Probiotic Properties of Escherichia coli Nissle in Human Intestinal Organoids

Escherichia coli strain Nissle has been used as a probiotic and therapeutic agent for over a century. Reports suggest that Nissle protects mice from enterohemorrhagic E. coli (EHEC) O157:H7 strains; however, mice are not very susceptible to O157:H7 and are not accurate models for O157:H7 infection in humans. Also, Nissle is closely related to uropathogenic E. coli (UPEC) strain CFT073, suggesting that Nissle could have pathogenic potential. To assess the safety of and protection conferred by Nissle, we modeled infection in stem cell-derived human intestinal organoids (HIOs). HIOs replicate the structure and function of human intestinal tissue. HIOs have a lumen enclosed by a single cell layer of differentiated epithelium, which is surrounded by a diffuse mesenchymal layer. An epithelial barrier which excludes the luminal contents from the surrounding cell layers and medium develops. Nissle appeared to be nonpathogenic; 10³ CFU were microinjected into the lumen, and after 3 days, 10⁷ CFU were recovered and the epithelial barrier remained intact. In contrast, microinjected EHEC and UPEC bacteria destroyed the epithelial barrier. To assess the protection conferred by Nissle, HIOs microinjected with Nissle were challenged after 18 to 24 h with EHEC or UPEC. Preincubation with Nissle prevented the loss of the epithelial barrier function, the loss of E-cadherin expression, the increased production of reactive oxygen species, and apoptosis. Nissle did not replicate in the HIO coculture, while the pathogenic strains did replicate, suggesting that Nissle conferred protection via activation of host defenses and not by eliminating competing strains. Nissle was shown to be susceptible to some Shiga toxin phage, and Nissle lysogens could produce Shiga toxin.IMPORTANCE Probiotic, or beneficial, bacteria, such as E. coli Nissle, hold promise for the treatment of human disease. More study is needed to fully realize the potential of probiotics. Safety and efficacy studies are critically important; however, mice are poor models for many human intestinal diseases. We used stem cell-derived human intestinal organoid tissues to evaluate the safety of Nissle and its ability to protect from pathogenic E. coli bacteria. Nissle was found to be safe. Human intestinal tissues were not harmed by the Nissle bacteria introduced into the digestive tract. In contrast, pathogenic E. coli bacteria destroyed the intestinal tissues, and importantly, Nissle conferred protection from the pathogenic E. coli bacteria. Nissle did not kill the pathogenic E. coli bacteria, and protection likely occurred via the activation of human defenses. Human intestinal tissues provide a powerful way to study complex host-microbe interactions.