The role of gastrointestinal microorganisms in developing and modulating the gastrointestinal immune response has been subject to investigation over the past few decades. However, early gastrointestinal tract stimulation and modulation of the systemic immune response is far from understood. This study explored the use of a non-pathogenic oral microbial inoculum to affect the composition of commensal microbiomes and subsequent systemic immune responses. Artificially raised piglets were divided into two groups: one group was orally inoculated (INOC) with non pathogenic gut microbiota, and the second group was uninoculated (UNINOC). In order to determine the effects of changes in the microbiome on systemic immune response, allergic type I) and delayed type (type IV) hypersensitivity responses were tested, as well as systemic immune responses via experimental infection with the respiratory pathogen hyopneumoniae. Pigs in group INOC had a lower severity of infection and stronger DTH response, suggesting a beneficial effect of the oral non-pathogenic microbial inoculation on commensal microbiomes and subsequent systemic immune responses. The 16S ribosomal RNA gene populations were amplified from DNA extracted from both fecal samples and nasal swabs collected temporally throughout the study. These amplicons were sequenced using 454 FLX-titanium technology to determine at great depth the effect of the oral microbial inoculum on both the gut and pulmonary commensal microbiomes. Preliminary analyses of the sequencing results reveal compositional differences in the pulmonary microbiomes between treatment groups, while analyses of the fecal microbiome are on-going. These results suggest the oral microbial inoculum is influential to our commensal microbiomes, and has a significant effect on systemic immune responses.