The objective of the study was to identify the predominant rumen bacterial groups that explained the variation in average daily dry matter intake (ADFI), average daily gain (ADG), and gain-to-feed efficiency (FE) in beef cattle using linear regression models. Data on individual intake and body weight were collected from a cohort of heifers (n = 125) fed a growing diet during 2009 and a cohort of steers (n = 122) fed a finishing diet during 2014. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region using the Illumina MiSeq platform. Statistical analyses were done within cohort due to the variation in sex and diet. To account for the inherent breed differences in ADFI and ADG, breed fractions were fitted as covariates in a linear model for both ADFI and ADG and residuals were regressed. Based on the regression of the residuals for ADG on residuals for ADFI, 4 animals were selected from each quadrant (n = 16) to determine differential features of the microbiome (operational taxonomic units (OTUs)) that explained variation in feed efficiency traits. Linear discriminatory analysis effect size was used to identify differential OTUs. The remaining samples from each cohort were used to perform forward stepwise regressions to identify subsets of predictive OTUs for the feed efficiency traits. To evaluate model accuracy, heifer data was used to assess the steer models and in turn the heifer models were assessed using the steer data. Across quadrants, α (P ≥ 0.40) and β (P ≥ 0.10) diversities were similar for both heifer and steer cohorts. OTUs belonging to the families Bifidobacteriaceae, BS11, Erysipelotrichaceae, Fibrobacteraceae, Lachnospiraceae, Prevotellaceae, Ruminococcaceae, S24–7, Spirochaetaceae, Veillonellaceae, and Victivallaceae explained the variation in ADFI, ADG, and FE in the heifer and steer cohorts. This study shows that the rumen microbiome is an important factor that influences feed efficiency in beef cattle and can contribute as much as 20% of the variation.