Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses

Our understanding of microbiomes, or the collection microorganisms and their genes in a given environment, has been revolutionized by technological computational advances. However, many undergraduate students do not get hands-on experiences with processing, analyzing, interpreting these types datasets. Recent global events have increased need for effective educational activities that can be performed virtually remotely. Here, we present module introduces STEM undergraduates to bioinformatic statistical analyses bacterial communities using combination free, web-based data processing software. These lessons allow engage studies microbiomes; gain valuable large, high-throughput datasets; practice science communication skills. The presented here walk through two platforms. first (DNA Subway) is an easy-to-use wrapper popular QIIME (pronounced “chime”) pipeline, which performs quality control analysis raw sequence outputs community matrix file assigned taxonomies. second, ranacapa, R Shiny App allows compare microbial communities, perform visualize data. Students may communicate findings written final report oral presentation. While use sample dataset based on gut-microbiome bean beetle (Callosobruchus maculatus), materials are easily modified original next-generation amplicon from any host environment. Additionally, options alternative datasets also provided facilitating flexibility within curriculum. Primary Image: Insects excellent example tractable biological system study relationship between organism its microbiome. Little currently known about insects, such as maculatus).