Buccal swabbing as an alternative way to stomach tubing to determine bacterial, archaeal, and eukaryotic community structure in the rumen of sheep. gut metagenome

Previously, rumen samples from ruminant animals were routinely collected via stomach tubing, and downstream analysis of microbial communities required freeze-drying, grinding and weighing of samples prior to DNA extraction. Our aim was to validate a less invasive buccal swabbing method that could potentially be performed on-farm in combination with a less laborious molecular sample preparation.