The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows

DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed four diets with different ratios of grass and maize silage.