The Next Bovine Genome: The Rumen Metagenome

The rumen harbors a dense (1011 organisms/ml of rumen contents) and complex microbial community (over 3,000 different species), or microbiome, the structure of which is shaped by the process of evolution and reflects the intrinsic dynamics of speciation and diversification and the impact of exogenous environmental influences.  The bovine rumen microbiome contains all three domains of life, Bacteria, Eukarya and Archeaea, and functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain volatile fatty acids, and methane.   With the advent of next generation sequencing technologies, it is now possible to explore in unprecedented phylogenetic depth the fine-grained structure of the rumen microbiome.  Deep hyper-variable SSU rDNA sequencing can be used to determine the phylogenetic composition of the rumen microbiome at unprecedented resolution.  Moreover, gene-centric comparative metagenomics can be used to predict the metabolic potentials in the rumen microbiome with respect to nutrient utilization.  These approaches seek to produce both phylogenetic and metabolic data about the microbiome, and to detect unique metabolic processes undertaken by these microbiomes, which can indicate the relative importance of these processes to both host and microbiome.  By applying high-resolution metagenomic analyses to the rumen microbiomes one can begin to understand the physiological ecology, differences in the microbial community structure and the metabolic potential which contributes to increased feed efficiency.  By doing so, once can contribute to our understanding of animal growth and nutrient utilization, and reveal strategies for improving this by manipulating the rumen microbiome.  Ultimately, these approaches will lead to strategies for improving meat and milk production and the nutritional value of milk.