In the presence of microbiota, specifically Pseudobutyrivibrio, Sodaliphilus and Oscillibacter, colonocytes in the apex of the crypts expressed Ceacam20, a known receptor for Gram-negative bacteria49 and a known colitis suppressor50, whereas goblet cells expressed high levels of Hif1a, a marker of a functioning mucosal barrier that is downregulated in IBD51 (Fig. 4d and Supplementary Table 4). This evidence concerns the gene HIF1A and colitis.