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An Integrated lab-on-chip system for genome sequencing of single microbial cells

用于单个微生物细胞基因组测序的集成芯片实验室系统

基本信息

批准号：
7692280
负责人：
Yu-Hwa Lo
金额：
$ 55.07万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-09-26 至 2011-07-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): There are approximately 100 trillion microorganisms inhabited in a human body. The intimate interactions between these microorganisms and the host have a profound impact of the physiology of the human body. The majority of these microorganisms have yet to be fully characterized, mainly due to the difficulties in growing them in laboratory conditions. Here we propose the development of an efficient and scalable method to obtain genome sequences from single microbial cells. This will eliminate the need to obtain pure laboratory culture, thus allow us to systematically characterize the genome structure of microbial communities that resides in different parts of the human body. The proposed project contains three major components. 1. Development of low-cost and disposable cell sorting devices that integrate microfluidics with micro- scale optical components. Such a lab-on-chip cell sorter will be able to identify and isolate single microbial cells from samples that contain hundreds to thousands of different species and often are contaminated with free DNAs from the host and other sources. 2. Development of a micro-well based polymerase cloning device for simultaneous amplification of genomes from hundreds to thousands of single microbial cells in parallel. Using such a device, we will prepare sufficient amount of DNAs from single cells for whole genome shotgun sequencing, a critical step to obtain genome sequences from single cells. 3. Development of an integrate pipeline for dissecting the genome composition of human microbiome at the single cell resolution. We will test this pipeline by isolating and sequencing genome from approximately 35 single microbial cells at different levels of relative abundance from the mouse distal intestine. The propose method will provide the research community a new tool to identify unknown microbial species, to study their metabolic functions and to better understand the host-microbe interactions under various physiological and disease conditions. PUBLIC HEALTH RELEVANCE: The distribution and activities of microorganisms in the human body have a profound impact on the health of the host. In this proposed project we will develop an efficient and scalable method to obtain genome sequences from single cells in complex microbial communities. Characterizing the genomic composition and structures of these microorganisms is a necessary step before their metabolic functions and the interactions with the host can be study in great detailed.

描述(申请人提供)：人体内约有100万亿个微生物。这些微生物与宿主之间的亲密相互作用对人体的生理产生了深刻的影响。这些微生物中的大多数还没有得到充分的表征，主要是因为在实验室条件下培养它们存在困难。在这里，我们建议开发一种高效且可扩展的方法来从单个微生物细胞中获取基因组序列。这将消除获得纯实验室培养的需要，从而使我们能够系统地表征驻留在人体不同部位的微生物群落的基因组结构。拟议的项目包括三个主要组成部分。1.开发集成了微流体和微型光学元件的低成本和一次性细胞分选设备。这样的芯片上实验室细胞分选器将能够从含有数百到数千个不同物种的样本中识别和分离单个微生物细胞，这些样本经常被来自宿主和其他来源的游离DNA污染。2.微孔聚合酶克隆设备的研制，用于同时扩增数百到数千个单个微生物细胞的基因组。使用这样的设备，我们将从单细胞中制备足够数量的DNA，用于全基因组鸟枪式测序，这是从单细胞中获得基因组序列的关键步骤。3.建立了一套完整的单细胞分辨率的人体微生物群基因组组成分析系统。我们将通过从小鼠远端肠道分离和测序来自不同相对丰度水平的大约35个单个微生物细胞的基因组来测试这条管道。提出的方法将为研究界提供一个新的工具来识别未知的微生物物种，研究它们的代谢功能，并更好地了解各种生理和疾病条件下宿主与微生物的相互作用。公共卫生相关性：微生物在人体内的分布和活动对宿主的健康有深远的影响。在这个拟议的项目中，我们将开发一种高效且可扩展的方法来从复杂微生物群落的单个细胞中获取基因组序列。在详细研究这些微生物的代谢功能和与宿主的相互作用之前，表征这些微生物的基因组组成和结构是必要的步骤。