microorganisms Article Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing Kelly A. Mulholland 1 , Monique G. Robinson 1, Sharon J. Keeler 1, Timothy J. Johnson 2, Bonnie W. Weber 2 and Calvin L. Keeler, Jr. 1,* 1 Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA;
[email protected] (K.A.M.);
[email protected] (M.G.R.);
[email protected] (S.J.K.) 2 Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA;
[email protected] (T.J.J.);
[email protected] (B.W.W.) * Correspondence:
[email protected]; Tel.: +1-302-831-2524 Abstract: 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 Citation: Mulholland, K.A.; detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection Robinson, M.G.; Keeler, S.J.; Johnson, with infectious laryngotracheitis virus.