Collaborative Research: ABI Development: VIROME, bioinformatics cyberinfrastructure for the next wave of scientific advancements in microbiome research

合作研究：ABI 开发：VIROME，微生物组研究下一波科学进步的生物信息学网络基础设施

• 批准号: 1356374
• 负责人: K. Wommack
• 金额: $ 61.7万
• 依托单位: University of Delaware
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2019-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1356374&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Development; VIROME

The University of Delaware and the University of Maryland Baltimore are awarded collaborative grants for improvements to a computational tool that will enable a broader community of life scientists, engineers, and geoscientists to access viral metagenomics for the next wave of scientific discoveries in microbiome research. Eight percent of the human genome derives from retroviruses; these viral sequences differentiate the human genome from that of other primates. Within microbial communities, including those living in association with animal hosts, viruses are the most numerically abundant microorganisms, outnumbering all cellular microbes by 10 to 1,000 fold. These natural viral communities are genetically diverse, containing a vast number of novel and unknown genes. In the oceans, viral breakdown of microbial cells contributes to the chemical transformation of carbon and nutrient elements. Ultimately, these transformations impact the productivity of marine ecosystems as well as regional and global climate. While understanding of extant viral diversity and the role of viruses within natural systems is still rudimentary, there is evidence that viruses play critically important roles in the biology, ecology, and evolution of life on earth. This project will enhance a newly developed computational tool, the Viral Informatics Resource for Metagenome Exploration (VIROME) to better facilitate the coming wave of discoveries surrounding the role of viruses in natural systems. In particular, we will pursue three specific developmental goals: 1) leverage sources of long-length DNA sequence data to improve the quality of the information output from the VIROME bioinformatics pipeline; 2) utilize the VIROME gene classification scheme to develop a sustainable database of unknown viral genes, i.e., viral genetic dark matter; and 3) advance the sustainability of the VIROME resource through virtualization of its underlying computational workflow.Given that viruses impact life on earth over evolutionary time and global scales, further development of VIROME will benefit researchers in the life sciences, engineering, and geosciences. The project?s impact will be enhanced by directly training graduate and undergraduate students and by conducting twice yearly workshops on the use of VIROME for the analysis of viral metagenome sequence data. The project will also advance public understanding of the emerging scientific consensus surrounding the nuanced and critical impacts of viruses on cellular life by hosting an informational booth at Ag Day, a public outreach event reaching thousands of residents in the quad state vicinity of the University of Delaware, Newark campus (DE, MD, PA, & NJ). Lastly, the team will reach out to K-12 students by hosting an annual ?Get to know viruses? STEM program at the Delaware Biotechnology Institute for groups of Cub Scouts and Girl Scouts in the Newark, Delaware area.

特拉华州大学和马里兰州大学巴尔的摩获得合作赠款，用于改进计算工具，使更广泛的生命科学家，工程师和地球科学家社区能够访问病毒宏基因组学，用于微生物组研究的下一波科学发现。 人类基因组的8%来自逆转录病毒;这些病毒序列将人类基因组与其他灵长类动物的基因组区分开来。在微生物群落中，包括那些与动物宿主生活在一起的微生物，病毒是数量最丰富的微生物，数量超过所有细胞微生物的10至1,000倍。 这些天然的病毒群落具有遗传多样性，包含大量新的和未知的基因。 在海洋中，微生物细胞的病毒分解有助于碳和营养元素的化学转化。 最终，这些变化会影响海洋生态系统的生产力以及区域和全球气候。 虽然对现存病毒多样性和病毒在自然系统中的作用的理解仍然是初步的，但有证据表明病毒在地球上的生物学，生态学和生命进化中发挥着至关重要的作用。该项目将增强新开发的计算工具，即用于宏基因组探索的病毒信息学资源（VIROME），以更好地促进即将到来的围绕病毒在自然系统中作用的发现浪潮。 特别是，我们将追求三个具体的发展目标：1）利用长长度DNA序列数据的来源来提高VIROME生物信息学管道输出的信息质量; 2）利用VIROME基因分类方案来开发未知病毒基因的可持续数据库，即，病毒遗传暗物质; 3）通过虚拟化其基础计算工作流程来提高VIROME资源的可持续性。鉴于病毒在进化时间和全球范围内影响地球上的生命，VIROME的进一步发展将使生命科学，工程和地球科学的研究人员受益。 项目？通过直接培训研究生和本科生，以及每年两次举办关于使用VIROME分析病毒宏基因组序列数据的研讨会，将增强该中心的影响力。 该项目还将通过在Ag Day举办一个信息摊位，促进公众对病毒对细胞生命的细微差别和关键影响的新兴科学共识的理解，Ag Day是一个公共宣传活动，在特拉华州大学纽瓦克校区（DE，MD，PA，NJ）附近的四个州有数千名居民。 最后，该团队将通过举办年度？了解病毒？特拉华州生物技术研究所的STEM项目，面向特拉华州纽瓦克地区的童子军和女童子军团体。

项目成果

CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes

• DOI: 10.1128/mbio.02651-18
• 发表时间: 2018-12
• 期刊: mBio
• 影响因子: 6.4
• 作者: Daniel J. Nasko;Barbra D. Ferrell;Ryan M. Moore;Jaysheel D. Bhavsar;Shawn W. Polson;K. E. Wommack

Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton

• DOI: 10.3389/fmicb.2019.00134
• 发表时间: 2018-11
• 期刊: Frontiers in Microbiology
• 影响因子: 5.2
• 作者: Amelia O. Harrison;Ryan M. Moore;Shawn W. Polson;K. E. Wommack