Assessment of cattle feedlots
The genomic DNA of strain NWUTAL1 was extracted from a pure culture grown on Bile Esculin Agar supplemented with vancomycin with a DNA extraction kit (Zymo Research, CA) according to the manufacturers protocol. The DNA quality and quantity were determined using a NanoDrop Lite spectrophotometer (Thermo Fischer Scientific, CA). The DNA was sent to Inqaba Biotec, a commercial next-generation sequencing (NGS) service provider in South Africa for 16S rRNA and whole-genome sequencing. The draft genome of E. durans NWUTAL1 was obtained with whole-genome shotgun sequencing using an Illumina paired-end library with an average insert size of 300 bp. We used 50 ng of the DNA sample to prepare the library with the Nextera DNA sample preparation kit (Illumina). The sample was fragmented with an ultrasonication approach (Covaris). The resulting DNA fragments were size selected (300 to 800 bp) with AMPure XP beads. The fragments were then end repaired, and Illumina-specific adapter sequences were ligated to each fragment. The sample was indexed, and a second size selection step was performed. The sample was then quantified with a fluorometric method, diluted to a standard concentration (4 nM), and then sequenced on Illuminas HiSeq X Five platform according to the kit protocol.