Effects of Diet and Feed Efficiency Status on Rumen Microbial Profiles in Sheep

The rumen microbiome plays a large role in fermentation of consumed feeds in ruminant livestock. Our objective was to determine the effects of diet and feed efficiency status on rumen microbial profiles in growing lambs. Wethers (initial BW = 51.3 ± 1.2 kg; n = 77) were randomly allocated to a concentrate (C; n = 39) or forage-based (F; n = 38) pelleted diet. Individual feed intake was measured with a GrowSafe System for 49 d and initial and final BW were recorded for estimation of residual feed intake (RFI), a measure of feed efficiency. DNA from rumen fluid was extracted for sequencing from the most (L-RFI; n = 8) and least efficient (H-RFI; n = 8) wethers. Pair-end reads were filtered, quality trimmed and compared with a database of known 16S rRNA genes. Operational taxonomic units (OTU) were defined as sequence clusters with ≥ 97% identity, and 349 prokaryotic OTUs were present in at least one animal. There were 33 OTUs affected (P ≤ 0.05) by the diet by RFI status interaction; 27 were of greater (P ≤ 0.05) abundance in L-RFI, C-fed lambs. There were 54 OTUs that differed (P ≤ 0.05) by diet; 26 were of greater (P ≤ 0.05) abundance in C-fed wethers. Finally, 14 OTUs differed (P ≤ 0.05) by RFI status; 8 were of greater (P ≤ 0.05) abundance in L-RFI lambs. Results suggested that key rumen microbial species are important to regulation of feed efficiency, and those species may differ with dietary composition.