16S rRNA gene amplicons and viral metagenomics sequencing of nasal swabs obtained from BRD diagnosed dairy calves and pen matched heathy controls

Nucleic acids were extracted and purified from nasal swabs obtained from BRD diagnosed calves (n=10) and pen matched healthy controls (n=10) at day of calf arrival to research farm (day-1), day of BRD diagnosis (day-BRD) and day 28 of the study (day-28). PCR amplification of an approximate 467 bp region within the hypervariable V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq Sequencer for all 3 timepoints. Day-1 and day-BRD nasal samples were also prepared for virus shotgun metagenomic sequencing by RT PCR to obtain cDNA, amplified and then sequenced on the Oxford Nanopore Mk1C and the Illumina NovaSeq.