16S rRNA nasopharyngeal gene amplicons from apparently healthy Holstein calves and calves diagnosed with bovine respiratory disease
Nasopharyngeal (NP) swabs were collected from 30 pre-weaned Holstein bull calves on days 0 (after transport), 7, and 14. Calves were screened for BRD clinical signs, if  signs were observed nasopharyngeal swabs were collected on day 0 (day of diagnosis) and days 1, 5, and 10 after antibiotic administration. Total healthy animals 20, and total BRD-affected animals 10. DNA was then extracted from the NP swabs  to construct the 16S rRNA gene library (V4 16S rRNA gene) following the protocol from the Schloss lab. The amplified DNA was normalized using the SequalPrep Normalization Plate (Invitrogen) and pooled to form a single library. The 16S rRNA gene amplicons were sequenced using Ilumina MiSeq (2x250, paired-end).