The study of microbiomes has skyrocketed over the last ten years. This growth has been driven by advances in DNA sequencing technologies, and by a paradigm shift in the field of microbial ecology sparked by culture-independent and metagenomic techniques. We saw in these rapid changes an opportunity to bring the excitement of microbiomes and metagenomics to students by providing training in the scientific process through their engagement in research. Using a course-based undergraduate research experience (CURE) model, we established the Urban Microbiome project at The City University of New York. Microbiome research allows students to conduct experiments that reveal the diversity and complexity of local environmental microbiomes and requires problem solving and quantitative skills. As the use of microbiome data in courses increases, there is a need to 1) set community standards, 2) adapt new technologies for use in microbiome CUREs, 3) provide training resources, and 4) to make available the growing microbiome datasets and analysis tools to students. We have established a national model for microbiome research and that provides support to faculty interested in incorporating the exploration of microbiomes into their courses. This is the perfect time for integrating microbiome studies as the tools for culture-independent study of microbial communities and for DNA sequencing are increasingly accessible and affordable.
Results/Conclusions:
There are a number of examples of how course-driven research can broaden participation and reach a larger demographic of STEM students who might not otherwise engage in original research. However, there are often barriers to adopting CUREs, including the major restructuring required for an existing course, the need to create a new course in some cases, and the significant time commitment required for faculty training. Aware of how these barriers prevent many instructors from adopting existing CUREs, we set out to offer an alternative CURE model that is easier for faculty to adopt. The Urban Microbiome CURE we developed is innovative because, 1) it uses a modular research project that instructors can easily insert into existing courses, 2) the richness and diversity of the microbiome data can be split into smaller, interconnected, research questions that can be divided among multiple student groups, and 3) because the addition of a microbiome component can complement existing faculty research efforts. The Urban Microbiome CURE has been incorporated into courses at numerous campuses (both four-year colleges and community colleges) in NYC and elsewhere, and has involved >4,500 students in microbiome research.