Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 4/16/2014
Publication Date: 4/15/2015
Citation: Li, R.W. 2015. Rumen Metagenomics. Book Chapter. New Delhi, India: Springer India. 379 p. doi: 10.1007/978-81-322-2401-3.
Technical Abstract: The rumen microbiome plays a critical role in normal physiology and nutrition of ruminants. Alterations in the rumen microbiome have important physiological and pathological implications. The advent of next-generation sequencing technologies and rapid development of computational tools and reference databases provide powerful tools in rumen microbiome studies. Rumen metagenomics enables studies on the collective genetic structure and functional composition of the rumen microbial community in a culture-independent manner and can be simply divided into functional metagenomics and sequencing-based computational metagenomics. Recent progresses in mining the rumen microbial community for novel enzymes, such as fibrolytic enzymes, or other biomolecules for industry and biotechnology applications using functional screening are discussed. Rapid advances in computational metagenomics tools and methods are summarized. Metagenomics has provided novel insights into the structure and function of the rumen microbiome. Recent efforts suggest that the core rumen microbiome consists of 8 phyla and 15 families, which likely contribute to the basic function of the rumen. Systematic investigations of the rumen microbiome, including its viral (virome) and plasmid (plasmidome) factions, have revealed previous unrecognized biodiversity in the rumen. Resistance and resilience of the rumen microbial community in response to perturbation is also discussed. Moreover, the need for mechanistic models and applications of general ecological theories and principles in rumen metagenomics studies are emphasized.