Periodic Reporting for period 1 - MarkEfficiency (Digestive and nutritional indicators of feed efficiency in cattle fed forage-based diets)
Reporting period: 2015-09-01 to 2017-08-31
Within the context of rarefaction of natural resources, climate change and global human population growth, achieving food security in a sustainable way is a present-day challenge facing mankind. The global demand of meat, dairy and eggs is increasing by more than two percent per annum, fuelled by the growing population, but also by changes in diet due to increased economic affluence, particularly in developing countries. Livestock animals are also a major source of greenhouse gas emissions and effluents. To comply with the current socio-economic context, it is essential for sustainable livestock production to target the efficient use of feeds not suitable for human consumption. Ruminants are particularly suitable as a result of their symbiotic rumen microbes, they can convert forages and low quality nitrogen sources into high protein and essential micronutrients present in meat and milk. Evaluation of the feed efficiency of ruminants fed non-competitive feed resources is a current focus of research to increase the profitability and sustainability of European ruminant farming systems. Feed efficiency is a complex trait and phenotyping this trait is lengthy and costly. In addition, newer sustainability parameters, such as methane emissions and nitrogen losses have to be incorporated for a more comprehensive evaluation of the “sustainable” phenotype. The general objective of this action is to explore potential biomarkers of feed efficiency in cattle fed forage-based diets that could be used to improve our understanding of the physiological basis of efficient animals and that could also be used as an early evaluation tool in young animals and/or on large numbers of animals in commercial settings for assessment of nutritional management problems and for selection purposes.
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.
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.
The notion of improving ruminant production efficiency and being able to effectively measure and rank this trait in young animals fed diets comprising ingredients which pose not threat to human food sources, is of increasing importance as the world’s human population continues to rapid expand. Food security is a growing concern and ruminant possess the unique ability to convert highly fibrous feeds not-readily consumable by humans to high protein products. The ability to exploit this process by selecting the most efficient animals would further benefit society by reducing the environmental impact of ruminants, for example due to greenhouse gas emissions. Further to this, another promising outcome of this project was the result, whereby methane emissions where reduced in calves when treated with an antimethanogenic compound from birth. If this pattern holds and the treatment of calves results in long lasting reductions in methane production this will have significant impacts on ruminant production systems if producers are rewarded for implementing this strategy on-farms.