Diet and feed efficiency status affect rumen microbial profiles of sheep

The rumen microbiota plays a large role in the digestion of consumed feeds in ruminant livestock and likely influences feed efficiency. The objective of this study was to determine associations of diet and feed efficiency status with rumen microbial profiles in growing lambs. Growing wethers 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 and initial, mid and final BW were recorded for estimation of feed efficiency. Rumen fluid samples were collected at the end of the trial, and DNA for sequencing was extracted from the rumen fluid of the 10% lowest ranking and highest ranking wethers for feed efficiency on each diet. Paired-end reads were filtered, quality trimmed and compared with a database of known 16S rDNA genes. Operational taxonomic units (OTUs) were defined as sequence clusters with ≥ 97% identity in a 16S rDNA database; 349 prokaryotic OTUs were present in at least one animal. Of these OTUs, 27 were affected (P ≤ 0.05) by the interaction of diet with feed efficiency status, 44 were affected (P ≤ 0.05) by the main effect of diet, and 11 were affected (P ≤ 0.05) by the main effect of feed efficiency status. These results confirm that diet is a major influence on composition of the rumen microbiome. Also, key microbial species may play important roles in the regulation of feed efficiency, and those species may differ according to diet composition.