16S rRNA nasopharyngeal gene amplicons from apparently healthy Holstein calves and calves diagnosed with bovine respiratory disease

This study focused on characterizing the dynamics of the nasopharyngeal microbiome of pre-weaned and post-transport Holstein calves during the first two weeks of life and how it changes during Bovine Respiratory Diseases (BRD) development and antibiotic treatment. From the study, nasopharyngeal (NP) swabs were collected from 30 pre-weaned Holstein bull calves on days 0 (after transport), 7, and 14. Throughout the study, calves were monitored for respiratory clinical signs like coughing, labored breathing, fever, dropping ears, eye, and/or nasal discharge, which are indicators of BRD development. Calves were diagnosed with BRD if they showed 2 or more physical BRD symptoms. After identifying and diagnosing a calf with BRD, nasopharyngeal swabs were collected on day 0 (day of diagnosis) and days 1, 5, and 10 after antibiotic administration. BRD-affected animals were treated after NP collection with either tulathromycin or florfenicol.To analyze the nasopharyngeal microbiome, the region V4 of the 16S rRNA gene was amplified and sequenced using Illumina MiSeq Sequencer.