A major goal in dairy research is to improve milk production efficiency (MPE). With the advent of next-generation sequencing and advanced methods for characterizing microbial communities, efforts are underway to improve MPE by manipulating the rumen microbiota. Recent work has demonstrated that MPE is correlated and directly linked to ruminal bacterial community composition (BCC) in cows. Moreover, the adult cow rumen microbiota is highly stable and returns to a baseline community structure even after extreme perturbation. We seek to influence the rumen microbiota by early intervention in pre-weaning dairy calves. Two cannulated Holstein donors of known and disparate MPE were selected. Three cohorts of 6 bull calves each were established. Calves were dosed by oral gavage with a blended inoculum of rumen contents sourced from the high-efficiency donor (HE), the low-efficiency donor (LE), or an autoclaved 50:50 mixture from the donors as a microbe-free control (C). Dosing occurred within 3 d of birth, then every 2 wk through 6 wk of age. Feces were collected at each dosing as a proxy for gut BCC. Calves were sacrificed at 8 wk to access rumen contents and rumen wall sections were collected to assess papillation. Qualitative histological analysis suggests greater papillation in the HE and LE cohorts than in the C cohort, but subsequent quantitative measures are needed. Fecal and rumen samples from the males were subjected to 16S rRNA amplicon sequencing. We found that BCC differed by cohort in fecal and rumen samples (P < 0.05), with HE calf samples most similar to adult rumen samples and C calves least similar. Several bacterial OTUs were observed to have differential abundances in rumen samples at 8 wk (P < 0.05), including several classified to genera Ruminococcus and Prevotella and family Veillonellaceae, previously implicated in bovine feed efficiency. Pre-weaning average daily gain did not differ between cohorts (HE: 0.90 ± 0.07 kg, LE: 0.76 ± 0.07 kg, C: 0.73 ± 0.05 kg, P = 0.186). These data demonstrate that the microbiota can be influenced by early intervention, providing a compelling avenue for future development of whole-rumen based probiotics to the end of MPE improvement.