Extended Data Fig. 5: scRNA-seq analysis of immune modulation by synthetic community colonization.
From: Mapping the T cell repertoire to a complex gut bacterial community
a, Left panel: Uniform manifold approximation and projection (UMAP) plot. These data represent three merged samples: hCom1d-colonized, hCom2d-colonized and germ-free mice. Right panel: Frequency of TCR clonotypes on the UMAP plot. Expanded TCRs (red) represent clonotypes observed in more than five cells, multiple (orange) are clonotypes found in 2–5 cells, and single (light blue) were seen in only one cell. Most of the expanded TCR clonotypes have an expression profile consistent with effector T cells, whereas naïve T cells are rich in unique (that is, non- expanded) TCR clonotypes. b, UMAP plot of intestinal immune cell clusters in each colonization condition. Immune cells were isolated from the large and small intestine from three groups of mice: hCom1d-colonized, hCom2d-colonized, and germ-free. c, Analysis of the frequency of T cell subsets in each group. The percentage of each T cell subset on the UMAP plot was calculated by the Seurat R package; fold changes compared to GF mice are shown. Colonization of germ-free mice with hCom1d and hCom2d increased pTreg, Th17, Fr4 Th and other effector T cells in the large intestine, and Th17 and other effector T cells in the small intestine. d, Analysis of expanded TCR clonotypes in each sample. Each dot represents one TCR clonotype found in multiple T cells (red, shared between effector T cells and pTreg cells; grey, effector T cell; black, pTreg). e, Differentially expressed genes in T cell subsets upon colonization with hCom1d and hCom2d. The FindMarkers function of Seurat was used to find differentially expressed genes. The two-sided non-parametric Wilcoxon rank sum test was used to calculate the adjusted p-value. White bars show mean values. Each dot represents one cell. ***p < 0.001. f, Criteria used to select TCR clonotypes for making hybridoma cells. Red genes: Upregulated by hCom1d and hCom2d colonization. Black genes: T cell subset markers.
