Diversity and composition of microorganisms in the lower gastrointestinal tract have been shown to affect health and weight in humans and other mammalian species. At least a portion of the microbial diversity is likely under host genetic control. Our objective was to determine whether animal feed intake and growth were genetically correlated with microbial taxonomic groups as measured in fecal samples from the lower gastrointestinal tract through metagenomic analysis. Fall born animals (n = 905) of various breed composition (crosses of 18 different breeds) had individual animal feed intake recorded during a 63d period. Steers (n = 491) received a high energy concentrate (finishing) ration, and heifers (n = 414) received a roughage (growing) ration. During these feeding trials, animals were weighed on 2 consecutive days both when feed intake collection began and ended with additional weights recorded at least every 3 weeks. Fecal samples were collected prior (once), during (at least 3 times), and after (once) the feed intake trial period and pooled as a composite sample by animal. Taxonomic composition of the fecal microbiome was quantified from shotgun metagenomic sequencing of total DNA. Common contigs within and among animals were pooled by phylogeny yielding a reference metagenome assembly of 87 taxonomic groups. These groups (each present in at least 75% of the animals) were quantified by mapping reads from individual animals onto the reference assembly. Genetic (co)variance components for feed intake, gain, and individual taxonomic groups were estimated using REML. Data were modeled with fixed effects of contemporary group (sex, year, season) and breed composition covariates. Random effects were animal direct genetic effect (pedigree derived relationships) and error. Seven taxonomic groups were estimated to be heritable (P ≤ 0.10). Genetic correlations were detected (P ≤ 0.10) for Blautia with feed intake (r = 0.61) and Cellulosilyticum with weight gain (r = −0.68). Ration (or sex) specific correlations were not estimable; however, it is likely that ration affects the lower gastrointestinal tract microbial composition. The USDA is an equal opportunity provider and employer.