Bioengineering a Probiotic to Bloom During Colonic Inflammation Promotes Reliable Efficacy in Translational Models of...

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. Escherichia coli Nissle 1917 (EcN), although 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 because 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 including an acute dextran sodium sulfate model and a chronic mucin 2-deficient model. To determine the role of interleukin (IL) 10 in EcN::ttr protection, we tested its efficacy in IL10-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 IL10 that limited leukocyte infiltration and decreased tumor necrosis factor-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 zonula occludens-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.