On July 17, 2025, a research team led by Weston R. Whitaker from Stanford University School of Medicine published an article in Science entitled "Controlled colonization of the human gut with a genetically engineered microbial therapeutic." This study used Genetically Engineered Microorganisms to controllably colonize the human gut for the treatment of enterogenic hyperoxaluria, demonstrating some efficacy in preclinical models and clinical trials, providing important evidence for precision microbiome programming therapy.
This research aimed to address the challenge of colonic colonization in precision microbiome programming therapy by constructing specific ecological niches to implant engineered bacteria into the human gut. Based on Phocaeicola vulgatus, a strain capable of utilizing Porphyran was constructed, and an oxalate degradation pathway was introduced to develop the therapeutic candidate strain NB1000S. In preclinical models, this strain effectively reduced urinary oxalate levels in rats; in a phase 1/2a clinical trial, it was tested in healthy volunteers and patients with enterogenic hyperoxaluria (EH) to evaluate its safety, tolerability, colonization performance, and therapeutic efficacy.
Oxalicate transport and degradation-related genes were introduced into P. vulgatus to construct a strain capable of efficiently degrading oxalate. Simultaneously, by replacing the natural regulatory element of arginyl-tRNA synthetase (argS), its expression was made dependent on porphyran induction, achieving reversible colonization of the strain.
A diet-induced EH rat model and a rat Roux-en-Y gastric bypass (RYGB) surgical model were established. P. vulgatus strains containing the oxalate degradation pathway were administered to rats orally by gavage, and changes in urinary oxalate levels were measured.
An adaptive phase 1/2a clinical trial (NOV-001-CL01) was conducted in the United States and Canada. Healthy volunteers were randomly assigned to 7 groups and given different doses of NB1000S and porphyran. Some volunteers received omeprazole to protect their stomachs. EH patients were given NB1000S, porphyran, or a placebo. Fecal and urine samples were collected periodically to measure bacterial colonization and urinary oxalate levels.
The constructed engineered bacteria rapidly degraded oxalate to formic acid in vitro. In EH rat models and RYGB surgical models, high-dose colonization with the strain containing the oxalate degradation pathway significantly reduced urinary oxalate levels.
By regulating the expression of key genes, the engineered bacteria were made to grow in dependence on porphyran. In mouse experiments, after the removal of porphyran, the NB1000S strain in the intestines of most mice carrying the strain decreased to below the detection limit. However, persistent colonization of the strain occurred in some mice due to related gene mutations.
In healthy volunteer trials, NB1000S colonization was related to the porphyran dose. In most volunteers, the strain was cleared from feces after cessation of porphyran administration. However, persistent colonization occurred in a few volunteers, and Gene Sequencing revealed mutations in the strain. Adverse events in the trials were mostly mild and transient, and no significant impact on native microbiome diversity was found.
The study discovered a mechanism for escape mutations from conditional attenuation. Constructing a three-layered conditional attenuation strain enhanced the attenuation effect. In mouse experiments, the density of the three-layered conditional attenuation strain in the intestines significantly decreased after the removal of porphyran, but persistent colonization still occurred in some mice; the mechanism remains unclear.
In the EH patient trial, NB1000S colonization levels were unstable, with some patients experiencing large-scale horizontal gene transfer (HGT) events. This resulted in the strain losing its oxalate degradation pathway and conditional attenuation module, or other gut bacteria acquiring porphyran utilization sites. Although urinary oxalate levels tended to decrease after treatment, the difference did not reach statistical significance.
Fig. 1 Bacteroidaceae with engineered oxalate degradation reduce urine oxalate in rat EH models. (Whitaker, et al. 2025)
This study successfully achieved controlled colonization of engineered bacteria in the human gut, providing a new strategy for treating EH. However, issues such as conditional attenuation escape and gene stability limited the therapeutic effect. Future research needs to further improve strategies for conditional attenuation and preventing HGT, reduce the adaptive burden of therapeutic activity, and conduct in-depth studies on the impact of engineered bacteria on gut ecology and Metabolism. Overall, this study provides an important reference for precision microbiome programming therapy and is expected to promote the development of related fields.
Reference
