Bonnie W. Weber4Calvin L. Keeler5Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USADepartment of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USADepartment of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USADepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USADepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USADepartment of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USAElucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.https://www.mdpi.com/2076-2607/9/4/721microbiomeavianrespiratorychickenviromebioinformatics |
| spellingShingle | Kelly A. Mulholland Monique G. Robinson Sharon J. Keeler Timothy J. Johnson Bonnie W. Weber Calvin L. Keeler Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing Microorganisms microbiome avian respiratory chicken virome bioinformatics |
| title | Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing |
| title_full | Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing |
| title_fullStr | Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing |
| title_full_unstemmed | Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing |
| title_short | Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing |
| title_sort | metagenomic analysis of the respiratory microbiome of a broiler flock from hatching to processing |
| topic | microbiome avian respiratory chicken virome bioinformatics |
| url | https://www.mdpi.com/2076-2607/9/4/721 |
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