The microbiota elicits specific transcriptional responses in different locations of the gut epithelium. (A) Immunostaining using epithelial cell type-specific antibodies and quantification. n = 8 (GF) and 9 (CR); *P < 0.05, ***P < 0.001 (two-way ANOVA). All pictures are in the same magnification. The scale bar indicates 100 μm. Data show mean ± standard error of the mean. (B) Schematic overview of the experimental setup. Tip and crypt epithelial fractions were harvested by LCM from ileum and colon of GF and CR mice and then used for microarray analysis. (C) Hierarchical clustering of the microarray data. (D) Venn diagram of microbiota-dependent genes (P < 0.001 for GF versus CR) in the four different LCM fractions.