Fig. 1: The LP niche supports the highest production of IL-10 in response to Hh colonization.

a, Diagram of tissue and lymphoid structures in the mouse gut, with representative images of CP, organized lymphoid structures and LAs in CD2^DsRed mouse. Scale bars, 1,000 μm. b, Schematic of transfer of naive TCR^Hh T cells into Hh-colonized hosts. c, Representative fluorescence-activated cell sorting (FACS) plots of TCR^Hh T cells at the indicated sites 14 days after transfer of naive TCR^Hh T cells. d, Frequency of TCR^Hh cells among total CD4 T cells at indicated timepoints after transfer of naive TCR^Hh T cells. e, Frequency of Ki-67⁺ TCR^Hh cells at the indicated sites 14 days after transfer of naive TCR^Hh T cells. f, Representative FACS plots (left) and frequency of T_reg cells of TCR^Hh (right) at 14 days after transfer of naive TCR^Hh T cells. g, Representative histogram overlay (left) and GFP MFI of TCR^HhNur77^GFP T cells (right) 11 days after transfer of naive TCR^Hh T cells. h, Representative FACS plots (left) and frequency of Il10⁺ cells among TCR^Hh T cells (right) 11 days after transfer of naive TCR^Hh T cells. i, Representative images of TCR^HhNur77^GFP (left and centre left) and TCR^HhIl10^GFP (centre right and right) T cells in the LA and LP. TCR^HhNur77^GFP and Il10-GFP-positive cells are indicated by white arrowheads. Scale bars, 50 μm. j, Frequency of Nur77^GFP (left) and Il10-GFP-positive (right) cells among TCR^Hh T cells in the LA and LP. a, Representative images from two individual mice over two independent imaging experiments. c–e, Four individual mice representative of two independent experiments. f, Seven individual mice representative of two independent experiments. g,h, Five individual mice representative of two independent experiments. i,j, Representative images and combined data from six individual mice over two independent imaging experiments. Scale bars, 50 μm. e–h, One-way ANOVA using Tukey’s multiple comparisons test. j, Two-tailed t-test.

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