Fig. 3

Immune cell composition of the small intestinal epithelium in IG and PW colonized mice at 8 weeks of age. A TCRβ + cells shown as a percentage of CD45 + EpCAM- Live cells. B CD4 + cells shown as a percentage of TCRβ + CD45 + EpCAM- Live cells. C CD8 + cells shown as a percentage of TCRβ + CD45 + EpCAM- Live cells. D CD8αα + TCRαβ Natural IELS (gated as CD8α + CD8β- TCRβ + cells as a percentage of CD45 + EpCAM- Live). E CD8αα + TCRγδ Natural IELs (gated as CD8α + CD8β-CD4- TCRγδ + cells as a percentage of CD45 + EpCAM- Live). F CD8αβ + TCRαβ Induced IELs (gated as CD8α + CD8β + TCRβ + cells as a percentage of CD45 + EpCAM- Live). G Representative flow plots of TCRγδ + Natural IELs in HD and SD IG mice. Cells were gated on the Live CD45 + EpCAM- population. H Granzyme A + cells shown as a percentage of CD8α + CD8β- CD4- TCRγδ + CD45 + EpCAM- Live cells (left) or CD8α + CD8β- TCRβ + CD45 + EpCAM- Live cells (right) within IG colonized mice. Data shown pooled between healthy donor colonized mice (3176 and 4142) and stunted donor colonized mice (4092 and 3114). Each point represents an individual animal. A-F n = 24/group [12 per donor] for IG groups, n = 18–20/group [7–10 per donor] for PW groups. * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001 by Two-Way ANOVA with Šídák’s multiple comparisons test. H n = 16–17/group [6–11 per donor], ** p ≤ 0.01 by Mann–Whitney U test