In vitro reproducible model of subgingival microbiome for high throughput screening for microbiome modulators

用于微生物组调节剂高通量筛选的龈下微生物组体外可重复模型

• 批准号: 9973103
• 负责人: Nezar Al-Hebshi
• 金额: $ 16.42万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-05 至 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9973103
• 关键词: 16S ribosomal RNA sequencing; Accounting; Address; Algorithmic Analysis; Algorithms; Animals; Coculture Techniques; Communities; Complex; Coupled; Culture Media; Dental Plaque; Devices; Disease; Economic Burden; Experimental Models; Feasibility Studies; Freezing; Gingiva; Glycerol; Growth; Health; Healthcare; Human; Immunologics; In Vitro; Individual; Laboratories; Literature; Measures; Microbial Biofilms; Modeling; Oral; Oral health; Patients; Periodontitis; Periodontium; Prevention; Prevention strategy; Probiotics; Problem Solving; Productivity; Reproducibility; Reproduction; Ribosomal RNA; Saliva; Sampling; Sucrose; Taxonomy; Temperature; Testing; Time; Tooth Loss; Translating; base; dental biofilm; dysbiosis; edentulism; global health; high throughput screening; in vitro Model; in vivo; indexing; innovation; keratinocyte; microbial; microbiome; microbiome analysis; microbiome composition; novel; oral microbial community; oral microbiome; pathobiont; pathogen; prebiotics; prevent; screening; subgingival microbiome; subgingival microbiota; tool; transcriptome sequencing; years lived with disability

Project summary Periodontitis continues to be a global health problem: combined with edentulism and severe tooth loss, it constitutes the 6th most prevalent long-term disease worldwide, accounting for 11 million years lived with disability and lost productivity of 117 billion USD. Currently, periodontitis is viewed as an immunological destruction of the periodontium, orchestrated by low abundance pathogens in an unbalanced subgingival microbial community--the so called microbial dysbiosis hypothesis. This entails that selectively targeting pathogens or/and stimulating growth of commensals to reverse subgingival microbial dysbiosis (or promote normobiosis) represents a promising strategy for prevention and adjunctive treatment of periodontitis. Such microbiome modulation can be achieved by using agents like prebiotics and probiotics. Remarkably, while a number of in vitro dental biofilm/microbiome models has been described in the literature, none has been developed for the purpose of exploring microbiome modulators. This two-year R03 has a single aim: to develop a robust, high- throughput, reproducible in vitro subgingival microbiome model specifically optimized for testing of microbiome modulators. The model will include a dysbiotic (experimental) microbiome grown from periodontitis-associated subgingival samples, and a normobiotic (reference) microbiome grown from health- associated subgingival plaques samples. The growth conditions will be fine-tuned to maximize similarity between the in vitro microbiomes and the original samples. We will also explore the possibility of reproducing the generated microbiomes by passaging or using frozen stocks, eliminating the need to obtain more patient samples. In addition, a novel subgingival microbial dysbiosis index (SMDI) as a measure of dysbiosis in the microbiomes will be developed. The microbial composition of the microbiomes as well as original samples will be assessed using 16S rRNA sequencing coupled with our BLASTN-based, species-level taxonomy assignment algorithm. Microbiomes will be compared using distance matrices, principle component analysis and a similarity index. The model characterized here will provide the scientific community with an important tool to screen large numbers of candidate modulators and quantitatively assess their effects on subgingival microbiome, before they can be considered for further testing in animals, and eventually, humans.

项目摘要 牙周炎仍然是一个全球健康问题：与脱牙和严重的牙齿脱落相结合， 在全球范围内构成第六个最普遍的长期疾病，占1100万年 残疾和生产率损失1170亿美元。目前，牙周炎被视为免疫学 牙周的破坏，在不平衡的副本中由低丰度病原体精心策划 微生物群落 - 所谓的微生物营养不良假设。这需要有选择地定位 病原体或//和刺激分子的生长以逆转尺寸的微生物营养不良（或促进 正常病）代表了预防和牙周炎辅助治疗的有前途的策略。这样的 可以通过使用益生元和益生菌等药物来实现微生物组调节。值得注意的是， 文献中已经描述了体外牙科生物膜/微生物组模型的数量，没有一个 为了探索微生物组调节剂而开发。这个为期两年的R03有一个目标：开发 可重现的强大，高吞吐量，可重现的体外副生物微生物组模型，专门针对测试进行了优化 微生物组调节剂。该模型将包括从 与牙周炎相关的近似样品，以及从健康中生长的正常生物生物（参考）微生物组 相关的尺寸斑块样品。生长条件将进行微调以最大化相似性 在体外微生物组和原始样品之间。我们还将探索复制的可能性 通过传递或使用冷冻库存来产生的微生物组，消除了获得更多患者的需求 样品。此外，一种新型的亚gingival微生物营养不良指数（SMDI）作为量度障碍的量度 将开发微生物组。微生物组和原始样品的微生物组成将 使用16S rRNA测序与我们的基于BLASTN的物种级分类学结合进行评估 分配算法。微生物组将使用距离矩阵，原理分析进行比较 和相似性索引。这里表征的模型将为科学界提供重要的工具 要筛选大量候选调制器，并定量评估其对尺寸的影响 微生物组，在可以考虑在动物乃至人类中进行进一步测试之前。

项目成果

Optimization of conditions for in vitro modeling of subgingival normobiosis and dysbiosis.

• DOI: 10.3389/fmicb.2022.1031029
• 发表时间: 2022
• 期刊: FRONTIERS IN MICROBIOLOGY
• 影响因子: 5.2
• 作者: Baraniya, Divyashri;Do, Thuy;Chen, Tsute;Albandar, Jasim M. M.;Chialastri, Susan M. M.;Devine, Deirdre A. A.;Marsh, Philip D. D.;Al-Hebshi, Nezar N. N.
• 通讯作者: Al-Hebshi, Nezar N. N.