Exploratory 16S rRNA pilot snapshot of tracheal bacterial communities in healthy and respiratory-diseased Cobb 500 broilers from Algeria
We used 16S rRNA V2-V3 amplicon sequencing to analyze the tracheal bacterial community composition of two identical 44-day-old Cobb 500 broiler flocks raised under different clinical conditions in Algeria. Community analysis was used to determine the most abundant taxa and to describe the differences in richness, diversity, and relative abundance of amplicon sequence variants (ASVs) between them.Flock 1 (P1): Pooled sample taken from birds showing active respiratory disease signs and having been treated with multiple antimicrobials at the time of sampling.Flock 2 (P2): Pooled sample from clinically healthy birds with no acute respiratory signs at sampling, but the flock had a history of respiratory disease.The working hypothesis was that the bacterial community profile of flock P1 was altered, with a decrease in the relative abundance of commensal Lactobacillus-associated features and an increase in the relative abundance of avian respiratory pathogens or opportunistic taxa, consistent with its clinical status and concurrent antimicrobial exposure.