Background: The respiratory tracts of turkeys are the main route of infection therefore plays important roles in the overall health and performance of the birds. Understanding the poultry microbiome has the potential to offer better diagnosis and rational management of many poultry diseases. Characterization of microbial communities in the upper respiratory tract of turkeys could help better understand the role of pathogenic bacteria and other commensal or symbiotic microorganisms in the infection. The aim of this study was microbiome characterization of upper respiratory tracks of commercial turkeys using next-generation sequencing technologies.
Results: The microbiome from samples collected from commercial turkey flocks was determined using 16S rRNA metagenomic approach. Taxonomic analysis of the microbiome was done by of the V3 and V4 regions of 16S rRNA gene (MiSeq, Illumina) amplification. The phylogenetic analysis identified the 10 bacterial phyla in turkey, the most abundant were phyla Firmicutes and Proteobacteria, accounting for >99% of all the sequences. The turkey sequences represent 144 established bacterial genera. Differences between bacterial abundances were found at the family and genus level. Several defining markers of microbiome succession were identified, including the presence of Ornithobacterium and Mycoplasma.
Conclusions: Understanding the turkey’s respiratory microbiome is very important. Unique informations about microbiome representing members of the four major phyla of the respiratory tract in turkeys was assembled. These results obtained in this study supply information about turkey microbiome and can be useful in controlling, diagnosing and treating commercial turkey flocks. Our study significantly broaden the knowledge of the upper respiratory tract microbiome of turkeys.