Submitted to: Journal of Dairy Science
Publication Type: Review Article
Publication Acceptance Date: 8/31/2017
Publication Date: 10/25/2017
Citation: Bickhart, D.M., Weimer, P.J. 2017. Bovine rumen metagenomics – moving beyond microbial diversity. Journal of Dairy Science. 101:1-10.
Technical Abstract: The rumen is a large bioreactor that enables dairy cattle to derive nutrition from otherwise inedible plant polymers and compounds. Despite the direct contribution of the rumen’s microbial community toward the nutrition of the dairy cow, only a general knowledge has been gained of the metabolic processes within the rumen, and less still is known about most of the individual microbial species that colonize the organ. What has been discovered is that the rumen contains a diverse community of microbial species from all of the major domains of life, and that the contents of the rumen can vary greatly among individual animals. There is also preliminary evidence that rumen microbial profiles are heritable and sustainable within an individual, and that rumen microbial community structure can revert back to its original profile within a short period of time following substantial perturbation. Much progress has been made in recent years to identify the diversity of microbial species in the rumen; however, the most popular methods used to identify microbial species often lack the predictive power necessary for metabolic modeling of the entire rumen microbial system. This represents the most significant barrier to the design of models that can estimate the direct effects of rumen microbial content on downstream dairy production traits. If such challenges can be overcome, then there is the possibility that rumen microbial content could be assessed as a new phenotypic trait in cattle. In the future, we may estimate dairy production using a “Genotype by Environment by Microbial Interactions” model that accurately combines all factors affecting milk production.