Traditionally, 16S data have been used to profile ruminal microbial communities and functionality has been inferred based on broad level taxonomic classifications. However, the accuracy of taxonomic calls is often lacking due to the poor resolution and lack of cultured representatives from the native rumen microbiome. The objective was to profile the metabolic capabilities of 20 native rumen microorganisms via in-depth analysis of their genomes coupled with metabolic modeling and flux balance analysis (FBA). For this study, 16 novel bacteria and 4 novel fungi were isolated from the rumen content of 3 healthy, mid-lactation Holsteins on TMR (16.3% CP, 37.3% NDF, 0.67 Mcal of NEI/lb). Strains were isolated using a diverse media panel and whole-genome sequenced (WGS) using Illumina Miseq and Oxford Nanopore sequencing platforms. Reads were assembled, annotated, and analyzed using metabolic modeling. All novel organisms shared less than 70% nucleotide homology to their closest neighbor in the NCBI database at the whole genome level, and were thus considered novel. Subsequent sequence analysis revealed the pivotal roles that these 20 microorganisms contribute to feed digestibility and milk production. For instance, isolates sequenced from the family Lachnospiraceae possessed a unique spectrum of genes associated with biohydrogenation and acetate production, which are commonly associated ruminal functions of Lachnospiraceae. The family Lachnospiraceae includes the genus Butyrivibrio, identified for xylan degradation and butyrate production in the rumen, and isolates from the genus Butyrivibrio displayed distinct metabolic profiles, with respect to amino acid metabolism and carbon source utilization. The Neocallimastigaceae isolates had unique polysaccharide metabolisms and docking mechanisms, suggesting that each fungal species may employ unique mechanisms to drive cellulolytic activity. These findings emphasize that functional capability can vary greatly between members of the same taxa. Looking beyond taxonomy can help us gain further insight into how bacterial communities affect ruminal health.