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Microbial Communities Present in the Lower Respiratory Tract of Clinically Healthy Birds in Pakistan

03 April 2015

Poultry Science journal

Based on examination of the respiratory tract samples from a number of birds from three farms in Punjab province, researchers found a diverse population of bacteria, including some opportunistic respiratory pathogens in apparently healthy birds.

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.

In the current issue of Poultry Science, Eric Harvill of Pennsylvania State University in the USand co-authors there and at the University of Veterinary and Animal Sciences at Lahore in Pakistan report that 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 characterisation of lower respiratory microbiome of birds including the identification of novel commensals and potentially merging pathogens.

In this study, the researchers collected tracheobronchoalveolar lavage of 14 birds raised at three different farms in the Punjab province of Pakistan.

To characterise the lower respiratory microbiome of these birds, they 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 interfarm 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, commented Harvill and co-authors.

They added that understanding and monitoring the respiratory microbiome of such populations may allow the early detection of future disease threats.


Shabbir M.Z., T. Malys, Y.V. Ivanov, J. Park, M.A.B. Shabbir, M. Rabbani, T. Yaqub and E.T. Harvill. 2015. Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan. Poultry Science. 94:612-620.

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April 2015

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