Metagenomics – Potential to Predict Feed Efficiency in Sheep

It is hypothesized that variation in feed efficiency of ruminant livestock is associated with differences in rumen microbial populations, and that diet type influences these populations.  For this study, growing wethers (initial BW 51.3 ± 1.2 kg) of Rambouillet, Hampshire, and Suffolk breed types were randomly allocated to receive a concentrate (n = 39) or forage-based (n = 38) pelleted diet for a 49 d trial period during which individual intake data was collected.  Residual feed intake (RFI) was estimated for each wether as an assessment of feed efficiency.   Wethers were ranked on RFI, and DNA from rumen samples collected from the most efficient (n = 3) and least efficient (n = 3) wethers within each diet group was sequenced.  Microbial taxa were identified by comparing filtered reads of 16S rRNA genes to a reference database.  The GENMOD procedure of SAS was used to determine differences in taxa abundance due to diet, RFI classification, their interaction, and breed type.  As expected, most differences in taxa abundance were due to diet. Of the 20 most abundant taxa, all but one differed (P < 0.001) between concentrate and forage-fed wethers.  Additionally, 7 of the 20 most abundant taxa differed (P ≤ 0.034) in frequency due to RFI classification, and 8 also differed (P ≤ 0.032) according to the diet by RFI classification interaction.  These results suggest that rumen microbial populations are influenced by diet type, and that differences in these populations are associated with variation in feed efficiency in sheep.