Dietary impacts on rumen microbiota in beef and dairy production

The reticulo-rumen is the largest compartment of the ruminant digestive tract, and it harbors a complex anaerobic microbial community capable of producing a wide array of enzymes, some of which are important for the breakdown of plant lignocellulosic and non-structural carbohydrate (starch, sugars) material through the process of fermentation (Russell and Rychlik, 2001). Important outcomes of microbial fermentation are the production of volatile fatty acids (or short-chain fatty acids) that serve as fuels for the animal’s tissues and the synthesis of microbial protein that provides amino acids for the animal to produce high-quality protein for human consumption, i.e., meat and milk. Studies over the last few decades have conclusively demonstrated that the ruminal microbial ecosystem (both of the neonate and mature ruminant) can be altered by nutritional management (McCann et al., 2014b). Therefore, nutrition represents an important tool for manipulating the microbial ecosystem to optimize rumen function while producing high-quality meat and milk for meeting the demands of a growing human population. The recent development of omic technologies, e.g., sequencing of the 16S and 18S ribosomal RNA gene, metagenomics, and metatranscriptomics, along with bioinformatics tools, have not only enhanced the understanding of the rumen ecology, but also our ability to predict the functional capacity of the microbiota (McCann et al., 2014b). From a production standpoint, it is believed that further gains in knowledge that in the medium-to-long term could lead to practical applications will arise from the integration of taxonomic and functional data with “classical” parameters of rumen digestion, metabolism, and performance (Morgavi et al., 2013). Our aim in this review is to provide recent examples demonstrating how nutrition can alter the structure, composition, and diversity of the rumen microbiota in beef and dairy production. In addition, we attempt to highlight points where there are knowledge gaps for further research.