Gram-positive lactic acid-producing bacteria including Lactobacillus rhamnosus GG (LGG) are commonly used as probiotics, while fewer gram-negative probiotics including Escherichia coli Nissle 1917 (EcN) are characterized. A mechanistic understanding of their individual and interactive effects on human rotavirus (HRV) disease and immunity is lacking. Noncolonized, EcN, LGG and EcN+LGG-colonized neonatal gnotobiotic (Gn) pigs were challenged with HRV. EcN colonization associated with greater protection against HRV, also induced the highest frequencies of plasmacytoid dendritic cells (DC), significantly increased natural killer (NK) cell function and decreased frequencies of apoptotic and TLR4+ mononuclear cells (MNCs). Consistent with the highest NK cell activity, splenic CD172+ MNCs (DC enriched fraction) of EcN colonized pigs produced the highest levels of IL-12 (activates NK cells) in vitro. LGG colonization had little effect on the above parameters, and those of EcN+LGG colonized pigs were intermediate, suggesting that the probiotics modulate each other’s effects. Additionally, in vitro EcN-treated splenic or intestinal MNCs produced a higher but balanced cytokine repertoire (IFN-α, IL-12 and IL-10), as compared to that of pigs treated with LGG. These results indicate that the EcN-mediated greater protection against HRV was associated with potent stimulation of the innate immune system and activation of the DC-IL-12-NK immune axis.