At birth, the calf gut is colonized by symbiotic microorganisms that associate into communities, which then undergo successive waves of compositional changes towards achieving a mature microbiome. Since these early stages are critical to the establishment of optimal gut communities that will later affect the health status and nutrient utilization of the adult, there is great interest in discovering feedstuffs that can modulate the composition of gut symbiotic microorganisms. A companion study found that Holstein calves fed pasteurized waste milk and starter pellets containing 8% (DM basis) of a microbially-enhanced soy protein product (MSP) had greater CP, NDF and ADF total tract digestibility compared to calves fed a control diet. As these results suggested differences in gut function, a comparative gut microbiome composition analysis was pursued using fecal samples collected from representative individuals from each treatment (n=5 / treatment) at 12 weeks of age. The bacterial 16S rRNA gene (V1-V3 region) was PCR-amplified from fecal microbial genomic DNA, then sequenced by Illumina MiSeq 2X300 to assess taxonomy and species diversity by Operational Taxonomic Unit (OTU) clustering. ACE and Chao1 estimates of total species richness were lower in MSP-fed calves compared to controls (P< 0.05). Calves fed MSP were found to have less variation in Firmicutes (79.8–83.8%) and Bacteroidetes (13.2–18.4%) compared to control-fed calves (Firmicutes: 56.0 - 83.6%; Bacteroidetes: 15.8 - 41.0%). While overlap in OTU composition was observed across different diets, three species-level OTUs were found to be associated with a particular treatment. OTUs SD_Bt-00990 and SD_Bt-01010, both corresponding to novel bacterial species affiliated to Ruminococcaceae, were found in higher abundance in control fed calves, while OTU SD_Bt-12535, likely a strain of Prevotell copri(99.2% sequence identity), was more highly represented in MSP-fed calves. Results suggest that MSP could be used to modulate the gut microbiome of growing calves.