Development of a Next Generation Engineered Live Microbiome Biotherapeutic, E Coli Nissle 1917-Ttr, for Ulcerative Colitis

Abstract Based on the known perturbations in microbiome composition and the efficacy of fecal microbial transplantation, microbiome therapies are promising new options for ulcerative colitis (UC). Bacterial consortia as therapeutics have not yet demonstrated effectiveness in UC. An oral microbiome therapeutic is an attractive option for treating mild to moderate UC as monotherapy and potentially in combination with other therapies across the spectrum of disease severity. While probiotics such as Escherichia coli Nissle 1917 (EcN) have marginal efficacy in treating acute flares, they have shown similar efficacy to 5-ASA therapy in remission maintenance. We hypothesized that probiotic and live biotherapeutic product (LBP) efficacy is limited because of failure to colonize the inflamed colon. This failure may be due to vulnerability to oxidative stress. To overcome this, we genetically engineered EcN to enhance colonization. We inserted the ttr operon from Salmonella enterica, which enables tetrathionate (TTR), a gut inflammation byproduct, to be an energy source, providing EcN with a selective advantage during inflammation. EcN::ttr is designed to replicate in response to the degree of underlying inflammation, based on TTR availability, providing a finely tuned therapeutic effect titrated to induce and maintain remission. In both DSS and Muc2-/- murine colitis models, EcN::ttr was significantly more effective in ameliorating colitis than both the unmodified parental strain and 5-ASA therapy. For clinical trials of EcN::ttr, we developed a proprietary oral microencapsulation formulation that optimizes colonic delivery to further enhance colonization. In a 7-day DSS porcine model of colitis, a single dose of orally administered EcN::ttr markedly reduced mortality, with untreated pigs having 20% mortality and severe illness, while treated animals resembled healthy controls clinically and histologically. EcN::ttr treatment preserved gut mucosal integrity and was well tolerated. Two dosing regimens were effective, with evidence of a dose-response for some parameters. This efficacy was achieved with modest doses that can be manufactured efficiently at low cost, providing compelling rationale to advance EcN::ttr as a next-generation microbiome therapeutic into human trials. EcN::ttr may be particularly effective in the maintenance of remission, where the parent EcN strain has previously shown some efficacy albeit in high dosing regimens. A phase 1 trial in 2026 will establish safety and tolerability, followed by an efficacy study initially focused on maintenance of remission and flare prevention in UC. We have shown that the addition of ttr enhances the efficacy of EcN’s anti-inflammatory effects resulting from successful colonization. EcN::ttr may be a novel therapy for UC due to its enhanced ability to successfully colonize the inflamed gut.