Using oral swabs to collect remnants of stomach content during rumination in dairy cows can closely replicate ruminal bacterial communities, making it beneficial for large-scale studies on the rumen microbiome.
The quality of these swabs can vary, affecting their ability to accurately reflect the microbiome due to factors such as sampling time, cow behavior, and swab color.
Our research shows that darker swabs correlate with increased bacterial diversity while lighter swabs display greater variation; darker swabs also relate to the ruminal fungal community, indicating their potential as a more accurate representation of the ruminal environment.