A Microbial Genome Reference Platform for Metagenomics

宏基因组学微生物基因组参考平台

• 批准号: 7645310
• 负责人: RICHARD A GIBBS
• 金额: $ 94万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-19 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7645310
• 关键词: Automated Annotation; Bacterial Genome; Biological Sciences; Cataloging; Catalogs; Cells; Communities; Complementary DNA; Complex; Data; Development; Disease; Future; Genome; Health; Human; Human Microbiome; Human body; Individual; Intestines; Metagenomics; Methods; Microbe; Oral cavity; Phase; Process; Sampling; Sequence Analysis; Shotguns; Software Tools; Techniques; Technology; Testing; Viral; Whole-Genome Shotgun Sequencing; base; cDNA Library; cost; experience; genome sequencing; improved; metagenomic sequencing; microbial; microbial community; microbial genome; microbiome; new technology; next generation; novel strategies; programs

DESCRIPTION (provided by applicant): The composition of the complex microbial communities inhabiting the human body has a tremendous influence on human health and disease. New DMA sequencing technologies offer the opportunity to study these communities by directly identifying the genome of individual microbial strains. Ideally, new sequences from metagenomic sampling can be compared to the known, full sequences of individual strains. It is estimated that there are more than 1,000 such reference strain sequences that are required and -600 that are either already determined, or else are in the process of being sequenced. The primary aim of this proposal is to generate reference DMA sequences of the remaining -400 strains to complete this reference catalogue. First, all 400 strains will be sequenced and assembled by shotgun methods. At least 60 will be finished to high quality using established methods and new approaches to convert the majority of the remainder to similarly high quality will be developed. The sequencing will use next-generation methods, based upon platforms developed by 454 Life Sciences, Illumina/Solexa and Applied Biosystems. All of the sequences wiN be annotated by an automated pipeline, and the 60 that are 'finished' will also be manually curated. The sequencing methods will also be applied to a selection of viral and fungal targets. Metagenomic sampling approaches will be tested using existing samples and methods, and these data will be refined by development of new technologies for selective DMA isolation and 16S and WGS sequencing of metagenomic samples, including microarray DMA chip capturing, electrophoretic techniques and cDNA tests. When all technical advances are combined, the cost of sequencing an individual bacterial genome will be less than $1,000.

描述（由申请人提供）：栖息在人体内的复杂微生物群落的组成对人类健康和疾病有着巨大的影响。新的DMA测序技术提供了通过直接识别单个微生物菌株的基因组来研究这些群落的机会。理想情况下，来自宏基因组采样的新序列可以与单个菌株的已知全序列进行比较。据估计，需要超过1，000个这样的参考菌株序列，并且约600个已经确定或正在测序过程中。本提案的主要目的是生成剩余约400株菌株的参考DNA序列，以完成本参考目录。首先，所有400个菌株将通过鸟枪法进行测序和组装。至少有60个将使用既定的方法完成高质量的工作，并将开发新的方法，将其余的大部分转换为同样高质量的工作。测序将使用下一代方法，基于454 Life Sciences，Illumina/Solexa和Applied Biosystems开发的平台。所有的序列都将由一个自动化的管道进行注释，而60个“完成”的序列也将由人工管理。测序方法还将应用于选择的病毒和真菌靶点。宏基因组采样方法将使用现有的样品和方法进行测试，这些数据将通过开发用于宏基因组样品的选择性DMA分离和16 S和WGS测序的新技术来完善，包括微阵列DMA芯片捕获，电泳技术和cDNA测试。当所有的技术进步结合在一起时，单个细菌基因组测序的成本将低于1000美元。