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

芝加哥洛约拉大学获得一项资助，建立一个多学科团队，开发和应用新工具，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通量和成本效益现在是可行的。作为许多生态位的关键成员，感染细菌的病毒物种（噬菌体）在维持群落内的细菌多样性和营养循环中起着重要作用。尽管测序技术取得了进步，但确定和/或分类存在于特定栖息地的病毒是一项重大挑战，因为地球上最丰富的物种可获得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，整合我们对病毒与宿主生物合成兼容性的知识。这项研究将与芝加哥洛约拉大学自家后院——密歇根湖近岸水域——的病毒多样性长期研究相结合。利用新颖的计算方法，本研究将确定噬菌体是否以及如何在这种环境中塑造细菌多样性和密度。开发的工具和产生的数据都将免费提供，这将有利于未来对环境病毒组的研究。这一项目具有广泛的影响，包括继续开展若干正在进行的指导少数民族和妇女学习多学科科学的倡议。此外，它将把计算和生物科学的本科生聚集在一起，在实验室和课堂上进行研究。通过新课程的开发和与现有课程的整合，学生将参与并推动课堂内的积极调查。例如，被更多计算方面吸引的学生将在实验室和课堂上参与独特的体验，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。这项研究的性质将引起芝加哥洛约拉大学大量学生的兴趣，为学生提供对他们所生活环境的更深入了解，并使下一代科学家接触跨学科研究方法。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/。

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/.