Muhammad Zubair Shabbir

A Metagenomic Analysis Of The Respiratory Microbiota Of Birds - 2013

The respiratory systems of birds are susceptible to and are a reservoir for numerous bacterial species, including those of significance to public health. A number of bacteria, either as primary or secondary infectious agents, have been associated with respiratory outbreaks in poultry and subsequent losses worldwide. A key component of a poultry development policy is the proper diagnosis and control of infectious diseases, which requires substantial knowledge of the microbiome in diseased and healthy birds. Because only a small proportion (< 1%) of organisms are culturable, limited as well as highly variable and time-consuming conventional microbiological procedures have typically excluded the normal flora present in the respiratory tract or have restricted the analysis to potential pulmonary pathogens. This limitation provides only a partial representation of the airway microbiota of birds and has little potential for determining or discovering novel organisms/pathogens and their association with clinical outcomes. Using the hypervariable region of the 16S rRNA gene, culture-independent techniques such as 454-pyrosequencing, can provide species-specific sequences of any bacteria in a given clinical sample. This approach has identified a number of novel bacterial species in recent years.
Based on the quality and quantity of the double-stranded gDNA, a total of 30 T-BAL samples including houbara bustard and ostrich, were collected from equal numbers of clinically diseased and healthy birds originating from flocks within different management systems, including free range, open house, and controlled house. Using 454 bar-coded pyrosequencing, the hypervariable regions of the 16S rRNA gene corresponding to V1 - V5 (~ 1,000 bp) were sequenced. Of the high-quality reads obtained (296,811) using the MOTHUR platform, the sequences were processed for sequence alignment with the 16S RDP database via BLASTn, and subsequent taxonomic analysis through MEGAN programs using a homology-based method to bin sequence reads.
Almost all of the read were classified to the bacterial domain and its subsequent descendants. The birds were shown to be susceptible to a diverse microbial community belonging to a variety of phyla, families, genera, and well-characterized bacterial species. The bacterial communities were relatively conserved at the phylum level; however, at lower taxonomic levels, differences were observed in the phylotypes and abundance between the clinically diseased and healthy birds as well as between different management systems. The biodiversity and richness in the taxonomic content was higher in the clinically healthy birds compared with the diseased birds, as indicated by the rarefaction plot and the Shannon-Wiener and Simpson-Reciprocal diversity indices. Regardless of the management type, bird species, and health status, a number of new bacterial species were identified. Although the clinical importance of these bacteria as part of the respiratory microbiome of birds has not been established, a number of these bacterial species have been found to be associated with infectious diseases in humans and other species.
The interactions of bacterial species with one another and, potentially, with the birds themselves provide a fascinating avenue for continued research. Further clinico-pathological studies will be needed to establish the links between causes versus effects. This information may help us gain insight into the ecological roles of these bacterial species and their potential co-evolution with birds.

Department of Microbiology


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