Viruses are the most abundant biological entities on the planet. Since the most abundant living organisms on Earth are bacteria, the majority of these viruses are phages, the viruses which infect bacteria. Through their diverse lifestyles and gene products, phages play important roles in horizontal gene exchange, in structuring natural microbial communities, and in global biogeochemical cycles. Phages carry genes for some of the deadliest toxins known and can also carry genes which confer adaptive advantages to the hosts they infect. Furthermore, phage genes and the proteins they encode are the outcome of evolution over eons, the products of which we would be able to exploit if only we could decode the information in the phage DNA sequences. The number of available phage genome sequences is increasing rapidly; on the other hand, they represent the largest global reservoir of uncharacterized genetic material. Bioinformatic tools necessary for interpreting this data has lagged behind the growth in genome sequences. Grants to develop a platform and toolbox of computational tools for phage genome analysis have been awarded to support collaborative research in the laboratories of Drs. Robert Edwards, Department of Computer Sciences, San Diego State University, Mya Breitbart, College of Marine Sciences, University of South Florida, Jeffrey Elhai, Biology Department, Virginia Commonwealth University and Matthew Sullivan, Department of Ecology and Evolutionary Biology, University of Arizona. Dr. Elhai is an Associate Professor, the other three investigators are Assistant Professors. This collaborative project is creating new computational tools to establish a consistent nomenclature for phage genomes, to annotate phage sequences, both from completely sequenced phage genomes and from environmental phage metagenome sequences. Most importantly, this project will engage a wide spectrum of researchers, regardless of their computational background, to access the wealth of information contained in phage genomes through familiar graphical interfaces. These collaborators have developed an extensive and far-reaching education plan that targets high school students, undergraduate students and graduate students. The students trained in the use of the tools will rotate into trainer roles via user forums and workshops. The postdocs will be working across all the labs and thereby gain an unparalleled panoramic view of phage biology.
The Phage Annotation Tools and Methods (PhAnToMe; www.phantome.org/) project was a collaborative project between researchers at San Diego State University, the University of Arizona, Virginia Commonwealth University, and the University of Southern Florida. The goal of the project was to enhance our understanding of the genomes of phages, viruses that infect bacteria. There are many different kinds of phages, sometimes killing the bacteria but sometimes helping them become more effective. Phages are important in many different areas: for example, particularly lethal phages are used to secure our food supply by eradicating Salmonella, but other phages help bacteria to cause disease, like the bacteria that causes cholera. Phages affect carbon cycles on the planet by infecting bacteria that fix carbon dioxide. Although viruses are not visible in our daily routine, understanding them is essential to appreciating how biology on our planet works. Scientists have been sequencing the genomes of phages for many years. In fact, the first complete genome ever sequenced was a small virus. However, there are many aspects of viral genomes that we don't yet understand. The PhAnToMe project built a database of over 1,000 phage genomes, and annotated them using an approach called Subsystems Technology. Fifty-seven different phage-related gene groups were identified and more than 100,000 proteins were annotated in those phage genomes. This annotation has lead to the identification of new functions for unknown proteins, and we have shared this annotation with scientists around the world through databases like the RAST database at Argonne National Laboratory. We also built several computational (bioinformatic) tools to analyze phage genomes and related data. All these tools are housed on our website, www.phantome.org. One of our tools, the phage biobike (http://biobike.phantome.org) allows users with limited programming ability to easily and quickly write programs to explore the phage genomes. Another program we wrote analyzes complete bacterial genomes to identify the phages that are sometimes lurking inside. Working with researchers at Argonne National Laboratory in Chicago we have used that software to analyze almost 5,000 bacterial genomes – our most advanced exploration of phages in bacteria to date. We have also created a tool that allows researchers to designed degenerate primers allowing them to amplify signature genes for specific groups of phages from the environment, which will greatly aid in the exploration of global phage diversity. Scientists are also working on new techniques to identify bacteria and their phages in their natural environments. One of those techniques is an area called "metagenomics", where scientists sequence all of the DNA in a sample (for example, 100's of liters of sea water) without purifying out individual organisms. This has been extensively used to study phages because the scientists are spared the impossible task of growing the phages in the laboratory before sequencing them. We have developed many tools and techniques to work with metagenomics data, and have also shared our data with our colleagues worldwide who are exploring the role of phages in different environments. The PhAnToMe team has helped many different scientists with their work, including organizing a workshop at the Biosphere 2 laboratory in Arizona. The tools developed through this project have enabled undergraduate classes to experience the process of scientific discovery, facilitating the development of the next generation of researchers. In addition, we have reached out beyond the university, working with Girl Scout Troops, kindergarten and high school teachers, and sharing our love and passion for science with members of the public through science fairs and expositions. The PhAnToMe project bought together many different researchers to explore the genomes and the biology of phages, and we have shared that information so that the greater research community and the public at large benefit from our work.