In this course-based undergraduate research experience, students extract DNA from insects and sequence that DNA with an Oxford Nanopore sequencer for the purpose of identifying gut microbiome bacteria. Specifically, in this research module, the DNA of individual bean beetles from two treatment groups, for example, beetles raised on two different host beans, is extracted. Then, students prepare extracted DNA for Polymerase Chain Reaction (PCR) of the full 16S rDNA (which is specific to bacteria). The instructor (teaching assistant or laboratory technician) uses the amplified products to complete the DNA library preparation, creates a combined pooled library sample with as many as 24 different samples, and loads a DNA sequencing flow cell (Oxford Nanopore Flongle flow cell) to start the sequencing process. A FASTQ file of the DNA sequence data will be created for each sample in a sequencing run that the instructor can process with free cloud-based GUI software (EPI2ME software). Processing the FASTQ files yields a taxonomy table showing the bacterial taxa and frequency of each taxon in each bean beetle sample. Students can conduct a community ecology analysis of the taxonomy table data to evaluate and compare the bacterial microbiome communities of two treatment groups of bean beetles.
Keywords: CURE, Bean Beetle Microbiome Project, course-based undergraduate research, Oxford Nanopore DNA sequencing, bacterial community ecology, Callosobruchus maculatus
University of Manitoba (2025)
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