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

外阴阴道念珠菌病(VVC)，一种以外阴瘙痒、炎症和皮损为特征的阴道感染， 每年影响140万美国女性。VVC主要由白色念珠菌引起，这种真菌 响应微生物组的扰动从共生酵母形态转换为致病菌丝形态 比如抗生素。虽然抗真菌药物治疗了许多VVC发作，但20%的确诊女性经历了 复发的VVC，这表明维持长期的健康需要恢复保护性的阴道 微生物群，而不仅仅是根除病原体。一个确定的阴道来源微生物联盟可以恢复 丧失微生物组功能-阴道壁龛的广泛定植和真菌抑制剂的产生，如 表面活性剂和乳酸--防止白念珠菌随后大量繁殖，防止VVC复发。 然而，产生一个最佳的治疗联盟需要彻底理解如何 微生物菌株在组合中发挥作用，这是微生物学中的一个突出挑战，目前还不能 仅从元基因组信息回答。高通量筛查(HTS)可以揭示微生物 执行特定期望功能的联合体；然而，复杂的液体处理是必要的 构建和测量数以百万计的微生物群落阻碍了这一战略的实际应用。协奏曲 生物科学公司使用KChip解决了这一问题，这是一个新型的HTS平台，可以构建和测量~50万 每天定义的微生物组合，并可用于执行数百万个 在一次筛选活动中的组合。在这个第一阶段的提案中，Concerto建议执行KChip 从10M种阴道来源微生物的多菌株组合中直接鉴定抑制 白色念珠菌的生长和菌丝形成是VVC的特征。我们的目标是(1)建立细菌菌株的生物库 取自健康捐献者的阴道样本，可作为设计微生物联合体的基础；(2) 在kChip筛选环境中开发白色念珠菌生长和菌丝形成的定量测量，以及 (3)确定抑制白色念珠菌生长和菌丝形成的菌株组合 环境，包括阴道提取物。此屏幕确定的顶级财团将经历额外的 开发--未来第二阶段提案的主题--产生一个牵头的治疗财团。这 治疗将是第一个明确的、多菌株微生物组修复治疗在妇女的健康 有可能安全有效地改善数百万美国人反复发作的VVC。更广泛地说， 成功实施kChip使能的发现将推动其他真菌治疗方法的快速发现 (脂溢性皮炎和毛霉菌病)和阴道(细菌性阴道病、早产和性传播感染 传播)疾病。

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.