Figure 1.

(a) Schematic of gastric pits, villi and crypts present in stomach (i), small intestine (ii) and colon (iii), respectively. The relative villus height in the small intestine is shown (millimetres); these structures are absent from the other intestinal compartments. The mucosa layer and its main components, such as the epithelium (continuous and dashes lines), lamina propria (blank spaces) and muscularis mucosa (black solid lines), are indicated. (b) Schematic of mucus layers present in the stomach, small intestine and colon. The mucus layer in the stomach (i) and colon (ii) is composed of a firm inner layer (represented in dark grey) and a loose outer layer (represented in grey). In the small intestine (iii scheme), the mucus is loose and arranged irregularly over the villus. MUC2 is enriched in all structural domains of the intestine, with the exception of the stomach, which is enriched in MUC5A. Relative mucus height (mm) in the stomach, small intestine and colon is shown. The intestinal lumen carries the microbiome and the eukaryome (non-represented). Some pathogens specific to each compartment are shown; these include bacteria (e.g. Helicobacter, Vibrio, Escherichia and Salmonella) and parasites (e.g. Giardia, Entamoeba and Cryptosporidium).