Bridging Biology and Data Science: Nanopore Sequencing-Based Lab Module for Biocomputational Engineering Students

Abstract Challenge The recently accredited Biocomputational Engineering (BCE) degree program seeks to provide students with a strong foundation in biology, quantitative problem solving, computation, and data science. Laboratory courses can strengthen comprehension of molecular biology and engineering principles and thus can support computational efforts, but there is a need for laboratory curriculum suited to BCE students. Novel Initiative To address this challenge, a two-week nanopore sequencing module was introduced to the required ENBC352 laboratory course. In lab, students extracted DNA from their saliva and prepared pooled libraries for 16S rRNA gene sequencing using the Oxford Nanopore Technologies (ONT) MinION instrument. Lectures supported the experimental workflow, and students characterized their oral microbiomes by analyzing species composition and diversity, linking their microbiome characterization results to personal survey data on health and habits. Learning outcomes were assessed via post-lab Likert-scale surveys. Reflection This module provided BCE students with valuable experience in experimental and analytical techniques, reinforcing connections between biology and data science. Students successfully extracted and sequenced DNA from their oral microbiomes, generating high-quality datasets that supported proper downstream analyses of microbiome composition; in Spring 2024, >100 Gb of data was produced, and in 2025, a shortened run generated ~1.2 M reads. Post-module surveys showed that all learning objectives were met, and the module received high scores for engagement, promoting interest in DNA sequencing, and perceived educational value. Personalized microbiome analysis enhanced student motivation, while nanopore sequencing offered a practical and modern platform for computationally inclined engineering students.