SEA-PHAGES: A Research Course for Freshman Undergraduates

Bacteriophages – viruses that infect bacterial hosts – are the most numerous biological entities in the biosphere, with an estimated 10³¹ phage particles. The phage population is not only vast but is dynamic and extremely old.  Not surprisingly it is also highly diverse, with phages of phylogenetically distal hosts showing little or no nucleotide sequence similarity. Early genomic characterization of fourteen mycobacteriophages  – sharing Mycobacterium smegmatis mc²155 as a single common host – suggested substantial diversity of the mycobacteriophage population, and showed that the genomes are architecturally mosaic and are replete with novel genes of unknown function. Establishment of the Phage Hunters Integrating Research and Education (PHIRE) in 2002 and the Howard Hughes Medical Institute’s Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program in 2008 has facilitated a large expansion of the collection of sequenced mycobacteriophages, providing novel insights into phage population structure, diversity, and evolution, within a context that introduces freshman undergraduates to research in microbiology. The SEA-PHAGES course is typically taught as a two-semester series for freshmen, with the first semester focusing on phage isolation, naming, purification, amplification, DNA isolation, and general characterization of their properties. Genomes are sequenced between the two semesters and then annotated and analyzed bioinformatically in the second semester. Currently, more than 80 US colleges and universities have participated in SEA-PHAGES, and a total of more than 5,000 students. A database and website (phagesDB.org) coordinates data assembly from participating students and faculty, and makes the collective data available for analysis. The SEA-PHAGES program has contributed to the isolation of over 4,500 newly discovered mycobacteriophages, over 650 of which have been completely sequenced. The SEA-PHAGES experience has a positive impact on student learning including enhanced retention in STEM. To date, PHIRE and SEA-PHAGES have generated more than a dozen publications with more than 200 undergraduate co-authors.