The gut microbiome drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

We investigate the microbial effects on DNA methylation and the transcriptome of intestinal epithelial cells (IECs) during postnatal development Overall design: C57Bl6/N female littermate mice were maintained under standard specific pathogen free or GF conditions in the laboratory for experimental biomedicine at University of Gothenburg. Mice were kept under a 12-h light cycle and fed autoclaved chow diet ad libitum (Labdiet, St Louis, MO, USA). Mice were sacrificed at three different stages: 1, 4 and between 12 to 16 weeks of age. Mice were killed by cervical dislocation and the small intestine removed for isolation of IECs. All animal protocols were approved by the Gothenburg Animal Ethics Committee. We collected IECs from the small intestine of 1-, 4- and 12 to 16-week-old mice, raised either in the presence or absence of a microbiota.