Evaluation of the upper respiratory and fecal microbiomes in neonatal beef calves
Twenty-eight late gestation commercial beef cows were transported from a local ranch near Clayton, NM to the Clayton Livestock Research Center two weeks prior to estimated first calf. Cows were housed in individual pens fitted with canvas tarps on shared fences to limit contact between unrelated calves and cows. Left nasal (LN), right nasal (RN), fecal, and vaginal swab samples were collected from cows at a single time point promptly after parturition. Swabs of the LN, RN, and rectum were collected from calves at birth (0 h), 6, 12, and 24 h post-parturition. Samples were flash frozen in an ethyl alcohol and dry ice solution then placed on dry ice and transported to the Veterinary Education, Research, and Outreach (VERO) laboratory in Canyon, TX. Samples were stored at -80C until processing. DNA was extracted from swabs using Power Soil Pro kit. Extracted DNA was used to prepare DNA libraries for full-length 16S rRNA gene sequencing on a MinION Mk1C device. Sequenced reads were classified using Centrifuge and used in microbiome analyses conducted in R to estimate the changes in the microbiome according to animal type (cow versus calf), time of collection, and sample type (nasal, fecal, or vaginal)