A broadly implementable research course in phage discovery and genomics for first-year undergraduate students

Abstract

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

Importance: Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

FIG 1

SEA-PHAGES students contribute to scientific knowledge. Results are from the first 5 years of the SEA-PHAGES program isolating new phages, showing the cumulative numbers of phages isolated (blue), cumulative numbers of genomes sequenced (orange), cumulative numbers of gene phamilies (purple), and total numbers of mycobacteriophages in GenBank (green). Not all genomes sequenced and annotated in year 5 are yet available in GenBank.

FIG 2

Student evaluation of learning gains. Mean learning gains for common survey items on the SURE (green diamonds), CURE (blue squares), and the SEA-PHAGES (red triangles) assessment instruments are shown. The SURE survey data represent 2,358 students who completed summer research in 2009; the CURE survey data represent 476 students who were enrolled in science courses that were described by their instructors as without a research element (data collected for fall 2007 through spring 2009); the SEA-PHAGES data represent 121 students who evaluated their course following the academic year 2008–2009. Error bars represent 2 standard errors around the mean.

FIG 3

(A) Retention of SEA-PHAGES participants (red) compared to other students at the same institution (blue), year 1 to year 2 of their college experience. Retention data were gathered from 20 institutions, with some institutions contributing data from multiple years, resulting in 27 sets of comparison data. Retention data were analyzed with a between-group analysis of variance with 3 levels of the independent variable (all majors, STEM majors, and SEA-PHAGES students) for 171 reports. The result was interpreted as significant at the 0.05 level. (B) SEA-PHAGES students (red) perform better than peers (blue) in traditional laboratory sections in the introductory lecture course. Results are for 127 SEA-PHAGES students and 1,120 students in the traditional laboratory course from six institutions. In the lecture course, SEA-PHAGES students averaged 2.95 on a 4.0 scale, compared to the 2.58 average of students in traditional lab sections. This difference was significant (t = 2.64; P < 0.05).