Compositional and Functional Seggregation of Rumen Microbiome in Beef Cattle with Different Feed Efficiency

The bovine rumen hosts a complex microbiome to ferment ingested plant materials and to provide the host animal with energy needed to perform daily functions. Compositional variation of the rumen microbiome is associated with variation in cattle feed efficiency, but the mechanisms remain unknown. To gain a better understanding of how the rumen microbial community contributes to the variation of cattle feed efficiency, 454 pyrosequencing was applied to generate the microbial metagenomes of rumen contents from beef cattle from distinct residual feed intake (RFI) classes. Phylogenic analysis of the obtained sequences identified compositional variation at different phylogenic levels for bacteria, archaea, eukaryote, and virus, and quantitative variation was observed for 16 microbial families. Under SEED subsystems assignment, 33 molecules were found to be RFI-group-specific, and 41 molecules were differentially abundant between H- and L-RFI steers. Correlations between RFI-dependent pathways and RIF-exclusive molecules were identified in both H- and L-RFI animals. KEGG pathway analysis further identified RFI-associated molecules from 11 different metabolic pathways. These results have provided a more detailed view of the differences between the rumen metagenomes of H- and L-RFI animals, and warrant further investigation of the rumen transcriptome and proteome to verify the hypothetical mechanisms contributing to variation in host feed efficiency.