Figure 1

Top: confocal micrographs of intestinal sections stained with UEA-1 (green) and DAPI (blue in epithelium, red in lumen). The UEA-1 glycan epitope is most abundant in the mouse distal colon and less so in the cecum and proximal colon. The epithelial boundary is overlaid (maroon). Middle: schematic of the distal mouse gastrointestinal tract. Bottom: schematic of key characteristics of each intestinal location after fixation with dry Carnoy’s fixative. Mucus structure and bacterial localization are heterogeneous along the longitudinal and transverse axes of the murine gastrointestinal tract. The MUC2-dependent layer becomes increasingly dense and impenetrable along the length of the intestines; the non-continuous appearance of the mucus in the ileum and proximal colon is potentially due to artefacts during mucus preparation. The density and diversity of bacteria increase along the longitudinal axis, with the small intestine favoring facultative anaerobic, proteolytic bacteria, and the colon favoring anaerobic, saccharolytic bacteria. Along the transverse axis, most bacteria are spatially segregated from the host tissue by immunological and physical barriers (Johansson et al., 2008; Vaishnava et al., 2011), with a few notable exceptions (Ivanov et al., 2009; Lee et al., 2013; Sonnenberg et al., 2012). Mucus structure in live animals is reviewed in (Pelaseyed et al., 2014). AMP, antimicrobial peptide; sIgA, secretory IgA; SFB, segmented filamentous bacteria.