Fig. 5

The microbiota may modulate host gene expression through DNA methylation. a Schematic analysis workflow. A 5-kb window up- and downstream of each microbially regulated gene was screened for CpG positions. Next, CpG regions were defined and tested for differential methylation (CONV-R vs GF) and p values of all differentially methylated CpG sites were corrected for multiple testing. It is noteworthy that any sequential analysis reflects a certain bias by the individual order of filter steps. b Microbial effects on gene expression and DNA methylation of Camk2b during postnatal development. c Genomic map of all methylation–transcription interactions dependent on the microbiota and postnatal development. The boxes in the outer circle depict the mouse chromosomes and their banding indicates the staining properties within the genomic locations (black = heterochromatin region, white = euchromatin region, gray = intermediate). The boxes in the inner circle represent genes that were both differentially expressed and methylated. The gene name is colored according to the expression difference in CONV-R vs GF comparison (red = upregulated, blue = downregulated). Box coloring corresponds to the developmental stage, in which a significant difference was detected (red = W1, green = W4, blue = W12/16). Width of the boxes indicates gene length, while methylation differences in CONV-R vs GF comparison are scaled along the height of the boxes. Red and blue dots within the gene boxes represent hyper- and hypomethylated CpG sites, respectively