To address this knowledge gap, we hypothesized that age (non-rumination, transition and rumination phases) and feeding type [supplemental feeding, (S) and grazing (G)] could modulateruminal microbiota, and further manipulate host mucosal innate immune function. To test this hypothesis, we applied a combination of MiSeq sequencing and relative RT-PCR analysis to investigate microbial diversity, as well as expression of genes encoding TLRs, inflammatory cytokines, and toll-IL-1 receptor (TIR)-domain containing adaptors.