Confining Single Cells to Enhance and Target Cultivation of Human Microbiome

限制单细胞以增强和定向人类微生物组的培养

基本信息

批准号：
8523446
负责人：
RUSTEM F ISMAGILOV
金额：
$ 18.35万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-08-01 至 2015-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8523446
关键词：
Abdominal Infection Address Affect Bilophila wadsworthia Biological Assay Biopsy Specimen Cells Colon Communities Data Daughter Development Disease Gases Gastrointestinal tract structure Genes Genetic Genome Growth Health Human Human Microbiome Individual Inorganic Sulfates Intra-abdominal Life Liquid substance Metagenomics Methodology Methods Microbe Microfluidics Modeling Organism Pathway interactions Persons Population Population Growth Production Public Health Role Science Screening procedure Sister Solid Sulfur-Reducing Bacteria System Technology Testing Ulcerative Colitis Unspecified or Sulfate Ion Sulfates Work acrosome stabilizing factor base cell killing data sharing density gene function improved interest killings microbial microbial community microbiome microorganism nanolitre new technology prevent public health relevance scale up success sulfate reducing bacteria technology development

项目摘要

DESCRIPTION (provided by applicant): Understanding the human microbiome is critical in maintaining human health and preventing disease, but it has been unclear how specific microbes affect health and disease because the majority of microbes cannot be cultivated using traditional methods. Technologies are needed that can both increase the success rate for cultivating microbes and target cultivation efforts towards microbes of high biomedical interest. This project will use microfluidic confinement to overcome the limitations of traditional cultivation and targeting methods by developing "single cell confinement technology". Stochastic confinement of single cells in droplets of small volumes (picoliters to nanoliters) will isolate microbial species and, potentially, enable cultivation of new microbes by initiating high-density growth from a single cell. The droplets created by this single cell confinement technology can be split to perform multiple assays in parallel on clonal sister populations, enabling killing assays to be performed to identify microbes in one sister population, and using of the other sister population for growth. In this technology, to target cultivation efforts towards microbes of biomedical interest, new species will be identified via two complementary approaches: gene-based assays and function-based assays. Gene-based assays, informed by existing metagenomic data, will identify desired functional genes and 16S sequences, and function-based assays will identify desired functions even if they are not associated with a known gene sequence. The identified microbial species will then be targeted for scale-up of microcolonies to make them available for sequencing and further study. We will develop and validate the single cell confinement technology by using sulfur-reducing bacteria from the human colon as the test system. Sulfur-reducing bacteria are of high biomedical importance, associated with Ulcerative Colitis and intra-abdominal infections, but are still poorly understood. We will first use a model consortium of gut-derived microorganisms, containing a representative sulfur-reducing bacterium Bilophila wadsworthia, to develop and optimize the technology. Next, we will develop gene-based and function- based assays and test them by identifying sulfate reducing bacteria in model mixtures. Finally, we will use these cultivation approaches and assays to cultivate and select new sulfur-reducing bacteria from the human colon. This technology will be generally applicable to identify and cultivate all classes of microbes in the human gut microbiome. This project will impact biomedical science and public health by developing and validating technologies for increasing our understanding of the relationship between genes and functions in the human gut microbiome, and therefore microbial contributions to both health and disease. PUBLIC HEALTH RELEVANCE: Statement Microbes are critical to the function of the gastrointestinal tract. Understanding their role in human health and disease requires cultivation, but the majority of the species in the human gut microbiome are difficult to cultivate. This application will develop confined-based technology to enhance cultivation of microbes from human colon and target the cultivation efforts by using complementary assays to identify microbes with genes and functions of high biomedical interest.

描述（由申请人提供）：了解人类微生物组对于维持人类健康和预防疾病至关重要，但目前尚不清楚特定微生物如何影响健康和疾病，因为大多数微生物无法使用传统方法培养。需要既能提高微生物培养成功率又能针对具有高度生物医学意义的微生物进行培养的技术。该项目将通过开发“单细胞限制技术”，利用微流控限制来克服传统培养和靶向方法的局限性。将单细胞随机限制在小体积（皮升到纳升）的液滴中将隔离微生物物种，并有可能通过启动单细胞的高密度生长来培养新的微生物。通过这种单细胞限制技术产生的液滴可以被分开，以对克隆姐妹群体并行进行多种测定，从而能够进行杀灭测定以识别一个姐妹群体中的微生物，并利用另一姐妹群体进行生长。在这项技术中，为了针对具有生物医学意义的微生物进行培养，将通过两种互补的方法来鉴定新物种：基于基因的测定和基于功能的测定。基于现有宏基因组数据的基于基因的检测将识别所需的功能基因和 16S 序列，而基于功能的检测将识别所需的功能，即使它们与已知的基因序列无关。然后，将确定的微生物物种用于扩大微菌落规模，使其可用于测序和进一步研究。我们将利用人类结肠中的硫还原菌作为测试系统来开发和验证单细胞限制技术。硫还原细菌具有很高的生物医学重要性，与溃疡性结肠炎和腹内感染相关，但人们对其仍知之甚少。我们将首先使用肠道来源的微生物模型联盟来开发和优化该技术，其中包含代表性的硫还原细菌Bilophila wadsworthia。接下来，我们将开发基于基因和功能的检测方法，并通过识别模型混合物中的硫酸盐还原菌来测试它们。最后，我们将利用这些培养方法和测定方法从人类结肠中培养和选择新的硫还原细菌。该技术将普遍适用于识别和培养人类肠道微生物组中所有类别的微生物。该项目将通过开发和验证技术来影响生物医学科学和公共健康，以增强我们对人类肠道微生物组中基因和功能之间关系的理解，从而了解微生物对健康和疾病的贡献。公共卫生相关性：声明微生物对于胃肠道功能至关重要。了解它们在人类健康和疾病中的作用需要培养，但人类肠道微生物组中的大多数物种都很难培养。该应用将开发基于限制的技术，以加强人类结肠微生物的培养，并通过使用补充测定来识别具有高度生物医学兴趣的基因和功能的微生物来确定培养工作。