Metagenomic approaches in harnessing gut microbial diversity

The mechanisms involved in the digestive process of the rumen are complex, and are accomplished by a diverse and dynamic group of microbes. Microbial diversity in the rumen has been predicted to enhance the resistance of the network of metabolic pathways by increasing the number of genes encoding the pathway, enabling the ecosystem to stabilize more rapidly after change to a new equilibrium. The more resistant metabolic pathways, and the more diverse source of novel pathways, will make the microbial system more resilient. A variety of molecular methods based on direct isolation and analysis of nucleic acids, proteins and lipids from environmental samples have been discovered, and they reveal structural and functional information about microbial communities. Molecular approaches such as genetic fingerprinting, metagenomics, meta proteomics, metatranscriptomics and proteogenomics are vital for discovering and characterizing the vast diversity of microbes and understanding their interactions with biotic and abiotic environmental factors. In this chapter, efforts are made to discover the possible applications of metagenomic tools for exploring the complex microbial diversity of ruminal microbes.