204 ● ● Verrucomicrobia Anaerostipes Streptococcus Bacteroidales Lachnoclostridium 0.00 0.05 0.10 0.15 Variation ● ● ● Marinifilaceae Lachnoclostridium CAG.56 Epsilonbacteraeota Dialister Prevotella_9 Bacteroidetes Actinobacteria.1 Burkholderiaceae Bacteroidaceae 0.00 0.04 0.08 0.12 Variation Epithelial cells CD8+ naive T−cells Plasma cells Endothelial cells Neutrophils Macrophages M1 Mast cells cDC Th2 cells Eosinophils Fibroblasts pDC CD8+ Tcm CD4+ Tcm NK cells NKT Tregs CD8+ Tem Tgd cells CD4+ naive T−cells Basophils Th1 cells CD4+ Tem Memory B−cells naive B−cells Class−switched memory B−cells Macrophages M2 basic factors medication inflammation location bacteria 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 ● ● ● ● ● ● ● ● ● ● ● ● ● 0.0 0.2 0.4 0.6 Epithelial cells CD8+ naive T−cells Plasma cells Endothelial cells Neutrophils Macrophages M1 Mast cells cDC Th2 cells Eosinophils Fibroblasts pDC CD8+ Tcm CD4+ Tcm NK cells NKT Tregs CD8+ Tem Tgd cells CD4+ naive T−cells Basophils Th1 cells CD4+ Tem Memory B−cells naive B−cells Class−switched memory B−cells Macrophages M2 Cell Variation ● ●● ● ● ●● ● ●● ● ● ● ● Lachnospiraceae_UCG.004 Bacteroidia Ruminococcaceae Bifidobacteriales Ruminiclostridium_5 Streptococcus Rikenellaceae Akkermansia Coriobacteriia Desulfovibrionaceae Lachnoclostridium Lachnospira Dialister Agathobacter 0.00 0.05 0.10 0.15 Variation Variation of Epithelial cells Variation of Macrophages M1 Variation of NK cells A B Figure 7 | Mucosal microbiota associate with distinct intestinal mucosal cell types. a, Boxplots show the amount of variation in intestinal cell type–enrichment that could be explained by mucosal microbiota. Heatmap shows the contribution of other fitted models in explaining intestinal cell type–enrichment, including ‘basic factors’ (age, sex and BMI), medication use, tissue inflammatory status and tissue location. Mucosal microbiota contributed most to the variation in enrichment of intestinal epithelial cells, M1macrophages, NK cells and eosinophils. b, Boxplots showing the contribution of the main bacterial taxa that explain the variation in mucosal enrichment of intestinal epithelial cells, M1-macrophages and NK cells—the cell types that interacted most strongly with the mucosal microbiota. Chapter 6
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