Improving knowledge of metagenome-assembled genomes (MAGs) through bioinformatics and article annotation

DNA from microbial communities can be sequenced and assembled to gain insight into the microbes that may be present in unique environments. Powerful computational tools, combined with more accessible sequencing technologies, have enabled metagenome-assembled genome (MAG) analysis in course-based settings. However, the computational methods and assumptions surrounding the creation of MAGs, as well as their application in understanding microbes in biomes, are often complex and intimidating to new users. The metagenomics course we designed enrolls undergraduate and graduate students in a half-semester lab experience. We hypothesized that collaborative annotation of specific bioinformatics research articles, paired with student application of tools using guided case studies on the powerful KBase bioinformatics web platform, would enhance learning of key MAG concepts. Student learning outcomes on conceptual quizzes, as well as learner perceptions of the assignment and confidence in using KBase and other bioinformatics tools, were analyzed. Assessments and surveys of student perceptions were collected over several semesters using consistent assignments, readings, and KBase narratives. Learning gains were identified for specific MAG analysis concepts and data interpretation. Nevertheless, misconceptions continue, and confidence in bioinformatics approaches varies. Additional exploration of qualitative data may suggest concepts to reinforce and resources to support learners. Combining KBase, collaborative annotation of primary literature, guided case studies, and aligned assessments effectively promotes students' conceptual and mechanistic understanding of MAGs and the assumptions underlying their creation and use.