Implementing DNA Barcoding and Metabarcoding for Course-Based Undergraduate Research Experience

Bruce Nash
Assistant Director for Science
Cold Spring Harbor Laboratory

Need: There is mounting evidence that early exposure to undergraduate research increases student retention and graduation rates in STEM disciplines. Educators rising to this challenge have incorporated course based undergraduate research experiences (CUREs) into large-enrollment freshman and sophomore core STEM courses. There are many barriers to developing and implementing CUREs, including lack of faculty time and expertise. The DNA barcoding and metabarcoding infrastructure developed by Cold Spring Harbor Laboratory’s DNA Learning Center (DNALC) leverages modular CURE activities ready for implementation, as exemplified by the first year DNA barcoding CUREs at James Madison University (JMU).Guiding questions: The project aims to determine if barcoding CUREs meet faculty needs as they aim to enrich student STEM education. The collaboration between the DNALC, JMU, Bowie State University, and New York City College of Technology aims to further develop, disseminate, and evaluate DNA barcoding and metabarcoding CURE modules. After refinement, we have trained and supported educators from across the country to implement these modules and test the effectiveness of these CUREs as they introduce authentic research to their classes.Outcomes: To reduce barriers to implementation, the biochemistry and bioinformatics for barcoding and metabarcoding have been improved. For barcoding, a new, faster DNA isolation method was developed and adapted for at-home use and BLAST searches improved. For metabarcoding, the biochemistry was streamlined to simplify sample processing and co-PI Enke adapted the DNALC’s techniques to support sequencing at JMU.At JMU, BSU, and City Tech, co-PIs Enke, Hyman, Seto, and Ude have implemented and refined their CUREs to provide participants with the best possible resources for implementation. Three DNA barcoding workshops have trained 35 university faculty, 26 college faculty, and 4 high school teachers. Meanwhile, two metabarcoding workshops have trained 47 university faculty, 27 college faculty, and 2 high school teachers. Two additional workshops at BSU introduced the CUREs (35) and trained faculty in metabarcoding (7).With extended support, including support with reagents, sequencing, pedagogy, and the biochemistry and bioinformatics supplied by project co-PIs and program participants acting as mentors, many faculty are implementing DNA barcoding and metabarcoding CUREs at their institutions. Although the pandemic impacted these efforts in many ways, 32 classes with 1418 students included DNA barcoding, while 25 classes included metabarcoding, reaching 431 students in 2021.Participation in barcoding and metabarcoding CURES both had significant impacts on students’self reported knowledge of these approaches and attitudes towards science. Over half also felt they were capable of going further in science and were more interested in technology, bioinformatics, and studying biology.Broader Impacts: The program positively affects student attitudes of science, promising to increase the number of people pursuing careers in STEM. Students also contribute to biodiversity research, identifying and tracking species. The program also promises to increase the diversity of students pursuing STEM. Toward this goal, 28% of faculty trained in DNA barcoding and 20% of faculty trained in metabarcoding were underrepresented minorities. As hoped, faculty reached a large proportion of URM students, with 38% of students identifying as URM in survey responses.


Bruce Nash, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; Oliver Hyman, James Madison University, Harrisonburg, VA; Ray Enke, James Madison University, Harrisonburg, VA; George Ude, Bowie State University, Bowie, MD; Jeremy Seto, New York City College of Technology, New York, NY