The effects of Saccharomyces cerevisiae fermentation product (SCFP) on the rumen bacterial function were studied in 8 rumen-cannulated lactating cows in a crossover study with 2 5-wk periods. Each period consisted of 4 wk of normal feeding and a 1-wk grain-based SARA challenge. A 3-wk washout period separated the experimental periods. During each period, 4 cows received 14 g/d of SCFP (Original XPC, Diamond V) mixed with 126 g/d ground corn and the other 4 received 140 g/d ground corn as control. Rumen fluid was collected during wk 4 and 5 of each period. DNA was extracted and V1-V3 region of 16S rRNA gene was amplified and subjected to pyrosequencing. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was used to impute metagenomic information based on 16S rRNA sequencing data. The SARA challenge and SCFP supplementation did not affect the α-diversity of the predicted functional gene families of rumen bacterial communities. However, the β-diversity was affected by SARA (P < 0.01), but not by SCFP. A total of 9 out of 36 level-2, and 39 out of 254 level-3 KEGG Orthology groups were found to be affected by SARA challenge (P < 0.01). At the KEGG level-2, pathways upregulated during SARA included cell motility, membrane transport, signal transduction and transcription, while pathways involved in the metabolism of terpenoids and polyketides, biosynthesis of other secondary metabolites, amino acid metabolism, signaling molecules and interaction, transport and catabolism were downregulated. However, SCFP supplementation and interaction between SARA challenge and SCFP supplementation were not significant. The relevance and accuracy of PICRUSt application to predict the function of microbiome in the rumen need further validation using shotgun sequencing approach.