Next generation informatics to elucidate viral ecology and ecosystem impacts in nature

下一代信息学阐明自然界中的病毒生态学和生态系统影响

• 批准号: 1759874
• 负责人: Matthew Sullivan
• 金额: $ 121.35万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2023-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759874&HistoricalAwards=false
• 关键词: Next; generation; informatics; elucidate; viral

Microbes are now appreciated for their roles in human health and disease, in promoting plant growth, and cycling nutrients in the oceans and soils. More recently, it has been recognized that the viruses that infect these microbes influence both the microbes and their communities through selective killing, moving genes between them, and reprogramming their host's metabolism during infection. Because viruses are so tiny, and most cannot be currently grown in laboratories, we are reliant upon decoding their biology through "reading" their stories via molecular sequencing techniques. This project seeks to augment iVirus, a collection of software tools (apps) and databases that leverages the NSF-funded CyVerse CyberInfrastructure (CI) to help researchers store, read and interpret these viral stories. Through development of new apps and curation of existing databases, the project will establish new analyses and features for researchers, directly train several undergraduate students, graduate students, and postdocs, and will provide two international training workshops to better "see" the viruses in their research.The microbiome is increasingly recognized to drive the nutrient and energy cycles that fuel Earth's diverse ecosystems, with their viruses modulating these impacts through killing, horizontal gene transfer, and metabolic reprogramming during infection. With the recent emergence of quantitative, sequence-based methods to comprehensively explore virus diversity in nature, the precise roles that viruses play can be increasingly elucidated. To perform these analyses, the iVirus platform was established in 2017 as part of the NSF-funded CyVerse CyberInfrastructure. iVirus currently includes apps, databases, and live documentation designed to enable researchers to better identify and analyze virus sequences by integrating and enhancing access to (meta)genomic sequence datasets and functions in the context of the NSF-funded CyVerse CyberInfrastructure. This project seeks to significantly augment iVirus in three ways: (i) aggregate and upgrade current viral ecogenomic capabilities, (ii) develop an integrated viral ecogenomic analytical pipeline, and (iii) establish direct connections and inter-operability across key databases and independent cyberinfrastructure environments. Beyond augmenting iVirus capabilities at CyVerse, we will actively seek to maximize its impact and utility for researchers through key partnerships with other existing tools (e.g., DOE Joint Genome Institute IMG/VR database). We will also continue to collect and be responsive to feedback provided through the CyVerse and the protocols.io reporting platforms, as well as collaborator and general user beta-testing and subsequent feedback on releases. Finally, we'll provide training at all levels through peer-reviewed publications, talks, and dedicated international workshops to enable the broader research community. The results of this project can be found at the iVirus website, http://ivirus.us/ .This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

微生物现在因其在人类健康和疾病中的作用而受到重视，促进植物生长，以及海洋和土壤中的营养物质循环。最近，人们已经认识到，感染这些微生物的病毒通过选择性杀伤、在它们之间移动基因以及在感染期间重新编程宿主的代谢来影响微生物及其群落。由于病毒非常微小，而且大多数病毒目前无法在实验室中培养，我们依赖于通过分子测序技术“阅读”它们的故事来解码它们的生物学。该项目旨在增强iVirus，这是一系列软件工具（应用程序）和数据库，利用NSF资助的CyVerse CyberInfrastructure（CI）帮助研究人员存储，阅读和解释这些病毒故事。通过开发新的应用程序和管理现有的数据库，该项目将为研究人员建立新的分析和功能，直接培训一些本科生，研究生和博士后，并将提供两个国际培训研讨会，以更好地“看到”他们的研究中的病毒。微生物组越来越被认为是推动营养和能量循环的动力，为地球多样化的生态系统提供燃料，它们的病毒在感染期间通过杀死、水平基因转移和代谢重编程来调节这些影响。随着最近出现的定量，基于序列的方法来全面探索病毒的多样性在自然界中，病毒发挥的确切作用，可以越来越多地阐明。为了进行这些分析，iVirus平台于2017年建立，作为NSF资助的CyVerse CyberInfrastructure的一部分。iVirus目前包括应用程序，数据库和实时文档，旨在使研究人员能够通过在NSF资助的CyVerse CyberInfrastructure的背景下集成和增强对（Meta）基因组序列数据集和功能的访问，更好地识别和分析病毒序列。该项目旨在通过三种方式显着增强iVirus：（i）聚合和升级当前的病毒生态基因组能力，（ii）开发集成的病毒生态基因组分析管道，以及（iii）在关键数据库和独立的网络基础设施环境之间建立直接连接和互操作性。除了增强CyVerse的iVirus功能外，我们还将积极寻求通过与其他现有工具（例如，DOE联合基因组研究所IMG/VR数据库）。我们还将继续收集并响应通过CyVerse和protocols.io报告平台提供的反馈，以及合作者和普通用户的beta测试和随后对版本的反馈。最后，我们将通过同行评审的出版物，讲座和专门的国际研讨会提供各级培训，以使更广泛的研究社区。该项目的结果可以在iVirus网站http://ivirus.us/上找到。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

项目成果

Diversity and ecological footprint of Global Ocean RNA viruses

• DOI: 10.1126/science.abn6358
• 发表时间: 2022-06-10
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Dominguez-Huerta, Guillermo;Zayed, Ahmed A.;Sullivan, Matthew B.
• 通讯作者: Sullivan, Matthew B.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

• DOI: 10.1093/nar/gkaa621
• 发表时间: 2020-09-18
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Shaffer, Michael;Borton, Mikayla A.;Wrighton, Kelly C.
• 通讯作者: Wrighton, Kelly C.

Perspective on taxonomic classification of uncultivated viruses

• DOI: 10.1016/j.coviro.2021.10.011
• 发表时间: 2021-11-12
• 期刊: CURRENT OPINION IN VIROLOGY
• 影响因子: 5.9
• 作者: Dutilh, Bas E.;Varsani, Arvind;Sullivan, Matthew B.
• 通讯作者: Sullivan, Matthew B.

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

• DOI: 10.1038/s41587-019-0100-8
• 发表时间: 2019-06-01
• 期刊: NATURE BIOTECHNOLOGY
• 影响因子: 46.9
• 作者: Jang, Ho Bin;Bolduc, Benjamin;Sullivan, Matthew B.
• 通讯作者: Sullivan, Matthew B.