| Summary: | Abstract Rumen microorganisms are primarily essential for feed decomposition and nutrition of the host animal, playing a key role in the health and well-being of cattle as well as the efficiency of milk or meat production. However, they also generate pollutant emissions such as methane. Analysing this microbiota under different farming conditions is therefore essential for optimizing production while minimizing its environmental impact. In this study, with metataxonomic sequencing and qPCR, we analysed the composition of the cow rumen microbiota sampled through the cannula and via esophageal tubing before morning feeding under two contrasting diets, low- and high-starch contents. Buccal swabs were also collected at the same sampling times to assess their potential as a proxy for the rumen microbiota. The two rumen sampling methods resulted in similar taxonomic compositions of bacteria, Archaea, fungi and protozoa and showed similar changes after the diet shift, indicating that the use of esophageal tubing is a reliable method for capturing the microbiota structure and its potential shifts following dietary changes. In contrast, the buccal swabs did not accurately reflect the rumen microbiota under the low- and high-starch diets, even after specific stringent filtering of the buccal sequences. Furthermore, we identified microbial markers of acidogenic challenge, with Dialister spp. also detected in buccal swab samples as potential indicators.
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