A comparative metagenomic approach to detect pathogenic bacteria in commercial broilers affected with respiratory disease complex

Abstract

Abstract 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.