CAREER: Quantitative Viral Metagenomics for Water Quality Assessment

职业：用于水质评估的定量病毒宏基因组学

• 批准号: 1653356
• 负责人: Kyle Bibby
• 金额: $ 50万
• 依托单位: University of Pittsburgh
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1653356&HistoricalAwards=false
• 关键词: CAREER; Quantitative; Viral; Metagenomics; Water

PI Name: BibbyProposal Number: 1653356 Current monitoring and regulatory approaches for microbial water quality, relying on the Fecal Indicator Bacteria (FIB), insufficiently protect public health due to a poor representation of viruses. Direct measurement of viral pathogens by conventional means is often incomplete due to the diversity of viral pathogens (200) that may be in the environment. In addition, due to a historical reliance on FIB, there is relatively little knowledge regarding viral pathogen presence and diversity in wastewater. The PI plans to develop quantitative viral metagenomics, sequencing of viral DNA/RNA, for viral water quality monitoring. The proposed technical developments will significantly advance not only water quality monitoring but also viral pathogen detection in other settings (e.g., food safety). The proposed efforts in viral water quality assessment will also offer an educational development opportunity for students (high school through graduate school), water quality professionals, and the general public. Specific technical goals include developing a rapid viral isolation and concentration approach and an improved methodology to remove free nucleic acids from non-viable viruses, an open-source bioinformatics pipeline to quantitatively identify viral pathogens from DNA sequence data, and a national survey of viral pathogen diversity in sewage. These developments may lead to new methods for monitoring microbial water quality as well as a methodology for viral water quality monitoring to elucidate the presence and diversity of viral pathogens in the water environment. Specifically, current metagenomics methods are applied non-quantitatively (e.g., on a relative abundance basis) and annotation accuracy is unverified; viral concentration methods are too slow for practical application and current methods for free DNA removal are inconsistent. Finally, little is known about viral pathogen diversity and dynamics in wastewater impacted systems. Application of viral metagenomics will help to inform investigations into the ecology of disease. Each task represents a discrete advance with applications beyond water quality in public health, microbiology, and bioinformatics. Additionally, bioinformatics tasks will be applicable to any sequencing platform and will be released as an open-access bioinformatic tool for use by researchers worldwide. Enabling quantitative and target-independent virus detection will facilitate improved water quality management, reducing overall human health impacts and informing infrastructure upgrades. Specific educational goals include a hands-on educational module for high school students to characterize microbial water quality, research experiences for high school and undergraduate students, expanding a current interactive exhibit established by the project PI at the Carnegie Science Center, and annual viral water quality webinars to be conducted through the Water Environment and Reuse Foundation. This effort will result in the release of an open-source bioinformatics viral annotation tool and an educational module for the high school classroom, extending the impact of technical and educational developments beyond the immediate project scope.

PI姓名：Bibby提案编号：1653356目前微生物水质的监测和监管方法依赖于粪便指示细菌（FIB），由于病毒的代表性差，不足以保护公众健康。由于可能存在于环境中的病毒病原体的多样性，通过常规方法直接测量病毒病原体通常是不完整的。此外，由于历史上对FIB的依赖，关于废水中病毒病原体的存在和多样性的知识相对较少。PI计划开发定量病毒宏基因组学，病毒DNA/RNA测序，用于病毒水质监测。拟议的技术发展不仅将大大推进水质监测，而且还将大大推进其他环境中的病毒病原体检测（例如，食品安全）。在病毒水质评估方面的拟议努力还将为学生（高中到研究生院）、水质专业人员和公众提供教育发展机会。具体的技术目标包括开发一种快速病毒分离和浓缩方法以及一种改进的方法，以从非活性病毒中去除游离核酸，开发一个开源生物信息学管道，以从DNA序列数据中定量识别病毒病原体，并对污水中的病毒病原体多样性进行全国调查。这些发展可能导致新的方法用于监测微生物水质以及病毒水质监测的方法，以阐明水环境中病毒病原体的存在和多样性。具体地，当前的宏基因组学方法是非定量地应用的（例如，在相对丰度的基础上）和注释的准确性是未经验证的;病毒浓缩方法对于实际应用来说太慢，并且目前用于游离DNA去除的方法是不一致的。最后，很少有人知道病毒病原体的多样性和动态废水影响的系统。 病毒宏基因组学的应用将有助于为疾病生态学的研究提供信息。每项任务都代表了一个独立的进步，其应用范围超出了公共卫生、微生物学和生物信息学中的水质。此外，生物信息学任务将适用于任何测序平台，并将作为开放获取的生物信息学工具发布，供全球研究人员使用。实现定量和目标无关的病毒检测将有助于改善水质管理，减少对人类健康的总体影响，并为基础设施升级提供信息。具体的教育目标包括为高中学生提供一个实践教育模块，以描述微生物水质，为高中和本科生提供研究经验，扩大卡内基科学中心PI项目建立的当前互动展览，以及通过水环境和再利用基金会进行的年度病毒水质网络研讨会。 这一努力将导致发布一个开源生物信息学病毒注释工具和一个高中课堂教育模块，将技术和教育发展的影响扩大到直接项目范围之外。