Rumen microbial community is important to host health and development in neonatal ruminants. However, molecular and host physiological changes associated with early bacterial colonization are largely unknown in cattle. The aim of this study was to investigate changes in host tissue transcriptomics (in liver and rumen), and in the rumen wall microbial metatranscriptomics in neonatal calves, treated with artificial dosing of exogenous rumen content. Ruminal content from adult cow was used as inoculum. Four newborn Holstein calves were treated with fresh inoculum, and 4 of them were treated with sterilized rumen inoculum at 2, 4, and 6 weeks. Bacterial community diversity of administered rumen inoculum was analyzed by 16S rRNA gene sequencing. All administered inoculum samples had Good’s coverage ≥97%, with Bacteroidetes as the most abundant phylum (53.31 ± 1.85% SE) followed by Firmicutes (34.32 ± 1.82% SE). Liver and rumen tissues were collected at 12 weeks at necropsy. Whole transcriptome RNA sequencing was used to characterize transcriptome changes. A total of 158 differentially expressed genes (DEGs) (fold-change, FC ≥ 1.5, P ≤ 0.05) was identified in rumen, and 338 DEGs (FC ≥ 1.5, P ≤ 0.05) was identified in liver. Functional annotation of these DEGs indicated enrichment of extra cellular matrix (P ≤ 0.001) and inflammatory response (P ≤ 0.001) in rumen, and enrichment in immune response (P ≤ 0.001) and sphingolipids metabolism (P ≤ 0.001) in liver. Specifically, upregulation of SGPLl, a polar sphingolipid metabolite, suggested an adaptive response in host to the influx of Bacteroidetes introduced by artificial dosing. Metatranscriptome analysis of rumen wall microbes indicated significant increase (P ≤ 0.001) of mRNA transcripts from Bacteroidetes and Firmicutes in treated calves, suggesting functional establishment of artificially dosed microbial communities. Our study provided insights into transcriptome changes in host and rumen microbial community resultant from early colonization of microbial species in young calves. Follow-up studies will focus on microbes mediated rumen development, health and nutrition in ruminants.