Characterizing the respiratory viral microbiome of a commercial broiler flock
Date
2020
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Publisher
University of Delaware
Abstract
The human microbiome has been extensively characterized and has been shown to play an essential role in health and metabolism. Research on the microbiome of agricultural animal species demonstrates similar roles. Although the intestinal microbiome has been extensively studied in poultry, the avian respiratory microbiome has not been characterized. Considering the importance and impact of avian respiratory health, an examination of the microbial community within the respiratory tract could lead to a better understanding of respiratory disease etiology and control. ☐ Respiratory Disease Complex (RDC) in poultry is an example of a complex microbial system with direct effects on poultry respiratory health. In RDC normal interactions between bacteria and viruses are disrupted resulting in a dysbiosis of the respiratory microbiome which causes acute respiratory disease. ☐ The primary objective of this project was to develop the methods needed to identify and enumerate the animal virus component of the avian respiratory tract. To preserve the integrity of viral RNA, it was determined that the optimal method of sample collection was storing tracheal swabs in a chaotropic buffer such as PV1, followed by immediate freezing in liquid nitrogen or on dry ice. Upon centrifugation of these samples, optimal viral recovery was obtained from processing the cellular debris in the pellet rather than the supernatant. The methodology for determining the poultry virome was evaluated by performing a longitudinal study in which commercial broiler chickens were sampled weekly from hatch until processing. A robust viral microbiome was identified in which a total of 11 viral species, both DNA and RNA, were detected in the respiratory passages of the flock. We found that the respiratory virome changes during the growth of a poultry flock, becoming more diverse as the flock ages. Certain viruses, such as coronaviruses, were found during the entire growth period. Other viruses, such as infectious bursal disease virus, were only found in the respiratory tract after the waning of maternal antibodies. Lastly, infectious laryngotracheitis virus was identified as the major viral species from clinical samples diagnosed with infectious laryngotracheitis virus. This virus was not found in the healthy flock. Therefore, we have successfully developed and evaluated a method to characterize the avian viral microbiome.
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Keywords
Chicken, Respiratory, Virus