title: Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan.
abstract: Commercial poultry is an important agricultural industry worldwide. Although dense living conditions and large flocks increase meat and egg production, they also increase the risk of disease outbreaks and zoonoses. Current pathogen identification methods mostly rely on culture-dependent techniques and, therefore, are limited to a very small number of bacteria present in the environment. Next Generation Sequencing allows for culture-independent characterization of lower respiratory microbiome of birds including the identification of novel commensals and potentially emerging pathogens. In this study, we collected tracheo-bronchoalveolar lavage of 14 birds raised at 3 different farms in the Punjab province of Pakistan. To characterize the lower respiratory microbiome of these birds, we sequenced hyper-variable regions of the 16S ribosomal subunit gene. Although dominated by bacteria belonging to a small number of taxonomic classifications, the lower respiratory microbiome from each farm was far more diverse and novel than previously known. The differences in microbiome among farms suggest that inter-farm differences affect the microbiome of birds more than breed, geographic location, or management system. The presence of potential and known pathogens in genetically similar specialty breeds of chickens kept at unnaturally high densities and under variable conditions presents an extraordinary opportunity for the selection of highly pathogenic bacteria. In some instances, opportunistic respiratory pathogens were observed in apparently healthy birds. Understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats.
authors: Quality Operations Laboratory, University of Veterinary and Animal Sciences Lahore 54600, Pakistan.
authors: Muhammad Zubair
authors: MZ
authors: Shabbir
authors: Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802.
authors: Tyler
authors: T
authors: Malys
authors: Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802.
authors: Yury V
authors: YV
authors: Ivanov
authors: Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802.
authors: Jihye
authors: J
authors: Park
authors: Quality Operations Laboratory, University of Veterinary and Animal Sciences Lahore 54600, Pakistan.
authors: Muhammad Abu Bakr
authors: MA
authors: Shabbir
authors: University Diagnostic Laboratory, University of Veterinary and Animal Science, Lahore 54600, Pakistan.
authors: Masood
authors: M
authors: Rabbani
authors: Quality Operations Laboratory, University of Veterinary and Animal Sciences Lahore 54600, Pakistan.
authors: Tahir
authors: T
authors: Yaqub
authors: Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park 16802 eth10@psu.edu.
authors: Eric Thomas
authors: ET
authors: Harvill
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D018893:Bronchoalveolar Lavage / Q000662:veterinary; D002645:Chickens / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D008168:Lung / Q000382:microbiology; D008297:Male; D064307:Microbiota; D008969:Molecular Sequence Data; D010154:Pakistan; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000662:veterinary; D014132:Trachea / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: culture-independent analysis; lower respiratory tract; microbiome; novel organism; poultry