The Phage Annotation Tools and Methods (PhAnToMe; http://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...

Please report errors in award information by writing to: awardsearch@nsf.gov.