RUI: Dynamics of Genomic Mosaicism in Non-Host Associated Escherichia Populations

RUI：非宿主相关大肠杆菌群体中基因组嵌合的动态

• 批准号: 1616737
• 负责人: Aaron Best
• 金额: $ 77.53万
• 依托单位: Hope College
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616737&HistoricalAwards=false
• 关键词: RUI; Dynamics; Genomic; Mosaicism; Non

This project aims to address whether Escherichia from watersheds can serve as a reservoir for horizontal gene transfer to host-associated strains such as Escherichia coli, which is a known source of human infections. Watersheds can become contaminated with Escherichia via treated sewage, livestock farming, wild animals, fowl, and sediment runoff from urban and agricultural environments. Several studies revealed that Escherichia may adapt and persist in these environments, and eventually may be able to pass the genes for new traits to host-associated strains such as Escherichia coli. In addition to examining this idea, the data from this study will allow the broader scientific community to evaluate existing water quality monitoring methods. The research for this project will be integrated into authentic research experiences for undergraduate students in STEM fields through course-based research experiences (CREs). In particular, undergraduates in first year and upper level laboratories will actively participate in all aspects of the project.This project focuses on two related scientific goals: 1) characterizing genomic diversity of environmentally derived Escherichia isolates to understand variation in naturally occurring populations over time; and 2) linking profiles of 16S community surveys to observed variation in Escherichia isolate genomes and to environmental changes in a watershed. Remarkable genetic diversity has been characterized by global studies of E. coli through analysis of representative fully sequenced genomes, and targeted studies of pathogen sub-types through hundreds of draft genome sequences of clinical isolates. The preponderance of genomic data is from clinical and host-associated environments. This project produces 720 draft genome sequences of environmentally derived Escherichia isolates. The longitudinal data enable testing hypotheses about genome structure and genetic exchange in naturally occurring, non-host-associated populations through comparative genomics of genome content, arrangement and single nucleotide polymorphisms. The data address long term persistence of Escherichia populations in non-host environments, potentially serving as reservoirs for genetic exchange and renewal of fecal indicator bacteria in bodies of water. Oligotyping will estimate diversity in the Escherichia populations; water samples will produce coupled isolate genome sequences and microbial community 16S rRNA sequences. It is asserted that single nucleotide changes in 16S rRNA represent diversity of genome structure; the data will be used to test this assertion. Fine scale sampling produces longitudinal 16S rRNA microbial community profiles used to understand changes in Escherichia and other microbial populations. Work linking 16S rRNA variation to genome variation enables prediction of population changes based on 16S rRNA surveys alone. High quality recreational and drinking water sources are essential for society, and as water quality monitoring shifts to molecular based approaches, the types of datasets produced here become critical to ascertaining effective and broadly applicable monitoring techniques. A third goal fully incorporates undergraduate students in STEM fields through individual and course-based research experiences (CREs). Over 100 students in courses will gain first-hand knowledge of authentic research. The effectiveness of these experiences will be assessed through convergent mixed methods approaches designed to gauge student attitudes toward STEM fields, comparing effects of individual research experiences and CREs on first year and upper level students.

该项目旨在解决来自流域的大肠杆菌是否可以作为宿主相关菌株（例如已知的人类感染源）水平基因转移的储存库。 流域可能通过处理后的污水、畜牧业、野生动物、家禽以及城市和农业环境的沉积物径流而受到大肠杆菌污染。几项研究表明，埃希氏菌可能会适应并在这些环境中生存，并最终可能能够将新性状的基因传递给宿主相关菌株，例如大肠杆菌。 除了检验这个想法之外，这项研究的数据将使更广泛的科学界能够评估现有的水质监测方法。该项目的研究将通过基于课程的研究体验 (CRE) 融入 STEM 领域本科生的真实研究体验中。 特别是，一年级和高年级实验室的本科生将积极参与该项目的各个方面。该项目侧重于两个相关的科学目标：1）表征环境来源的大肠杆菌分离株的基因组多样性，以了解自然发生的种群随时间的变化； 2) 将 16S 群落调查概况与观察到的埃希氏菌分离株基因组变异以及流域环境变化联系起来。通过分析代表性的完全测序基因组对大肠杆菌进行全球研究，并通过数百个临床分离株的基因组草图序列对病原体亚型进行有针对性的研究，其特点是显着的遗传多样性。大部分基因组数据来自临床和宿主相关环境。该项目产生了 720 个来自环境的埃希氏菌分离株的基因组序列草案。纵向数据能够通过基因组内容、排列和单核苷酸多态性的比较基因组学来测试有关自然发生的非宿主相关群体中的基因组结构和遗传交换的假设。这些数据说明了埃希氏菌种群在非宿主环境中的长期存在，可能作为水体中粪便指示菌的遗传交换和更新的储存库。寡分型将估计埃希氏菌种群的多样性；水样将产生耦合的分离基因组序列和微生物群落 16S rRNA 序列。断言16S rRNA中单核苷酸的变化代表了基因组结构的多样性；数据将用于测试这一断言。精细采样产生纵向 16S rRNA 微生物群落概况，用于了解埃希氏菌和其他微生物种群的变化。将 16S rRNA 变异与基因组变异联系起来的工作可以仅根据 16S rRNA 调查来预测种群变化。高质量的娱乐和饮用水源对社会至关重要，随着水质监测转向基于分子的方法，这里生成的数据集类型对于确定有效且广泛适用的监测技术变得至关重要。第三个目标是通过个人和基于课程的研究经验 (CRE) 让本科生充分融入 STEM 领域。超过 100 名课程学生将获得真实研究的第一手知识。这些经验的有效性将通过收敛混合方法进行评估，旨在衡量学生对 STEM 领域的态度，比较个人研究经验和 CRE 对一年级和高年级学生的影响。