metagenome of beef calves
Extracted DNA was used to prepare DNA libraries for full-length 16S rRNA gene sequencing. The SQK-16S024 from Oxford Nanopore Technologies was utilized following the manufacturers instructions, while modifying the input and PCR number of cycles depending on the sample type as follows: 10 ng of extracted DNA and 25 cycles for fecal swabs, 50 ng of extracted DNA and 30 cycles for nasal and vaginal swabs. Each pooled DNA library consisted of 23 samples and one PCR blank (i.e., molecular grade water instead of extracted DNA). Each pooled DNA library was loaded onto a R9.4.1 flow cell (ONT, UK) and sequenced on a MinION Mk1C device for 24 hours. Real-time base calling and barcode demultiplexing was performed via the MinKNOW software version 22.10.7 (fast model basecaller in Guppy version 6.3.9).