Structural differences between rumen and caecum microbiota of growing cattle fed a control or linseed and nitrate supplemented diet
Genomic DNA (gDNA) was extracted from each rumen and caeca sample using bead-beating and on-column purification (Popova et al., 2010). DNA extracts were quantified on the Nanodrop 1000 Spectrophotometer (Thermo Fisher Scientific, France) and run on a FlashGel System (Lonza, Rockland, Inc) to check integrity. Approximately 3 µg of gDNA were sent to Roy J. Carver Biotechnology Center (Urbana, IL61801, USA) for fluidigm amplification and MiSeq Illumina sequencing. Selected primers (V4_515F_New V4_806R_New) amplified specifically bacterial 16S rDNA