Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding

Abstract

We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow. The CURE is designed to take students with little to no technical and bioinformatic experience through key steps of the protocol through scaffolded laboratory and computational practicals. Our students extract and amplify human microbiome DNA using 16S ribosomal RNA specific primers, then construct a sequencing library for Oxford Nanopore based sequencing. They taxonomically assign the sequencing reads, and determine the ecological community composition using relevant software packages. Our students were able to successfully prepare sequencing libraries and analyse the data to produce relevant figures, demonstrating they met the learning objectives of the CURE. Students identified that they had developed higher level learning as defined by Blooms taxonomy, and that their confidence in practical work significantly increased as a result of doing the CURE. We share recommendations for implementation of the CURE in undergraduate curricula, and adaptations of the methods for use in schools outreach. Our CURE successfully provides training for students in genetic analysis in an enjoyable and relatively time and cost efficient manner, preparing them for future research or careers in modern molecular biology techniques.