Effects of feeding a rapeseed-based diet containing various protein concentrations and a soybean-based diet with a commercial protein level on nitrogen use efficiency and the rumen microbial community in lactating dairy cows

Eighty-eight dairy cows (22 cows per treatment) were offered three rapeseed-based diets (14%, 15,5% and 17% crude protein [CP]) and one soya-based diet with 15.5% CP for 250 days. Rumen samples were collected at weeks 0, 4, 8, 12, 20 and 28 post calving. Residual feed intake (RFI) was estimated for each cow during five 5-week periods (weeks 2-6, 6-10, 10-14, 18-22, and 26-30 post calving), with these periods centered on the rumen sampling occasions at 4, 8, 12, 20 and 28-weeks post calving. Cows from each treatment were ranked from high-RFI to low-RFI and six least efficient cows with high-RFI and six most efficient cows with low-RFI from each treatment (12 cows per treatment * 4 treatment* 6 time points = 288 samples) were selected for DNA extraction and sequenced via Illumina NovaSeq 6000 shotgun metagenome approach.