In line with our results, colonization with lactobacilli has previously been reported to associate with lower cytokine responses following allergen stimulation. Also, in a recent paper, intranasally administered lactobacilli to mice resulted in a diminished expression of several pro-inflammatory cytokines, via a TLRindependent pathway, suggesting that Lactobacillus species generally seem to suppress immune responses. As for lactobacilli, the early presence of bifidobacteria species has been associated with immune function and allergy development. Although we did not find any consistent associations between early colonization with bifidobacteria and cytokine production at two years of age in this study, early colonization with Bifidobacterium species is associated with higher levels of secretory IgA in saliva and reduced allergy prevalence at five years. Gut colonization with the skin/nasal passage bacteria S. aureus is common during infancy and probably caused by increased hygienic conditions in the Westernized Countries. Here, we show that S. aureus gut colonization two weeks after birth associates with significantly increased numbers of IL-42 and IL10 secreting cells, after PHA XL880 stimulation at two years of age. S. aureus colonization and exposure to its enterotoxins have been associated with asthma and rhinitis, and also in our study S. aureus seems to be more frequently detected early in infants being allergic at the age of five. In children co-colonized with both lactobacilli and S. aureus compared to children colonized with S. aureus alone, suppressed numbers of IL-42, IL-102 and IFN-c secreting cells were found from these children at two years of age. This indicates that the simultaneous presence of lactobacilli early in life might modulate an S. aureus induced effect on the immune system. Children negative for both species had cytokine-producing cell numbers in the same magnitude as children colonized with lactobacilli, indicating that it is the presence S. aureus, and not solely the absence of lactobacilli, that triggers an increased number of cytokine-producing cells. As the majority of infants are colonized with S. aureus early in life, we speculate that other species, such as certain Lactobacillus spp, might be needed to regulate S. aureus triggered responses to avoid an inappropriate immune stimulation. Further, our in vitro PBMCs stimulations with S. aureus 161.2 and LGG support the idea that S. aureus induces a cytokine response, which can be suppressed by lactobacilli. The opposing findings regarding IL-10 in relation to S. aureus 161.2 may be an in vitro and in vivo consequence and due to the differences in our experimental set-ups. For the association-study we measured PHA-stimulated T cell cytokine responses, while for the in vitro studies we investigated the direct effects of the bacterial species on PBMCs. Thus, other cells, e.g. monocytes, may produce IL-10, which could then explain these contradictory results. Several potential mechanisms, by which lactobacilli potentially exert their immunosuppressive effects, have been reported. For instance, lactic acid produced by lactobacilli, has been shown to degrade gram-positive bacterial lipoteichoic acid and reduce pathogen-induced cell cytotoxicity. In addition, metabolites from lactic acid producing bacteria have been reported to reduce TLR-induced inflammatory responses. Also, T helper responses, in PBMCs cultures after PHA stimulation, were down regulated, by lactobacilli, in an monocyte-induced IL-10 dependent manner supporting our in vitro findings of increased IL10 levels in LGG stimulated cultures. Supplementation with different Lactobacillus species has been used in allergy prevention, but the results vary between studies.