Phanning the Phlames: Expansion of the Phage Hunters Integrating Research and Education (PHIRE) Program
Summary: Graham Hatfull's project uses bacteriophage discovery and characterization—phage hunting—to engage undergraduate and high school students in authentic scientific research. Student researchers identify previously unknown bacteriophages (viruses that infect bacteria), analyze their genomes, and design experiments to determine the function of specific bacteriophage genes.
In 2002, we established the Phage Hunters Integrating Research and Education (PHIRE) program. Our goal was to develop a platform in which novice scientists—primarily undergraduate and high school students—could become engaged in authentic scientific research. The research focuses on the discovery and comparative genomics of bacteriophages, viruses that infect bacteria, and takes advantage of the abundance and diversity of the phage population. Each student in the program isolates a novel virus from the environment, names it, and learns how it is related to other viruses through genomic characterization. The initial steps are technically and conceptually simple, but the project becomes more complex and abstract as it progresses. The excitement of discovery and the power of project ownership motivates students to tackle the more challenging tasks.
We have focused on a particular type of phages called mycobacteriophages—those that infect mycobacterium bacterial hosts. Through the PHIRE program, we have sequenced more than 60 phage genomes to create the largest collection of phages known to infect a common host, Mycobacterium smegmatis. The mycobacteriophages not only show broad DNA diversity but also fantastic genetic novelty, as more than 80 percent of the gene families have an unknown function. PHIRE students contribute new scientific information that promises to significantly advance our understanding of how viruses work and the genetics of tuberculosis.
Because of the simplicity of phage isolation and the structure of the PHIRE program, entering students do not need to be have advanced knowledge of biological concepts or techniques, but they must have the curiosity and the motivation to explore. To date, we have engaged over 275 undergraduate and high school students in the program, from a variety of academic and demographic backgrounds. Over 95 percent of all students who have graduated from this program are now studying or working in science-related fields.
Students in the PHIRE program learn that the chance to engage in cutting-edge scientific exploration comes with the responsibility to teach others how to do the same. Because each student follows a parallel set of procedures and protocols, advanced students in the program have the opportunity to mentor those that are just starting. We also expect students to coauthor submission of their annotated phage genome sequence to the public databanks and to coauthor manuscripts for publication in peer-reviewed scientific literature. Thirty-six undergraduate or high school PHIRE students have coauthored genome sequence and annotation entries in GenBank since the program started. In addition, 23 undergraduates are coauthors of published or submitted manuscripts in peer-reviewed scientific journals describing discoveries in phage genomics and evolution.
Dissemination of the PHIRE program has taken three main forms. The first is HHMI’s Science Education Alliance (SEA) initiative, in which phage hunting is offered nationally as a research-based course for freshman undergraduates. In its first two years, the SEA course has reached 517 students at 24 schools. The program has been highly successful at retaining students and encouraging them to think more closely about science research. The second outreach effort is a phage discovery module for students at local high schools. The third is a series of summer workshops for teachers nationwide who are trained to implement phage-hunting activities in their schools. Sixty-three teachers have attended the workshops and more than 10,000 students have conducted phage-hunting activities in 77 schools.
One possible limitation of the PHIRE program is that its primary focus on discovery and genomic characterization provides little opportunity for students to learn about experimental design and open-ended investigations. With new funding from HHMI, we plan to address by introducing avenues for determining the function of the genes in the new phages that students discover. Two key technical developments will help facilitate this. First, next-generation sequencing technologies enable much more rapid sequencing of complete phage genomes. As a result, students can progress through phage isolation, sequencing, and genome annotation in a shorter timeframe that was previously possible. Second, we have developed a relatively simple and effective means of constructing bacteriophage mutants and recombinants, enabling students to learn how to design experiments to address specific questions about phage biology. For example, a student may isolate and sequence a phage that has an unexpected gene whose function is unknown. The student can then design an experiment to knock out that gene, characterize the mutant, determine its phenotype, and generate a model for the gene function. The PHIRE platform thus provides a foundation for students to learn about experimental design, data analysis, and interpretation, and how to advance independently to address more complex questions. Through research experiences in this program, students learn how questions of significant scientific importance can be addressed through the scientific method.
Related HHMI Project Publications
Pedulla, M. L., et al. "Origins of Highly Mosaic Mycobacteriophage Genomes." Cell 113 (2003):171-82.
Hanauer, D. I., et al. "Inquiry Learning. Teaching Scientific Inquiry." Science 314 (2006):1880-1.
Hatfull, G. F., et al. "Exploring the Mycobacteriophage Metaproteome: Phage Genomics as an Educational Platform." PLoS Genet 2 (2003):e92.
Pham, T. T., et al. "Comparative Genomic Analysis of Mycobacteriophage Tweety: Evolutionary Insights and Construction of Compatible Site-Specific Integration Vectors for Mycobacteria." Microbiology 153 (2007):2711-23.
Morris, P., et al. "Genomic Characterization of Mycobacteriophage Giles: Evidence for Phage Acquisition of Host DNA by Illegitimate Recombination." J. Bacteriol 190 (2008):2172-82.
Hanauer, D., G.F. Hatfull, and D. Jacobs-Sera. Active Assessment: Assessing Scientific Inquiry. New York, NY: Springer, 2009.
Hatfull, G. F., et al. "Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size." J Mol Biol 397 (2010):119-143.
My lab is interested in the exploration and exploitation of mycobacteriophages, viruses that infect mycobacterial hosts such as Mycobacterium tuberculosis. Discovery and genomic analysis of a large set of mycobacteriophagesall known to infect a common M. smegmatis hostreveals them to be enormously genetically diverse and contains vast numbers of genes of unknown function with no homologues in the sequence databases. Nevertheless these phage genomes contain many genes related to host genes suggesting that they may act to modify the physiology of their hosts. Mycobacteriophages are therefore rich topics for discovery and genomic analysis, presenting an effective platform for an introduction to research for novice scientists. They also present an abundance of mysteries about gene function, regulation, and evolutionary mechanisms.
Mycobacteriophages represent terrific toolboxes for mycobacterial genetics. On one hand, they have evolved to efficiently introduce their DNA into their bacterial hosts and can thus be used as vehicles to introduce transposons, reporter genes, and recombination substrates into M. tuberculosis. On the other hand, many of their component parts function as well-oiled machines, and can be adapted for use to modify their hosts; these including integration systems for inserting foreign DNA into bacterial genomes, mycobacterial-specific recombineering, and nonantibiotic selectable markers.