Essential role of the electroneutral Na+–HCO3− cotransporter NBCn1 in murine duodenal acid–base balance and colonic mucus layer build‐up in vivo

•  In the upper intestinal tract, luminal acidity due to intermittent release of gastric juice needs to be counteracted by basolateral HCO3− import. In the lower gastrointestinal tract, the build‐up of a thick mucus layer is a major defence mechanism against pathogens, and HCO3− is of the utmost importance for this process. The pathways for HCO3− transport that play a role in these mucosal defence strategies are, however, unknown. •  We recently identified the electroneutral Na+–HCO3− cotransporter NBCn1 as a major regulator of intracellular pH in duodenal villous enterocytes. The present study shows that the murine duodenocytes, whose intracellular pH was monitored by in vivo two‐photon confocal microscopy in anaesthetized NBCn1 knock‐out mice, are unable to recover rapidly from intracellular acidification imposed by a short pulse of low‐pH solution in the duodenal lumen. Likewise, they are not able to respond to contact of the surface with low pH by a protective HCO3− secretory response. •  The cotransporter NBCn1 is also expressed in the basolateral membrane of colonic crypt cells, many of which stain positive for mucin granules. We found only a minor role for NBCn1 in colonic epithelial HCO3− secretion, but the build‐up of a mucus layer, measured in the exteriorized colon of anaesthetized mice by in vivo microscopy, was significantly delayed in the absence of NBCn1 expression. •  Therefore, NBCn1 plays major but different roles in mucosal protective functions in the upper and lower intestine.