The Effect of Diet on Rumen Microbial Profiles in Sheep

ABSTRACT: The ruminal microbial ecosystem plays a large role in fermentation of consumed feeds in ruminant livestock. The objective of this study was to determine the effects of diet on rumen microbial profiles in lambs fed either a concentrate or forage-based diet. Growing wethers (initial BW = 51.3 ± 1.2 kg; n = 77) of Rambouillet, Hampshire, and Suffolk breed types were randomly allocated to receive a concentrate (n = 39) or forage-based (n = 38) pelleted diet. Individual feed intake was measured with a GrowSafe System for 49 d and BW was recorded weekly to allow for estimation of feed efficiency. Rumen fluid samples were collected at the end of the feeding trial and DNA was extracted for sequencing from the most (n = 6) and least efficient (n = 6) 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 318 prokaryotic OTUs were present in at least one animal. There were differences (P < 0.001) in frequency of the 12 most abundant OTUs between concentrate and forage-fed wethers. The most abundant OTU across diets was Prevotella ruminicola, which had greater (P < 0.001) abundance in forage-fed lambs compared with concentrate-fed lambs; however, 9 of the 12 most abundant OTUs had greater (P < 0.001) abundance in concentrate-fed lambs.  These data suggest an effect of diet on microbial profiles in sheep.