CAREER: How do phage drive bacterial diversity in Lake Michigan near-shore waters? A bioinformatics perspective

职业：噬菌体如何驱动密歇根湖近岸水域的细菌多样性？

• 批准号: 1149387
• 负责人: Catherine Putonti
• 金额: $ 70.65万
• 依托单位: Loyola University of Chicago
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1149387&HistoricalAwards=false
• 关键词: CAREER; How; do; phage; drive

Loyola University of Chicago is awarded a grant to establish a multidisciplinary team for the development and application of new tools for the synthesis of next-generation viral metagenomic sequence data. With the advent of next-generation sequencing (NGS) instrumentation, the throughput and cost-effectiveness of studying entire complex environmental communities is now feasible. A critical member of many ecological niches, the viral species which infect bacteria (phage) play an important role in maintaining the bacterial diversity within the community as well as nutrient cycling. Despite advances in sequencing technology, identifying and/or classifying the viruses present in a particular habitat is a significant challenge as relatively little genomic data is available for this the most abundant species on earth. Classifying novel species will be achieved by fusing existing and new tools, integrating our knowledge of viral biosynthetic compatibility with their host. This will be conducted in concert with a long-term study of the viral diversity present within Loyola University Chicago's own backyard - the near-shore waters of Lake Michigan. Utilizing novel computational methods, this research will ascertain if and how phage are shaping the bacterial diversity and density in this environment. The tools developed and data generated, both of which will be made freely available, will benefit future studies of environmental viriomes.This project has broad impacts, including the continuation of several ongoing initiatives for the instruction of minorities and women in multidisciplinary science. Furthermore, it will bring together undergraduate students in computational and biological sciences to do research both in the laboratory as well as in the classroom. Through the development of new courses and integration into existing courses, students will be engaged in and drive active investigation within the classroom. For instance, students drawn to the more computational aspects would be engaged in a unique experience in the laboratory and classroom, contributing to the development of a large project, directly applying concepts of data structure and algorithm design. The nature of this study will be of interest to a large number of students at Loyola University Chicago, providing students with a greater understanding of the environment in which they live as well as exposing the next generation of scientists to interdisciplinary approaches in research. For more information about the project visit the PI's lab website at http://sites.google.com/site/putonti/.

芝加哥的洛约拉大学被授予一笔赠款，建立一个多学科的团队，用于开发和应用新的工具，用于合成下一代病毒宏基因组序列数据。随着下一代测序（NGS）仪器的出现，研究整个复杂环境群落的吞吐量和成本效益现在是可行的。作为许多生态位的重要成员，感染细菌（噬菌体）的病毒种类在维持群落内细菌多样性以及营养循环方面发挥着重要作用。尽管测序技术取得了进展，但对特定栖息地中存在的病毒进行鉴定和/或分类仍是一项重大挑战，因为地球上最丰富的物种的基因组数据相对较少。新物种的分类将通过融合现有的和新的工具来实现，整合我们对病毒生物合成与宿主相容性的知识。这将与洛约拉大学芝加哥自己的后院-密歇根湖的近岸沃茨内存在的病毒多样性的长期研究相一致。利用新的计算方法，这项研究将确定噬菌体是否以及如何在这种环境中塑造细菌的多样性和密度。开发的工具和生成的数据都将免费提供，这将有利于今后对环境病毒体的研究，该项目具有广泛的影响，包括继续开展几项正在进行的倡议，为少数群体和妇女提供多学科科学方面的指导。此外，它将汇集计算和生物科学的本科生在实验室和课堂上进行研究。通过新课程的开发和融入现有课程，学生将参与并推动课堂内的积极调查。例如，被吸引到更多计算方面的学生将在实验室和课堂上获得独特的体验，为大型项目的开发做出贡献，直接应用数据结构和算法设计的概念。这项研究的性质将感兴趣的大量学生在洛约拉大学芝加哥，为学生提供更好地了解他们生活的环境，以及暴露下一代的科学家跨学科的研究方法。有关该项目的更多信息，请访问PI的实验室网站http://sites.google.com/site/putonti/。

项目成果

virMine: automated detection of viral sequences from complex metagenomic samples

• DOI: 10.7717/peerj.6695
• 发表时间: 2019-04-10
• 期刊: PEERJ
• 影响因子: 2.7
• 作者: Garretto, Andrea;Hatzopoulos, Thomas;Putonti, Catherine
• 通讯作者: Putonti, Catherine

Pseudomonas Diversity Within Urban Freshwaters

• DOI: 10.3389/fmicb.2019.00195
• 发表时间: 2019-02-15
• 期刊: FRONTIERS IN MICROBIOLOGY
• 影响因子: 5.2
• 作者: Batrich, Mary;Maskeri, Laura;Putonti, Catherine
• 通讯作者: Putonti, Catherine