Comparison of the digestive tract microbiota and resistome in grass-fed and grain-fed cattle

These data are from a study done to compare the microbiota (abundance and type of bacterial species) and resistome (antibiotic resistance genes) in grass-fed (system A) versus conventionally raised grain-fed beef (system B). Fecal swabs were collected from system A calves at multiple time points including pre-weaning, post-weaning, summer, and winter. Fecal swabs were collected from system B cows at four dietary stages: preweaning, transition, backgrounding, and finishing. Preharvest fecal swabs were also collected from cows in both agricultural systems. DNA was extracted from fecal swabs and Illumina-based shotgun metagenomic sequencing was used to characterize the microbiome.