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Supplementary Material Supplementary Figure 1 Significant Treg depletion in intestines and gut associated lymphoid tissues (GALT). DEREG mice were gastrically gavaged with C. rodentium strain ICC 180 and then injected i.p. with DT or PBS day 0 and 1 p.i. At day 2 p.i., mice were sacrificed for cell isolation from different organs. Isolated cells from different organs were stained with anti-CD4, anti-CD4 and anti-FoxP3 for FACS analysis of depletion efficiency of regulatory T cells in spleen, mesenteric lymph nodes (mLN), Peyers Patches (PP), colon (CO) and small intestines (SI). Supplementary Figure 2 Frequency of Treg cells after each round of DT- mediated depletion shows significant reduction in the blood. (a) Schematic picture of protocol of Treg depletion and C. rodentium infection used in this study. DEREG mice were infected with C. rodentium strain ICC 180 orally and then injected i.p. with DT on day 0, 1, 7 and 8 p.i.. At day 2 (b) and 9 p.i. (c), mice were bled to collect blood for lysing, and staining with anti-CD4 and antiFoxp3 in order to check depletion efficiency of regulatory T cells. Bar of blood Treg cell frequency from different groups represents mean ± S.E.M. from one representative of at least 3 individual experiments (n = at least 3 mice per group). *<0.05, **<0.01, ***<0.001. Supplementary Figure 3 Immune response in the colons at early phase after infection show impaired IL-17A-producting T cell response but not IL-22-producing innate lymphoid cell response. Mice were orally infected with C. rodentium strain ICC 180 and treated with DT in 100 μl of PBS on day 0 and 1 p.i.. On day 6 post infection, mice were sacrificed for analysis. Colonic LPLs were isolated and restimulated at 37 ℃ for 4 h with ionomycin and PMA, and Brefeldin A within the last 2 h of restimulation. Restimulated cells were further stained with anti-CD4 and anti-CD3 antibodies for surface staining and anti-RORγt, and anti-IL-22 intracellularly. FACS data show immune responses from ILCs (gated with CD3-RORγt+ for ILC population). Dot plots represent different colonic LPL subsets. Data are one representative from 3 individual experiments (n = 3 mice per group) and represent mean ± S.E.M.. Statistics are analysed according to student’s T test. Supplementary Figure 4 Treg depletion impairs expression of Th17-associated cytokines or surface markers. (a) Treg depleted mice showed impaired colonic IL-17A and IL-17F production by CD4+CD3+TCRβ+ cells (upper panels) but not in CD4-CD3+TCRβ- cells (lower panels) 10 days post C. rodentium infection. Colonic lamina propria lymphocytes (cLPLs) were isolated from Treg depleted hosts or non-depleted controls 10 days after C. rodentium infection and further restimulated at 37 ℃ for 4 h with ionomycin and PMA, and Brefeldin A within the last 2 h of restimulation. Restimulated cells were further stained with anti-CD4, anti-CD3 and anti-TCRβ antibodies for surface staining and anti-IL-17A, anti-IL-17F intracellularly. Data represent one experiment, with 3 mice per group. (b) Treg depletion decreased total cell number of CCR6 expressing CD4+ T cells in the colon 10 days after C. rodentium infection. Colonic lamina propria lymphocytes (cLPLs) were isolated from Treg depleted hosts or non-depleted controls 10 days after C. rodentium infection and further stained with anti-CD3, anti-CD4, anti-CCR6 antibodies. Data, shown as mean ± S.E.M., represent one experiment (n = 3 mice per group). (c) Treg depletion decreased mRNA level of Il23r, Ccr6 and Ifng in colonic CD4+CD3+ T cells in the colon 10 days after C. rodentium infection. LP cells were FACS sorted according to the expression of CD4 and CD3, and pooled from the individual mice of each group. 300,000 cells either from Treg-depleted or control group were further restimulated with 0.5 µg/ml anti-CD3 mAb for 24 hours and RNA isolated from these cells was used to analyse gene expression by RT-PCR. Gene expression was normalized to expression of -actin and is shown as fold difference. Data represent one experiment, with 2 to 4 mice per group. 2 Supplementary Figure 5 Treg depletion has no impact on systemic Th17 cell response in the spleen and mesenteric lymph nodes but enhances Th1 cell response 10 days after infection. Erythrocyte-lysed splenocytes were restimulated in RPMI complete medium containing phorbol 12-myristate 13-acetate (PMA) and ionomycin for 4 h, stained with anti-CD3 and anti-CD4 mAbs, fixed and permeabilized, and intracellularly labeled with anti-IFN-γ and antiIL17A, and analyzed by FACS. Dot plots of different splenic cell subsets (upper panel). Data are pooled from 3 individual experiments. Data represents mean. *<0.05, **<0.01. Cells from mesenteric lymph nodes were restimulated in RPMI complete medium by PMA and ionomycin for 4 h, stained with surface anti-CD3 and anti-CD4 mAbs, fixed and permeabilized, and intracellularly labeled with anti-IFN-γ and anti-IL17A, and analyzed by FACS. Dot plots of different cell subsets (lower panel). Data are pooled from 3 individual experiments. Data represents mean. *<0.05, **<0.01. Supplementary Figure 6 Treg depletion in C. rodentium infected mice show no difference in the production of anti-microbial peptide/protein by colonic epithelial cells (ECs) compared to non Treg deplete controls 10 days post C. rodentium infection. Colons from Treg-depleted mice or controls, sacrificed 10 days after C. rodentium infection, were treated with 30mM EDTA for 30 min and ECs were pooled from the rinsed buffer after vigourously shaking and several rounds of PBS wash and further collected by centrifugation at 250 x g at 4°C for 10 min. RNA from ECs were isolated by TRIzol, reverse transcribed, and further analyzed by RT-PCR. Gene expression was normalized to expression of -actin and is shown as fold difference. Data are pooled from 3 individual experiments and represent mean ± S.E.M. ( n = 3 to 4 mice per group). 3 Supplementary Figure 7 Anti-IL-2 mAbs treatment enhanced systemic Th1 cell response in the spleen. C. rodentium-infected DT-treated DEREG mice or control groups were intraperitoneally treated either with anti-IL-2 mAbs or PBS on daily basis for 9 days before analysis on day 10 p.i.. Splenocytes were collected from each group for FACS analyses. FACS-plots showing IFN-γ and IL-17A expression of splenocytes. Dot plots of different splenic cell subsets (upper panel). Data pooled from 3 individual experiments (lower panel). Data represents mean. *<0.05, **<0.01, ***<0.001. 4