title: Shotgun metagenomics of Bos taurus: fecal samples from healthy cows
design: Fecal DNA was extracted from 250 mg of selected samples using the Quick-DNA Fecal/Soil Microbe Miniprep Kit, quantified by Qubit, and equal DNA masses were pooled per cow and treatment period, resulting in 12 shotgun metagenomic pools. Libraries were prepared with the Illumina DNA Prep kit and sequenced on an Illumina NextSeq 1000 with a 2% PhiX spike-in, generating ~25 million clusters per pool. Reads were quality-trimmed using Trimmomatic and taxonomically classified at the genus level with Kaiju using the NCBI nr-based database. Bacterial diversity analyses were performed in R using phyloseq after rarefaction to even sequencing depth. Antimicrobial resistance genes were characterized using the nf-core AMR++ pipeline with MEGARes 3.0, producing ARG abundance profiles across treatments and time points.