Understanding the Respiratory Microbiome of Commercial Poultry (Broilers)
PI: Calvin L. Keeler, Jr. and Jack Gelb, Jr.
For years avian researchers have studied the respiratory disease complex (RDC) in the context of the individual microbial components that are involved. We plan to study those interactions by determining what microbial elements are present in the broiler bird and how the relative abundance of those components changes with time. We will first develop and validate the methodology to evaluate the microbial respiratory microbiome (bacterial and viral). Using a combination of metagenomic sequencing approaches (including 16S rRNA gene analysis, shotgun sequencing (Illumina and Pac-Bio), and RNA transcript sequencing (RNASeq)), followed by a robust bioinformatic analysis, we aim to determine the bacterial and viral community (the respiratory microbiome) in the respiratory tract of normal broiler chickens. Commercial broiler flocks will be utilized for this analysis. In the next phase of the project, the respiratory microbiome will be determined for broiler flocks challenged by respiratory disease. Compared with the control microbiome profiles obtained in the first phase of the project, we expect to identify changes in the viral and/or bacterial respiratory microbiome. These changes are expected to vary with the type of respiratory challenge faced by the flock (bacterial, viral, mixed).
Yearly Goals:
Year 1:
Identify partners within the commercial broiler industry. Identify and characterize broiler flocks for experimental studies (traditional and organic). Develop methods for collecting biological materials from the upper respiratory tract. Preliminary determination of bacterial microbiome through 16S analysis at 1, 3, 5, and 7 weeks of age.
Year 2:
Develop methodologies to enrich for the viral component of the avian respiratory microbiome and the metagenomics and bioinformatics tools to determine the viral microbiome.
Year 3:
Combine the approaches developed in years 1 and 2 to perform longitudinal studies on the composition of the bacterial and viral respiratory microbiomes in flocks of commercial broilers grown under varying environmental and nutritional conditions.
Years 4 & 5:
Expand studies to determine the composition of the avian respiratory microbiome (bacterial and viral) in birds experimentally infected with respiratory disease agents(s) and in commercial flocks experiencing respiratory disease.
Potential Impact and Expected Outcomes:
Ultimately, based on the technology developed through this project, we will be able to examine how the microbiome in the bird’s respiratory tract (both viral and bacterial) reacts to changes during growth and development and in response to changes in nutrition, environmental management, and disease. This will lead to improvements in flock management and disease control.
