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了一笔赠款，用于建立一个多学科团队，开发和应用合成下一代病毒元基因组序列数据的新工具。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方面发挥着重要作用。尽管测序技术取得了进步，但识别和/或对特定栖息地存在的病毒进行分类是一项重大挑战，因为对于这种地球上资源最丰富的物种，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，整合我们对病毒生物合成与宿主的兼容性的知识来实现。这项研究将与对芝加哥洛约拉大学自家后院密歇根湖近岸水域存在的病毒多样性的长期研究协调进行。利用新的计算方法，这项研究将确定噬菌体是否以及如何塑造这种环境中的细菌多样性和密度。开发的工具和生成的数据都将免费提供，这将有助于今后对环境病毒的研究。该项目产生了广泛的影响，包括继续开展对少数群体和妇女进行多学科科学教育的若干持续倡议。此外，它还将召集计算科学和生物科学的本科生在实验室和课堂上进行研究。通过开发新课程和融入现有课程，学生将参与并推动课堂上的积极探索。例如，被更多计算方面吸引的学生将在实验室和课堂上进行独特的体验，直接应用数据结构和算法设计的概念，为大型项目的发展做出贡献。这项研究的性质将引起芝加哥洛约拉大学的大量学生的兴趣，使学生更好地了解他们所生活的环境，并使下一代科学家接触到跨学科的研究方法。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/.

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/.