Illuminating the "black boxes" of microbiome sequencing

Research on microbiomes is becoming common in undergraduate laboratory courses. These course-based undergraduate research experiences (CUREs) address many important microbiology and bioinformatics learning objectives related to science process skills. However, certain steps of the process for studying microbiomes represent "black boxes" for students. They never actually see any bacteria, but just extract bacterial DNA. Furthermore, how sequence data get translated into bacterial taxonomy tables is often opaque. We describe a protocol for evaluating communities of cultured bacteria that are sequenced with Oxford Nanopore technology. Then, students use BLAST on a subset of sequencing reads to identify the bacteria in the community. This approach illuminates these black boxes in typical microbiome CUREs.