The UCSD Microbiome and Metagenomics Center

加州大学圣地亚哥分校微生物组和宏基因组学中心

• 批准号: 10386327
• 负责人: Jack Anthony Gilbert
• 金额: $ 54.98万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-23 至 2026-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10386327
• 关键词: Address; Algorithms; American; Archaea; Area; Artificial Intelligence; Assimilations; Bacteria; Benchmarking; Bioinformatics; Biological Markers; California; Collaborations; Collection; Communication; Communities; Community Outreach; Computer software; Consensus; Core Facility; Cost efficiency; DNA; Data; Data Analyses; Data Provenance; Detection; Development; Elements; Ensure; Eukaryota; Faculty; Feces; Feedback; Fellowship; Generations; Goals; Health; Human; Infrastructure; International; Investments; Laboratory Research; Leadership; Libraries; Metagenomics; Microbe; Mission; National Institute of Diabetes and Digestive and Kidney Diseases; Nutritional Study; Participant; Persons; Pilot Projects; Planet Earth; Positioning Attribute; Precision Health; Preparation; Procedures; Process; Production; Protocols documentation; Quality Control; Quality of life; RNA; Recording of previous events; Reproducibility; Research; Research Design; Research Support; Resolution; Sampling; Scientific Advances and Accomplishments; Scientist; Services; Sum; Supercomputing; System; Taxonomy; Technology; Time; United States National Institutes of Health; Universities; Virus; Visualization; base; beta diversity; biobank; bioinformatics infrastructure; cost; cost efficient; data access; data format; data management; data sharing; data visualization; density; detection sensitivity; experience; improved; innovation; innovative technologies; interest; laptop; metagenome; metaproteomics; metatranscriptomics; microbial; microbiome; microbiome analysis; microbiome research; multidisciplinary; nutrition; open source; operation; precision nutrition; recruit; sample collection; statistics; stool sample; success; synthetic construct; tool; ultra high resolution; undergraduate student

Project Summary The University of California San Diego (UCSD) Microbiome and Metagenomics Center (MMC) as part of the Nutrition for Precision Health (NPH) consortium will provide rapid, robust stool sample processing, high-quality metagenomic and metatranscriptomic data generation, and best-in-class bioinformatic analysis. We will optimize our protocols for DNA and RNA extraction from stool, metagenomic and metatranscriptomic library preparation, sequencing, and bioinformatics for ultra-high resolution taxonomic and functional profiling of the microbiome, including bacteria, archaea, eukaryotes, and viruses. We will offer analytical services and expertise on study design, sample collection, statistics, artificial intelligence, and host-microbe data interpretation to support other NPH centers and develop standard operation procedures with the Research Coordinating Center (RCC). Our team has developed uniquely innovative approaches to provide metagenomic and metatranscriptomic data at a cost that facilitates application to all 17,500 samples provided by the BioBank, with robust quality control to ensure high-quality raw and processed data products. We are also able to provide absolute quantification of microbial load through our recent innovation in synthetic DNA ‘spike-ins', which also facilitates rigorous assessment of contamination and extraction efficiency. Beyond bringing cutting edge technology that we have developed to the consortium, we also propose 3 Pilot Projects: (i) long-read data assembly; (ii) multiplexed metaproteomics; and (iii) automated stool sample collection and processing, so as to improve the taxonomic and functional resolution of profiling and improve biomarker detection sensitivity using dense timeseries. Importantly, our team is also optimally positioned to develop community consensus for the analysis strategies agreed on during the planning year, as well as to address the challenges of integrating microbiome data into the NPH consortium, due to our: existing high-throughput sample processing, sequencing, and data analysis cores; tight integration among disciplinary groups; access to supercomputing infrastructure; data visualization expertise; and tight coordination with an international braintrust of scientists who have been selected based on their complementary expertise in different areas of microbiome and precision nutrition research. This center will also benefit from cross-campus institutional commitment to provide 4 undergraduate, 5 postgraduate, and 6 postdoctoral fellowships, enabling faculty engagement and the development of innovative technologies and algorithms to advance NPH consortium goals. Additionally, our existing community outreach experiences can further support the NPH consortium’s goal to provide respectful, accessible and engaging feedback to the participants. Essential to the success of the MMC is the 35% time-commitment of the PI who has an outstanding track record in leading similar scale efforts. As a key part of the NPH consortium, we aim to democratize microbiome data by reducing cost, time, and computational requirements and coordination of multidisciplinary expertise required for data analyses and interpretation to achieve the ambitious goals of precision nutrition.

项目摘要 加利福尼亚大学圣地亚哥分校（UCSD）微生物组和宏基因组中心（MMC） 精确健康的营养（NPH）财团将提供快速，健壮的粪便样本处理，高质量 宏基因组和元文字数据生成以及一流的生物信息学分析。我们将优化 我们从粪便，元基因组和元文字图库制备中提取DNA和RNA的方案， 测序和生物信息学用于超高分辨率分类学和功能分析，微生物组的功能分析 包括细菌，古细菌，真核生物和病毒。我们将提供分析服务和研究专业知识 设计，样本收集，统计，人工智能和宿主 - 微叶数据解释以支持其他 NPH中心并通过研究协调中心（RCC）制定标准操作程序。我们的 团队已经开发了独特的创新方法，以在一个 促进生物库提供的所有17,500个样本的成本，并具有强大的质量控制 确保高质量的原始和处理的数据产品。我们还能够提供绝对的量化 微生物负载通过我们最近在合成DNA“ Spike-Ins”中创新，这也有助于严格 评估污染和提取效率。除了带来我们拥有的尖端技术 我们还提出了3个试点项目：（i）长阅读数据组件； （ii）多路复用 元蛋白质组学； （iii）自动凳样品收集和处理，以改善分类学和 使用密集的时间表的分析和提高生物标志物检测灵敏度的功能分辨率。重要的是， 我们的团队也处于最佳状态，以建立社区共识，以达成共识的分析策略 在计划年度，以及解决将微生物组数据集成到NPH的挑战 财团，由于我们的：现有的高通量样本处理，测序和数据分析核心；紧的 纪律群体之间的整合；访问超级计算基础架构；数据可视化专业知识；和 与国际科学家的国际脑子的紧密协调 在微生物组和精确营养研究的不同领域中完全专业知识。这个中心也将 跨校园机构承诺提供4个本科生，5个研究生和6个 博士后奖学金，使教师参与和创新技术的发展和 推进NPH联盟目标的算法。此外，我们现有的社区外展经验可以 进一步支持NPH财团的目标，以提供尊重，可访问和引人入胜的反馈 参与者。对MMC成功至关重要的是PI的35％时间承诺 领先的规模努力中的记录。作为NPH财团的关键部分，我们旨在民主化 微生物组数据通过降低成本，时间和计算要求以及多学科的协调 数据分析和解释所需的专业知识，以实现精确营养的雄心勃勃的目标。