Deconvolution and Assembly of Metgenomes Using Chromatin Conformation Capture

使用染色质构象捕获对元基因组进行反卷积和组装

• 批准号: 9046257
• 负责人: Ivan Liachko
• 金额: $ 21.62万
• 依托单位: PHASE GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2017-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9046257
• 关键词: Agriculture; Bacterial Genome; Biomass; Cell physiology; Cells; Chromatin; Chromosomes; Clinical; Communities; Complex; Computer software; Cytolysis; DNA; DNA Sequence; DNA purification; Development; Disease; Ecosystem; Environment; Faculty; Genetic Variation; Genome; Genomics; Health; Health Benefit; High-Throughput Nucleotide Sequencing; Human; Industry; Legal patent; Libraries; Metagenomics; Methods; Molecular; Molecular Conformation; Nutritional; Organism; Phase; Plants; Plasmids; Population; Predisposition; Process; Production; Protocols documentation; Research; Sampling; Shotgun Sequencing; Site; Soil; Technology; TimeLine; Veterans; cell preparation; chromosome conformation capture; commercialization; crosslink; deep sequencing; genome sequencing; human disease; insight; member; metagenomic sequencing; microbial; microbiome; microbiota; microorganism; microorganism culture; novel; phase 2 study; public health relevance; tool; whole genome

 DESCRIPTION (provided by applicant): The diversity of communities of microorganisms ("microbiota") in our bodies, in soils, and throughout all ecosystems known on Earth has only recently been realized. Different microbiota are found at multiple body sites - where some provide health benefits and others cause disease. Analysis of these communities will reveal new ways to determine predisposition to diseases and will enable manipulation of the human microbiota to optimize human health. Other microbiota are found in and around plant cells, where some provide nutritional and anti-disease benefits, while others cause disease. Understanding plant microbiota will identify and define new ecologically compatible and sustainable agricultural practices and enable agricultural expansion to currently unsuitable land. Furthermore, the unprecedented diversity of microorganisms throughout all ecosystems provides for tremendous and uncharted genetic diversity, with far-reaching industrial applications. Technology Hurdle: Much of the information we have about microbiota derives from high-throughput sequencing technologies. Because the vast majority of microorganisms are unknown and cannot be purified, the microorganisms in microbiota must remain mixed and are co-sequenced ("metagenomics"). Using conventional methods, it is difficult to decipher which sequences belong to specific microorganisms ("deconvolution") because information regarding the cell of origin is lost upon breaking cells and preparation of DNA for sequencing - especially for complex genomes with multiple chromosomes or plasmids. Our Technological Advance: We used "chromosome conformation capture", to make both intra- and inter-chromosomal DNA crosslinks (stable linkages) - prior to breaking cells and processing of DNA. This allowed us to know which sequences originated in the same cell during deconvolution. In our initial studies, we successfully assembled artificially mixed populations of microorganisms (fungal, bacterial, and archaeal species), including those with complex genomes. Hypothesis: We hypothesize that our method can be applied to natural microbiota with unknown species at unknown concentrations. Specific Aims: 1) To adapt wet-lab chromosome conformation capture methods to real-world metagenomic samples, including difficult and low-biomass samples; and 2) develop production-quality software optimized for assembling low-abundance genomes, strain deconvolution, and plasmid assignment. Overall Impact: Upon completion, we believe our methods will become the standard for metagenomic sequencing - to better realize the potential that discoveries of human, plant, and ecosystem microbiota have to offer.

 描述（由申请人提供）：我们体内、土壤中以及地球上已知的所有生态系统中的微生物群落（“微生物群”）的多样性最近才被认识到。不同的微生物群存在于多个身体部位-其中一些提供健康益处，另一些导致疾病。对这些群落的分析将揭示确定疾病易感性的新方法，并将使人类微生物群的操纵能够优化人类健康。其他微生物群存在于植物细胞内和周围，其中一些提供营养和抗病益处，而另一些则导致疾病。了解植物微生物群将识别和定义新的生态兼容和可持续的农业实践，并使农业扩展到目前不适合的土地。此外，所有生态系统中微生物的空前多样性提供了巨大和未知的遗传多样性，具有深远的工业应用。技术障碍：我们拥有的关于微生物群的大部分信息都来自高通量测序技术。由于绝大多数微生物是未知的并且不能被纯化，因此微生物群中的微生物必须保持混合并且被共测序（“宏基因组学”）。使用常规方法，很难破译哪些序列属于特定微生物（“去卷积”），因为关于起源细胞的信息在破碎细胞和制备用于测序的DNA时丢失-特别是对于具有多个染色体或质粒的复杂基因组。我们的技术进步：我们使用“染色体构象捕获”，在破碎细胞和处理DNA之前，使染色体内和染色体间的DNA交联（稳定的连接）。这使我们能够知道在反卷积过程中哪些序列起源于同一细胞。在我们最初的研究中，我们成功地组装了人工混合的微生物种群（真菌，细菌和古细菌物种），包括那些具有复杂基因组的微生物。假设：我们假设我们的方法可以应用于未知浓度的未知物种的天然微生物群。具体目标：1）使湿实验室染色体构象捕获方法适应真实世界的宏基因组样品，包括困难和低生物量样品; 2）开发优化用于组装低丰度基因组、菌株解卷积和质粒分配的生产质量软件。总体影响：完成后，我们相信我们的方法将成为宏基因组测序的标准，以更好地实现人类，植物和生态系统微生物群的发现所提供的潜力。

项目成果

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen.

• DOI: 10.1038/s41467-018-03317-6
• 发表时间: 2018-02-28
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Stewart RD;Auffret MD;Warr A;Wiser AH;Press MO;Langford KW;Liachko I;Snelling TJ;Dewhurst RJ;Walker AW;Roehe R;Watson M
• 通讯作者: Watson M