The UCSD Microbiome and Metagenomics Center

项目摘要 加州大学圣地亚哥分校(UCSD)微生物组和元基因组学中心(MMC)作为 精确健康营养(NPH)联盟将提供快速、可靠的粪便样本处理、高质量 元基因组和元翻译数据生成，以及一流的生物信息学分析。我们将优化 我们从粪便、后基因组和后转录文库制备中提取DNA和RNA的方案， 用于微生物组的超高分辨率分类和功能描述的测序和生物信息学， 包括细菌、古菌、真核生物和病毒。我们将提供分析服务和研究方面的专业知识 设计、样本收集、统计、人工智能和宿主-微生物数据解释，以支持其他 NPH中心，并与研究协调中心(RCC)一起制定标准操作程序。我们的 团队开发了独特的创新方法，以在 成本，便于应用于生物库提供的所有17,500个样本，并具有强大的质量控制，以 确保高质量的原始和加工数据产品。我们还能够提供绝对量化的 通过我们最近在合成DNA‘尖峰’方面的创新来加载微生物，这也促进了严格的 污染和提取效率的评估。除了带来我们拥有的尖端技术 发展到联合体，我们还提出了3个试点项目：(I)长读数据汇编；(Ii)多路传输 (3)自动收集和处理粪便样本，以改进分类学和 利用密集时间序列分析和提高生物标记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地位，能够就达成一致的分析战略达成社区共识 在规划年期间，以及解决将微生物组数据纳入国家卫生机构的挑战 财团，由于我们现有的高通量样本处理、测序和数据分析核心； 学科小组之间的整合；超级计算基础设施的使用；数据可视化专业知识；以及 与国际智囊团密切合作，这些科学家是根据他们的 在微生物组和精确营养研究的不同领域的互补专业知识。该中心还将 受益于跨校园机构承诺，提供4名本科生、5名研究生和6名 博士后奖学金，促进教师参与和创新技术的开发 推进NPH联盟目标的算法。此外，我们现有的社区外展体验可以 进一步支持NPH联盟的目标，即向 参与者。MMC成功的关键是PI 35%的时间承诺，他拥有出色的 在领导类似规模的努力方面有过往记录。作为NPH联盟的关键部分，我们的目标是实现民主化 通过减少成本、时间和计算要求以及多学科的协调来获取微生物组数据 数据分析和解释所需的专业知识，以实现精准营养的宏伟目标。

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.