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Microbial exposure early in life influences immune maturation and potentially also the development of immune-mediated disease. Here we studied early-life gut colonization in relation to cytokine responses at two years of age. Fecal samples were collected from infants during the first two months of life. DNA was extracted from the fecal samples and  Bifidobacterium (B.) adolescentis ,  B. breve ,  B. bifidum , a group of lactobacilli ( L. casei ,  L. paracasei  and  L. rhamnosus ) as well as  Staphylococcus (S.) aureus  were detected with real time PCR. Peripheral mononuclear cells were stimulated with phytohaemagglutinin (PHA) and numbers of IL-4−, IL-10− and IFN-γ secreting cells were evaluated using ELISpot. We further stimulated peripheral blood mononuclear cells with bacterial supernatants  in vitro  and assessed the IL-4−, IL-10− and IFN-γ inducing capacity by flow cytometry and ELISA. Early  S. aureus  colonization associated with higher numbers of IL-4− (p = 0.022) and IL-10 (p = 0.016) producing cells at two years of age. In contrast to colonization with  S. aureus  alone, co-colonization with lactobacilli associated with suppression of IL-4− (p = 0.004), IL-10− (p = 0.004) and IFN-γ (p = 0.034) secreting cells.  In vitro  stimulations of mononuclear cells with bacterial supernatants supported a suppressive role of  L. rhamnosus  GG on  S. aureus -induced cytokine responses. We demonstrate that the early gut colonization pattern associates with the PHA-induced cytokine profile at two years of age and our  in vitro  findings support that specific bacterial species influence the T helper cell subsets. This suggests that dysbiosis in the early microbiota may modulate the risk of developing inflammatory conditions like allergy.

Early-Life Gut Bacteria Associate with IL-4−, IL-10− and IFN-γ Production at Two Years of Age