What is the Composition of the Avian Respiratory Microbiome?

Applebaum, Jessica
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University of Delaware
The microbiome of an organism is as critical to its health as is any other organ. Characterizing the microbial communities associated with agricultural animals, such as poultry, is important for understanding the relationships between these animals and their environment. My research goal is to develop the technology and methods needed to enumerate and characterize the bacterial microbiome in the respiratory tract of the broiler chicken. Bronchoalveolar lavage fluid was collected from several four-week old broiler chickens, some of which were infected with a cocktail of respiratory viral vaccine strains, infectious bronchitis virus (IBV), New Castle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). The bronchoalveolar lavage fluid from two control and two infected birds was processed, and the bacterial and viral communities were extracted and counted. Using 16S rRNA analysis by highthroughput Illumina sequencing followed by bioinformatic analysis, we plan to identify the bacterial species present in the bronchoalveolar lavage fluid and determine their relative abundances. The results of this project can ultimately allow scientists to track how the microbiome changes during growth and disease and in response to variations in nutrition and environment.