A Microbial Genome Reference Platform for Metagenomics

描述（由申请人提供）：居住在人体中的复杂微生物群落的组成对人类的健康和疾病有着巨大的影响。新的DMA测序技术通过直接鉴定单个微生物菌株的基因组，为研究这些群落提供了机会。理想情况下，宏基因组取样的新序列可以与已知的单个菌株的完整序列进行比较。据估计，有超过1000个这样的参考应变序列是需要的，-600个要么已经确定，要么正在测序过程中。本提案的主要目的是生成剩余的-400株的参考DMA序列，以完成该参考目录。首先，所有400个菌株将通过鸟枪法测序和组装。将使用既定方法至少完成60个项目，使其达到高质量，并将制定新办法，使其余大多数项目达到同样高质量。测序将使用下一代方法，基于454生命科学公司、Illumina/Solexa公司和Applied Biosystems公司开发的平台。所有的序列都将由一个自动化的流水线进行注释，而“完成”的60个序列也将被手动整理。测序方法也将应用于病毒和真菌目标的选择。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选择性DMA分离和宏基因组样品16S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起来，单个细菌基因组测序的成本将低于1000美元。

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.