A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R

Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusion in the curriculum may be hindered by several barriers, including lack of faculty expertise, student resistance to computational work, and few examples in the pedagogical literature. An 8-week wet-lab and in silico research experience for undergraduates was implemented. Students performed DNA purification and metagenomics analysis to compare the diversity and abundance of microbes in two samples. Students sampled snow from sites in northern Minnesota and purified genomic DNA from the microbes, followed by metagenomic analysis. Students used an existing metagenomic dataset to practice analysis skills, including comparing the use of Excel versus R for analysis and visualization of a large dataset. Upon receipt of the snow data, students applied their recently acquired skills to their new dataset and reported their results via a poster. Several outcomes were achieved as a result of this module. First, YouTube videos demonstrating hands-on metagenomics and R techniques were used as professional development for faculty, leading to broadened research capabilities and comfort with bioinformatics. Second, students were introduced to computational skills in a manner that was intentional, with time for both introduction and reinforcement of skills. Finally, the module was effectively included in a biology curriculum because it could function as either a stand-alone course or a module within another course such as microbiology. This module, developed with Course-based Undergraduate Research Experience guidelines in mind, introduces students and faculty to bioinformatics in biology research.