Rumen Microbiota Differences Associated with Diet and Feed Efficiency Status in Sheep

The rumen microbiota plays a large role in the digestion of consumed feeds in ruminant livestock and likely influences the efficiency of feed use. Our objective was to determine differences in rumen microbial profiles of growing lambs attributable to effects of diet and feed efficiency status. Growing wethers (initial BW = 51.3 ± 1.2 kg; n = 77) were fed either a concentrate- (C; n = 39) or forage-based (F; n = 38) diet. Individual feed intake was measured over a 49 d intake trial to allow for estimation of residual feed intake (RFI), a measure of feed efficiency. Rumen fluid samples were collected at the end of the trial, and microbial DNA was extracted for sequencing from the 10% lowest ranking RFI (n = 4) and highest ranking RFI (n = 4) wethers on each diet. Resulting paired-end reads were compared with a database of known 16S rDNA genes. Operational taxonomic units (OTUs) were defined as sequence clusters with ≥ 97% identity.  Differences in OTU abundance according to the main effects of RFI status and diet, and their interaction were determined, using total OTU abundance as a covariate. Of 349 OTU identified, abundance differences (P ≤ 0.05) were observed with respect to diet (n = 52), RFI status (n = 17), and their interaction (n = 28). These results not only confirm that diet influences the rumen microbiome, but also that key microbial species may influence feed efficiency status, and those species may differ with diet composition.