Discovery of bacterial consortia to treat recurrent vulvovaginal candidiasis: a generalizable platform for phenotypic microbial community screening

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Vulvovaginal candidiasis (VVC), a vaginal infection characterized by vulval itching, inflammation, and lesions, affects 1.4 million American women per year. VVC is primarily caused by Candida albicans, a fungus that switches from a commensal yeast form to a pathogenic hyphal form in response to microbiome perturbations such as antibiotics. While antifungals treat many VVC episodes, 20% of diagnosed women experience recurrent VVC, suggesting that maintaining long-lasting health requires restoration of a protective vaginal microbiome, not just eradication of a pathogen. A defined consortium of vaginal-derived microbes could restore lost microbiome functions—broad colonization of vaginal niches and production of fungal inhibitors such as surfactants and lactic acid—to resist subsequent blooms of C. albicans and prevent recurrent VVC. Nevertheless, generating an optimal therapeutic consortium requires a thorough understanding of how microbial strains function in combination, an outstanding challenge in microbiology that cannot yet be answered from metagenomic information alone. High-throughput screening (HTS) could reveal microbial consortia that perform specific desirable functions; however, the complex liquid handling necessary to construct and measure millions of microbial communities has prevented practical use of this strategy. Concerto Biosciences solves this problem using kChip, a novel HTS platform that can construct and measure ~500,000 defined microbial combinations per day, and can be leveraged to perform direct functional assays of millions of combinations during a screening campaign. In this Phase I proposal, Concerto proposes to perform a kChip screen of 10M multistrain combinations of vaginal-derived microbes to directly identify consortia that suppress C. albicans growth and hyphae formation, hallmarks of VVC. We aim to (1) build a biobank of bacterial strains derived from healthy donors’ vaginal samples that can form the basis of designed microbial consortia, (2) develop quantitative measures of C. albicans growth and hyphae formation in a kChip screening context, and (3) identify strain combinations that suppress C. albicans growth and hyphae formation across multiple environments, including vaginal extracts. The top consortia identified by this screen will undergo additional development—the subject of a future Phase II proposal—to generate a lead consortium therapeutic. This therapeutic will represent the first defined, multistrain microbiome restoration therapeutic in women’s health with the potential to safely and effectively ameliorate recurrent VVC of millions of Americans. More broadly, successful implementation of kChip-enabled discovery will fuel rapid discovery of treatments for other fungal (seborrheic dermatitis and mucormycosis) and vaginal (bacterial vaginosis, preterm birth, and STI transmission) diseases.