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

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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/.