Fig. 2

Microbial effects on the host epithelial transcriptome during postnatal development. a Principal component analysis displaying overall gene expression profiles across all samples. The first dimension explained 63% variation and separated W1 and the other two stages. The second dimension explained 8% variation and separated both W4 versus W12/16 and samples of a stage for their microbiota status. b Transcription factor binding sites enriched among microbially regulated genes (differentially expressed in CONV-R vs GF) for each of the three developmental stages. The bar plot depicts the 15 most significantly enriched transcription factors of either up- or downregulated genes. All p values were corrected for multiple testing using the Benjamini–Hochberg method. c Hierarchical clustering of microbially regulated genes identified 12 groups with specific expression profiles, e.g., group 3 genes that were repressed by the presence of the microbiota at W4 and W12/16 or conversely group 8 genes induced by the microbiota