Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: March 28, 2010
Publication Date: January 9, 2011
Citation: Li, R.W., Sparks, M., Connor, E.E. 2011. Dynamics of the rumen microbiota. In: Li, R.W., editor. Metagenomics and its Applications in Agriculture. New York, NY: Nova Science Publishers. p. 135-164. Technical Abstract: Optimizing rumen microbial ecosystem output by manipulating ruminal fermentation has long been attempted in order to satisfy the rapidly increasing need for meat, dairy and wool from the world’s burgeoning human population and to mitigate the environmental footprint of animal agriculture. The rumen microbiota is highly responsive to changes in diets and supplements, management practices, host physiology and genetics, as well environmental factors. Metagenomic analysis suggests that from cattle fed a hay-based diet, DNA sequences from over 500 genera can be identified from a single rumen microbial community. In this community, genus-level rank-abundance curves of the rumen microbial community exhibit a long right-hand tail pattern, which is characteristic of complex microbial ecosystems. The top 6 phyla, in terms of numbers of sequence hits, are Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, Spirochaetes and Euryarchaeota. The diversity is reflected by a broad phylogenetic representation of organisms in the rumen, from fungi, green algae, and protists, to parasitic nematodes; although some of these organisms could be transient species not having contributed directly to the biological functions of the rumen ecosystem. During rumen development, especially when the diet is switched from milk to hay, conspicuous changes in the rumen microbiota include diminishment of microaerophic species, as well as a significant expansion of Gram+ bacteria. Accompanying the changes in the rumen microbiota is the establishment of the ecosystem function, reflected by a rapid enrichment of fibrolytic enzymes associated with a hay diet, such as cellulases and xylanases. Ecological and physiological consequences of changes in rumen microbiota and implications of rumen functional diversity in terms of the rumen ecosystem resistance and resilience are also discussed in this chapter.