Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique

The study aimed at investigating the rumen microbiome composition and functional activity in mid lactating cows of Italian Holstein (IH) and Italian Simmental (IS) breeds. Eight IH and eight IS pluriparous cows with days in milking (DIM) ranging from 90 to 180 were selected and rumen contents were sampled with oesophageal tube. Rumen metagenome was analysed using a whole shotgun sequencing. Data were analysed for taxonomic classification and microbial genes. The relative abundance of Archaea, the Archaea to Bacteria ratio and the Archaea to Eukarya ratio were higher (<i>p</i> Bactroidaceae, <i>Bacteroides</i>, <i>Prevotellaceae</i> and <i>Prevotella</i> lower (<i>p</i> Euryarchaeota (<i>p</i> Methanosphera (<i>p</i> Methanothermobacter (<i>p</i>