Work Package (WP) 8 – Novel tools for end-users

WP Leader: John Wallace
Email: John.Wallace[at]abdn.ac.uk

The large volume of data generated in WP1-6 will be of great value to geneticists, nutritionists and microbiologists who study ruminants. The challenge of this Work Package is to make the information more useful to end users, who would include researchers, breeders, practical nutritionists and producers aiming to minimize their environmental emissions and thereby improve the efficiency of production (or vice-versa probably). Bioinformatics systems must be translated into tools for breeders. A metabarcoding system would enhance the value of next-generation sequencing to microbial ecologists, by increasing the accuracy of microbiome analysis, while reducing its cost dramatically. Another of the chief limitations to doing microbial ecology work is the need to obtain samples of ruminal digesta, which is a moderately invasive process. Here we propose to find if oral or faecal samples can provide proxy measurements of rumen microbial ecology as determined by 16S rRNA gene technology.

Aims

• To develop and publicize metabarcoding protocols suitable for the analysis of the rumen microbiome;
• To characterize the metaproteome in selected samples of ruminal digesta taken from WP3 and WP4;
• To create a data warehouse for open online use;
• To determine if fatty acids in milk fat or faecal archaeol concentration can be used as an on-farm proxy for methane emissions;
• To compare the bacterial and archaeal communities in samples of buccal, ruminal digesta and faeces taken in WP3 in order to establish if either buccal samples, containing regurgitated digesta, or faeces can be surrogate samples for assessing ruminal microbiomes, production efficiency or emissions;
• To establish a selection index for metabolic efficiency.

Major Outcomes

• Detailed standardized protocol for studying the rumen microbiome;
• Report on the analysis of the ruminal metaproteome: comparison with the microbiome and emissions;
• Report on the relations between ruminal archaea and methane emissions, and milk fatty acid and faecal archaeol concentrations;
• Report on the comparison of the bacterial and archaeal communities in samples of buccal digesta, ruminal digesta and faeces;
• Report on models for genomic breeding values estimation for environmental impact AND efficiency;
• Report on models for genomic breeding values estimation for environmental impact and efficiency traits;
• Report on breeding schemes, selection equations, expected rate of genetic progress;
• Data repository available on the data warehouse system to collect public metagenomic rumen experiments.