In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.

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Respiratory disease complex is a serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide. A metagenomic approach was used to investigate bacterial abundance and diversity using Whole genome shotgun sequencing of clinically diseased and healthy broiler affected with respiratory disease complex. The data were analyzed using best hit approach through MG-RAST. Sequences predominantly aligned with the phyla Proteobacteria followed by Bacteroidetes in samples from clinically diseased broiler affected with respiratory disease complex, whereas Chlamydiae followed by Proteobacteria in sample from apparently healthy broiler birds. At the species level Escherichia coli, Ornithobacterium rhinotracheale and Pseudomonas aruginosa were predominant in diseased birds, Chlamydia psittaci, Mycoplasma gallisepticum, Lactobacillus agilis and Gallibacterium anatis were predominated bacterial species found in the apparently healthy birds. Higher alpha diversity indices and richness values were found for the bacterial communities in clinically diseased broiler birds as compared to healthy birds. The present study findings may help in formulating strategies for the prevention, control and treatment of respiratory infections in birds and consequently also reducing economic losses in poultry industries.