Fig. 2: Cr predominantly attaches to DCCs.

scRNA-seq was performed on epithelial cells from mid–distal colons of C57BL/6 mice without infection (naive) and on day 9 of Cr infection. (n = 2). a, UMAP analysis of Ly6g and Fabp2 expression. b, IECs from mid–distal colons of naive mice were stained for LY6G, FABP2, EPCAM1, CD45 and LIVE/DEAD (L/D) dye, and analysed by flow cytometry. n = 3 mice and n = 2 independent experiments. c–e, Tissue from distal ileum (c; scale bar, 1,000 μm), colon (d; scale bar, 1,000 μm) and middle colon region (e; scale bar, 50 μm) from naive mice were stained with LY6G and FABP2 antibodies and DAPI (3–4 mice per region, n = 2 independent experiments). f,g, IECs from distal ileum (green), proximal colon (blue) and distal colon (red) of naive mice were stained as in b and analysed by flow cytometry (f) or sorted as EPCAM1⁺CD45⁻L/D⁻ IECs, and mRNA expression was analysed by PCR with reverse transcription (RT–PCR) (g) (2 or 3 mice pooled per sample; n = 2 independent experiments). One-way ANOVA. h, Mid–distal colon IECs mice on day 8 of Cr-GFP infection were sorted for EPCAM1⁺CD45^–GFP^– or EPCAM1⁺CD45^–Cr-GFP⁺ cells. i, mRNA expression of indicated genes in sorted Cr-GFP^– and Cr-GFP⁺ IECs was analysed by RT–PCR (2 or 3 mice pooled per sample; n = 2 independent experiments). Two-tailed unpaired t-test. j–l, Proximal (j), middle (k) and distal (l) colon tissue from mice on day 8 of Cr infection was stained for LY6G, FABP2, Cr-LPS and DAPI. White arrows identify rare Cr in proximal colon, green arrows identify FABP2⁺ PCCs, and red arrows identify Cr-laden LY6G⁺ DCCs. Scale bar, 100 μm. 3 or 4 mice per experiment; n = 2 independent experiments. Data are mean ± s.e.m. *P ≤ 0.05, **P ≤ 0.01 and ***P ≤ 0.001.