Linking nasopharyngeal microbiome to clinical, ultrasonographic and bacteriological diagnosis of calf respiratory disease
This study investigated the respiratory microbiome of calves from Norwegian dairy and fattening herds with bovine respiratory disease. Nasal swabs, deep nasopharyngeal swabs, and non-endoscopic bronchoalveolar lavage samples were collected to compare upper- and lower-airway microbiome composition. The V3-V4 region of the bacterial 16S rRNA gene was sequenced to identify microbial signatures associated with clinically relevant respiratory disease phenotypes defined using clinical examination, thoracic ultrasonography, and bronchoalveolar lavage bacteriology. The study aimed to determine whether deep nasopharyngeal swabs could provide a practical upper-airway proxy for lower-airway microbiome composition and identify bacterial pneumonia-associated microbiome signals.