Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan

Muhammad Zubair Shabbir, Tyler Malys, Yury V. Ivanov, Jihye Park, Muhammad Abu Bakr Shabbir, Masood Rabbani, Tahir Yaqub, Eric Thomas Harvill

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)612-620
Number of pages9
JournalPoultry science
Issue number4
StatePublished - Jul 31 2014

All Science Journal Classification (ASJC) codes

  • Animal Science and Zoology


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