WP1. Relationship between natural abundance of 15N, rumen microbial signatures and feed efficiency in growing cattle.
Alongside measurements of FCE and δ15N, we estimated changes in body composition and used diet treatments and rumen metagenomics to explore these effects. Nitrate fed steers had reduced FCE and δ15N enriched plasma compared to non-nitrate containing diets. The negative relationship between FCE and δ15N was strengthened with the inclusion of fat depth change at the 3rd lumbar vertebrae, but not with the addition of average daily gain. We identified 1700 microbial genes with a relative abundance >0.01% of which, 26 genes were associated with δ15N. These genes explained 69% of variation in δ15N and showed clustering in two distinct functional networks. However, there was no clear relationship between their relative abundances and δ15N, suggesting that rumen microbial genes contribute little to δ15N. Conversely, we show that changes in the composition of gain, specifically fat accretion, can provide additional strength to the relationship between FCE and δ15N.
WP2. Assessment of the potential of natural abundance of 15N and rumen microbial signatures to evaluate feed efficiency in young animals.
Study 1:
A total of 54 Charolais bulls were ranked according to RFI with extremes classified as either efficient (Neg-RFI) or inefficient (Pos-RFI) as well as for FCE. No differences were detected in carcass conformation, fat scores, hot carcass weight or dressing percentage. Yet, heart and bladder weights were heavier in Pos-RFI, and rumen weight tended to be heavier in Pos-RFI bulls. RFI did not affect bulk 15N or 13C fractionation. A negative correlation was observed between FCE and δ15Nplasma proteins-diet. Inefficient bulls (Pos-RFI) had higher δ15N in glycine compared to Neg-RFI bulls. Similarly, metabolomic analysis showed a tendency for concentrations of glycine and sarcosine to be elevated in Pos-RFI and Neg-RFI bulls, respectively. Among vitamins, only flavin adenine dinucleotide concentration was higher in the blood of bulls with High FCE. These results suggest that the two feed efficiency metrics differ in the underlying mechanisms of metabolism, where RFI is driven by differences in the energetic requirements of visceral organs and the extent of AA catabolism. This part of the study was published in the Journal of Agricultural and Food Chemistry (Meale et al., 2017 in press).
For the RFI phenotype, no differences in alpha diversity, a measure of the diversity within a population, were observed within the rumen or feces, for either Archaea or Bacteria. However, ruminal archaeal populations (beta-diversity) between high- and low-RFI bulls tended to differ, suggesting there may be differences related to feed efficiency in the form of FCE. There were, however, no differences in diversity observed in the feces of these bulls. Comparing the archaeal taxa present in the rumen of divergent RFI bulls showed that the abundance of all Methanobrevibacter clades combined was higher in the rumen of low- vs. high-RFI bulls. Whereas, in the feces, Rikenellaceae from the Bacteriodetes phylum, was more abundant in low- vs. high-RFI bulls. For the FCE-phenotype, rumen bacteria of high-FCE bulls had greater evenness and abundance of OTUs, compared to that of the low-FCE bulls. Similarly, fecal bacteria of high-FCE bulls displayed greater species richness compared to low-FCE bulls. Analysis of the beta-diversity between high- and low-FCE bulls showed a tendency for separation between the two feed efficiency groups. Additionally, a comparison of the bacterial taxa indicated Paraprevotellaceae was more abundant in rumen of low-FCE and cecum of high-FCE bulls, compared to the rumen of high-FCE and cecum of low-FCE, respectively.
Study 2: Assessment of early life treatment on methanogenesis and gut microbiota.
Eighteen female dairy calves were randomly assigned at birth to either a treatment or control group . Treatment and placebo was administered daily via an oral gavage and lasted until week 14 of life. Calves were weaned at week 11. Calves were sampled for rumen content, fecal matter and saliva at week 1, 4, 11, 14, 23 and 61 weeks of life. Additionally, blood samples were taken at weeks 11, 14, 23 and 61. Following weaning, until week 23, calves were tested for methane emissions using the GreenFeed system. Calves were re-examined for methane emissions at approximately 1 year of age. DNA from rumen content and feces will be sequenced using primers for bacteria, archaea, fungi and protozoa.
