A Microbial Genome Reference Platform for Metagenomics

描述(申请人提供)：居住在人体内的复杂微生物群落的组成对人类健康和疾病有巨大的影响。新的DNA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，从元基因组样本中获得的新序列可以与已知的单个菌株的全序列进行比较。据估计，有1000多个这样的参考菌株序列是必需的，-600个要么已经确定，要么正在进行测序。这项建议的主要目的是生成剩余-400株菌株的参考DNA序列，以完成该参考目录。首先，所有400个菌株将通过鸟枪法进行测序和组装。将使用既定的方法完成至少60个高质量的工作，并将开发新的方法，将剩余的大部分工作转化为同样高质量的工作。测序将使用下一代方法，基于454生命科学公司、Illumina/Solexa和应用生物系统公司开发的平台。所有的序列都将由自动化管道进行注释，而完成的60个序列也将进行手动整理。测序方法还将应用于一些病毒和真菌靶标的选择。将使用现有的样本和方法测试元基因组抽样方法，并将通过开发选择性DMA分离和元基因组样本的16S和WGS测序的新技术来完善这些数据，包括微阵列DMA芯片捕获、电泳技术和cDNA测试。当所有技术进步结合在一起时，对单个细菌基因组进行测序的成本将不到1,000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.