Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing

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

doi:10.3390/microorganisms9040721

Kelly A Mulholland, Monique G Robinson + Show 4 more

Open Access

https://doi.org/10.3390/microorganisms9040721

Copy DOI

Journal: Microorganisms	Publication Date: Mar 31, 2021
Citations: 10	License type: CC BY 4.0

Affiliation: University of Delaware, University of Minnesota

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 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.

Highlights

Microbiomes are complex environments consisting of eukaryotic viruses, bacteria, archaea, bacteriophage, fungi, and protozoa; and microbiomes exist throughout the body in the oral cavity, intestinal tract, respiratory tract, vaginal tract and skin of both animals and humans [1,2]
This preliminary study will be confirmed and expanded by examining the respiratory microbiome of multiple flocks from multiple companies, by examining multiple grow-out cycles from the same flock in order to determine seasonal effects and flock consistency, and by examining flocks grown under different production systems. These results could be compared with multi-age backyard flocks from the same geographic area. Ecological niches such as the avian respiratory tract are complex microbial environments consisting of eukaryotic viruses, bacteria, archaea, bacteriophage, fungi, and protozoa, all of which contribute to its microbial ecology
We developed and employed a bioinformatics pipeline to examine a healthy flock of chickens throughout their grow out cycle

Summary

Introduction

Microbiomes are complex environments consisting of eukaryotic viruses, bacteria, archaea, bacteriophage, fungi, and protozoa; and microbiomes exist throughout the body in the oral cavity, intestinal tract, respiratory tract, vaginal tract and skin of both animals and humans [1,2]. The composition within these different microbiome environments varies as the microbial communities participate in unique biological functions. Viruses can affect infection by other viral pathogens This can occur due to interference, a phenomenon by which a viral infection causes a cell to be temporarily resistant to infection by other viruses.

Objectives

Methods

Results

Conclusion