Cattle
The rumen contents were collected from rumen canulated animals and solid digesta (~5g) was filtered from rumen fluid with a bodum coffee filter press and then immediately flash frozen in liquid nitrogen and stored at -80oC for further processing. The collected solid digesta was ground under liquid nitrogen and RNA was extracted using Trizol extraction as per manufacturers protocol followed by a column clean-up with the Megaclear kit as per manufactures protocol. RNA was enriched for mRNA using Illumina TruSeq mRNA library kit and 100 bp SE reads were sequenced with an Illumina Hi-seq 2000 at Genome Quebec sequencing centre.