Illuminating the "black boxes" of microbiome sequencing

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Microbiome research is increasingly integrated into undergraduate laboratory courses through course-based undergraduate research experiences (CUREs).
• Current microbiome CUREs often present "black box" challenges for students, particularly in visualizing bacteria and understanding the translation of sequence data to taxonomic information.

Purpose of the Study:

• To describe a protocol for evaluating cultured bacterial communities using Oxford Nanopore sequencing.
• To enhance student understanding of microbiome analysis by illuminating opaque steps in typical CUREs.

Main Methods:

• A protocol was developed for culturing bacterial communities.
• Communities were sequenced using Oxford Nanopore technology.
• Bioinformatics analysis involved using BLAST on sequencing reads for bacterial identification.

Main Results:

• The protocol allows for the evaluation of bacterial communities through direct sequencing.
• Student use of BLAST on sequencing reads successfully identified bacteria within the community.
• This method demystifies the process of translating sequence data into bacterial taxonomy.

Conclusions:

• The described protocol effectively addresses "black box" issues in undergraduate microbiome CUREs.
• It provides a hands-on approach for students to visualize and identify bacteria in their samples.
• This method improves learning outcomes related to microbiology and bioinformatics processes.