Ruminants are dependent on the microbiota (bacteria, protozoa, archaea and fungi) that inhabit their reticulo-rumens for digestion of feedstuffs. Nearly 70% of energy and up to 85% of the protein requirements for dairy cows are met from microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to comprehend the functional relevance of microbial genomes. Particularly, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients to more fully understand the physiology of feed digestion in the rumen. The need to increase energy and protein content of feeds to meet high nutrient demands of lactation in the dairy sector are well appreciated. Application of these genomic-based approaches offers the promise of unraveling specialized microbial niches and their gene repertoires that have the potential to enhance fiber digestion, microbial protein synthesis and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.