Evaluation of the upper respiratory and fecal microbiome in neonatal dairy calves

Commercial Holstein dairy cows (n = 26) and their calves (17 heifer and 12 bull calves; 3 cows delivered twins) were selected based on calving order. Cow sampling included left nasal swabs (LNS), right nasal swabs (RNS), vaginal swabs (VS), and fecal swabs (FS) using proctology swabs at 0h. Samples (LNS, RNS, and FS) were collected from calves at 0 h, 6 h, 12 h, and 24 h post-parturition and flash-frozen. DNA was extracted from swabs using Power Soil Pro kits, where extracted DNA was used to prepare DNA libraries for full-length 16S rRNA gene sequencing on a MinION Mk1C device.