Mulholland Kelly A, Robinson Monique G, Keeler Sharon J, Johnson Timothy J, Weber Bonnie W, Keeler Calvin L
Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.
Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA.
Microorganisms. 2021 Mar 31;9(4):721. doi: 10.3390/microorganisms9040721.
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.
阐明生物环境中复杂的微生物相互作用不仅需要鉴定和表征细菌成分，还需要鉴定和表征真核病毒、噬菌体和真菌。在一项概念验证实验中，利用下一代测序方法，并结合新型计算和生物信息学工具的开发，来研究健康商业肉鸡群生长过程中禽气管微生物生态的演变。从雏鸡入舍开始，每周对鸡群进行采样，直至49日龄（即屠宰前一天）。利用DNA和RNA的宏基因组测序来检测鸡群生长过程中的细菌、病毒、噬菌体和真菌成分。通过检测诊断为感染传染性喉气管炎病毒的肉鸡禽呼吸道病毒组中的生态失调，证实了使用宏基因组方法研究禽呼吸道病毒组的实用性。本研究首次对禽呼吸道微生物组的生态进行了全面分析，并证明了该方法在未来禽呼吸道疾病研究中的可行性。
