Polysaccharides Enable Controlled Colonization and Aid Hyperoxaluria Treatment
On July 17, 2025, Weston R. Whitaker et al. from Novome Biotechnologies, Stanford University School of Medicine, and other institutions published their research results, titled "Controlled Colonization of the Human Gut with a Genetically Engineered Microbial Therapeutic," in Science. This study, using Genetically Engineered Microbes to enable controlled colonization of the human gut for the treatment of enteric hyperoxaluria, demonstrated promising results in preclinical models and clinical trials, providing important evidence for precision microbiome programming for therapeutics.
This study aims to address the challenge of colonization in precision microbiome programming for therapeutics by creating a specific ecological niche for engineered bacteria to be introduced into the human gut. Based on Phocaeicola vulgatus, a strain capable of utilizing Porphyran and incorporating an oxalate degradation pathway was constructed, resulting in the development of the therapeutic candidate strain, NB1000S. In preclinical models, this strain effectively reduced urinary oxalate levels in rats. In a Phase 1/2a clinical trial, the drug was tested in healthy volunteers and patients with enteric hyperoxaluria (EH) to evaluate its safety, tolerability, colonization, and therapeutic efficacy.
Genes related to oxalate transport and degradation were introduced into P. vulgatus to construct a strain capable of efficiently degrading oxalate. Furthermore, by replacing the native regulatory elements of arginyl-tRNA synthetase (argS), its Expression became dependent on porphyran-induced induction, achieving reversible colonization of the strain.
A diet-induced EH rat model and a Roux-en-Y gastric bypass (RYGB) rat model were established. P. vulgatus strains harboring the oxalate degradation pathway were administered orally to the rats, 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 divided into seven groups and given varying doses of NB1000S and porphyran. Some volunteers also took omeprazole for gastric protection. EH patients were given NB1000S, porphyran, or a placebo. Fecal and urine samples were collected regularly to assess bacterial colonization and urinary oxalate levels.
The engineered bacteria rapidly degrade oxalate into formic acid in vitro. In EH rat models and RYGB surgery models, high-dose colonization with a strain containing an oxalate-degrading pathway significantly reduced urinary oxalate levels.
By Manipulating the Expression of Key Genes, the engineered bacteria were made dependent on porphyran for growth. In mouse experiments, removal of porphyran reduced the NB1000S strain to below the detection limit in the intestines of most mice. However, some mice showed persistent colonization due to mutations in the relevant genes.
In healthy volunteer trials, NB1000S colonization correlated with porphyran dosage, and most volunteers cleared the strain from their feces after stopping porphyran. However, a few volunteers maintained persistent colonization, and genetic sequencing revealed this was due to mutations. Adverse events in the trial were mostly mild and transient, with no significant impact on the diversity of the native microbiome.
The study identified a mechanism for conditional attenuation escape mutations, enhancing attenuation efficacy by constructing a three-layer conditionally attenuated strain. In mouse studies, the intestinal density of the three-layer conditionally attenuated strain was significantly reduced after porphyran was removed, but some mice still maintained persistent colonization, and the mechanism remains unclear.
In trials with EH patients, NB1000S colonization levels were unstable, with some patients experiencing large-scale horizontal gene transfer (HGT) events, resulting in the strain losing the oxalate degradation pathway and conditional attenuation module, or acquiring porphyran utilization sites by other intestinal bacteria. Although there was a downward trend in urinary oxalate levels after treatment, the difference did not reach statistical significance.
Fig.1 Combining porphyran utilization and essential gene regulation enables reversible engraftment. (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 with conditional attenuation escape and genetic stability limit therapeutic efficacy. Future work is needed to further refine conditional attenuation and prevent HGT strategies, reduce the adaptive burden of therapeutic activity, and further investigate the effects of engineered bacteria on intestinal ecology and metabolism. Overall, this study provides important insights for precision microbiome programming therapy and is expected to advance related fields.
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