Bioengineering a probiotic to bloom during colonic inflammation promotes reliable efficacy in translational models of colitis.

Abstract

Emerging insights into the gut microbiome have sparked interest in exploring microbial therapeutics for treating inflammatory bowel diseases (IBD). However, no microbial therapeutics have yet shown clinical efficacy for IBD. E. coli Nissle 1917 (EcN) while effective for maintenance of remission, is only marginally effective for treating active colitis. We postulated that EcN effectiveness is hindered by the inflamed intestine, which prevents colonization since EcN lacks stress-resistance mechanisms necessary to persist during colitis. To address this, we introduced a fitness advantage, the ttr operon, to EcN (EcN::ttr), enabling tetrathionate, a byproduct of intestinal inflammation, to be used as fuel. We hypothesized that EcN::ttr bioengineered to bloom during colitis would effectively treat colitis. We evaluated the efficacy of EcN::ttr in murine colitis: acute DSS and a chronic mucin 2-deficient model. To determine the role of IL-10 in EcN::ttr protection, we tested its efficacy in IL-10-deficient mice. Finally, we co-incubated EcN::ttr with human colonoids to understand its effect on barrier proteins. EcN::ttr ameliorated colitis more effectively than EcN and 5-aminosalicylate. EcN::ttr bloomed during inflammation and promoted immunoregulatory responses reliant on IL-10 that limited leukocyte infiltration and decreased TNF-α⁺ myeloid resident cells. EcN::ttr induced functional changes in the gut microbiome related to mucosal healing, increased butyric acid, reduced bacterial translocation, and improved ZO-1 organization. We provide a proof-of concept study that bioengineering ttr into EcN unlocks a robust therapeutic effect during colitis. EcN::ttr may be a novel microbiome therapeutic for IBD due to its enhanced ability to successfully colonize the inflamed gut.