RECOVERY OF MICROBIOME FUNCTIONAL PATHWAYS INVOLVED IN STICKLAND FERMENTATION IN PATIENTS RECEIVING VE303, A DEFINED BACTERIAL CONSORTIUM FOR CLOSTRIDIOIDES DIFFICILE INFECTION (CDI)

Background: VE303 is a rationally defined consortium of 8 bacterial strains, designed to promote the establishment of a gut environment resistant to CDI. VE303 is manufactured from clonal cell banks and thus overcomes limitations of fecal microbiota transplantation and other donor-derived treatments for patients with recurrent CDI (rCDI). Donor-derived treatments have inherently variable composition and quality, are difficult to scale, and have resulted in transfer of harmful emerging pathogens. Here we assessed the functional potential of the microbiomes of VE303 recipients and placebo controls, to examine if VE303 recovered metabolic pathways that promote a gut environment antagonistic to C. difficile. Specifically, proline and glycine metabolism potential were examined since species with Stickland fermentation capabilities can compete with C. difficile.

Methods: The CONSORTIUM Study was a Phase 2 randomized, double-blind, placebo-controlled, dose-finding study in individuals at high risk of rCDI. After completing standard-of-care antibiotics for a lab-confirmed CDI episode, subjects were randomized 1:1:1 to low-dose (LD) VE303 (1.6 x 10⁸ CFU), high-dose (HD) VE303 (8 x 10⁸ CFU), or placebo orally once daily for 14 days. Subjects were followed for 24 weeks to monitor safety, rCDI episodes, and gut microbiota composition. Fecal samples for metagenomic sequencing were collected during dosing and at weeks 4 and 8. Short read metagenomic sequence data were assembled and annotated to characterize the functional potential of the microbiota. The diversity of genes involved in glycine and proline metabolism was compared between responders and non-responders after the first week of VE303 or placebo dosing.

Results: VE303 HD had an acceptable safety profile and significantly reduced the risk of rCDI compared with placebo. The HD also induced superior VE303 strain colonization at 14 days than LD. Several VE303 strains encode genes involved in glycine and proline metabolism, suggesting that colonization may provide nutrient competition with C. difficile (Fig. 1). VE303 recipients had a significantly larger number of detected glycine and proline reductase-related genes at 7 days than placebo recipients (Fig. 1, Fig. 2, Wilcoxon rank sum, p < 0.01). Although not statistically significant, there tended to be more of these genes in subjects who did not recur than in subjects who did recur (Fig. 1, Fig. 2, Wilcoxon rank sum, p = 0.16).

Conclusion: Examination of the functional potential across assembled metagenomes suggests that VE303 colonization may contribute to recovery of the antibiotic-perturbed microbiome with diverse organisms that can reduce glycine and proline, and thus compete with C. difficile for nutrients associated with spore germination and outgrowth.