16S sequencing of nasal swab from Cow
Total nucleic acids were extracted from NP swabs as described previously (Holman et al., 2017). DNA extraction from the vaginal swabs followed the same protocol. To obtain DNA from fecal samples, the feces were first freeze-dried and then mixed with a ball grinder. A total of 250 mg of the homogenized fecal material was used for the DNA extraction process and followed the manufacturer's guidelines (Cat# 47016, DNeasy PowerSoil Pro Kit, QIAGEN). In DNA from all samples, the V4 region of the 16S rRNA gene was amplified using primers 515-F (5-GTGYCAGCMGCCGCGGTAA-3) and 806-R (5-GGACTACNVGGGTWTCTAAT-3) (Holman et al., 2019). The amplicon was sequenced on a MiSeq instrument (PE250, with 25,000 read coverage, Genome Quebec, Montreal, Quebec, Canada) with the MiSeq Reagent Kit v2.