Metagenomic analysis of the respiratory microbiome of a broiler flock from hatching to processing

Kelly A. Mulholland, Monique G. Robinson, Sharon J. Keeler, Timothy J. Johnson, Bonnie W. Weber, Calvin L. Keeler

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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.

Original languageEnglish (US)
Article number721
Issue number4
StatePublished - Mar 31 2021

Bibliographical note

Funding Information:
Funding: This project was supported by Agriculture and Food Research Initiative Competitive Grant #2015-68004-23131 from the USDA National Institute of Food and Agriculture. Computational infrastructure support by the University of Delaware Center for Bioinformatics and Computational Biology Core Facility was made possible through funding from Delaware INBRE (NIH P20 GM103446) and the Delaware Biotechnology Institute.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.


  • Avian
  • Bioinformatics
  • Chicken
  • Microbiome
  • Respiratory
  • Virome

PubMed: MeSH publication types

  • Journal Article


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