Evolution of an 8‐week upper‐division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis

Abstract

Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8‐week metagenomics laboratory course has the objective of introducing upper‐level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high‐throughput sequencing before transitioning to computer‐based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre‐ and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting‐edge field of metagenomics.

Sharing Notes Is Encouraged: Annotating and Cocreating with Hypothes.is and Google Docs †

“…We introduced the use of Hypothes.is and collaborative notes in the fall of 2019 in an 8-week upper-division undergraduate and graduate student Metagenomics course (19). The course has weekly lectures of 1 hour 50 minutes and 5-hour labs with a course-based research project that relies heavily on the assigned readings.…”

Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules

“…Metagenomics ( Goller and Ott, 2020 ) is an inquiry-based course that provides advanced level undergraduate and graduate students hands-on exposure to a wide-variety of methods for analyzing unique and complex microbial communities. A focus is on computational skills to evaluate interactions between microbial populations and their surroundings.…”

“…Reasons for additional rounds of Development include activities not working as intended, or assessments revealing that scaffolding of the material was insufficient to achieve the learning objectives. Through the 5D process, MBLEMs have been created and disseminated over the years ( Witherow and Carson, 2011 ; Srougi and Carson, 2013 ; Ott and Carson, 2014 ; Lentz et al, 2017 ; Chen and Goller, 2020 ; Goller and Ott, 2020 ; Samsa et al, 2020 ; Garcia et al, 2021 ), ranging in topics from protein-protein interactions, signal transduction to metagenomics. This model has proven effective as demonstrated by the successful achievement of student learning outcomes and technical skills acquisition in these courses as assessed from quantitative course data (i.e., lab reports, exams, lab notebooks, and projects) and through analysis of qualitative student survey data.…”

A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning

“…Numerous active learning modules have been developed for students to explore microbial communities. These include inquiry-based activities, where students formulate hypotheses and either conduct experiments or analyze existing data sets to form conclusions ( Wang et al, 2015 ; Freeman et al, 2016 ; Lentz et al, 2017 ; Genné-Bacon and Bascom-Slack, 2018 ; Goller and Ott, 2020 ; Sewall et al, 2020 ); simulations and/or modeling activities ( Estes, 2015 ; Robertson-Albertyn et al, 2016 ; Rabelo-Fernandez and Rios-Velazquez, 2021 ); and gamification activities ( Coil et al, 2017 ). Some of these activities provide novice learners the opportunity to explore the physiological connection between the gut microbiome and its host.…”

“…For example, Freeman et al (2016) detailed a project where students collected data on their own facial microbiomes, along with demographic and lifestyle variables, to address novel questions, such as how one’s diet impacts their microbial diversity. While these active learning modules provide an effective mechanism to teach the physiological relevance of the microbiome, many are laboratory-based activities ( Freeman et al, 2016 ; Genné-Bacon and Bascom-Slack, 2018 ; Goller and Ott, 2020 ; Sewall et al, 2020 ) that are not feasible for a non-laboratory course. Additionally, many of these published activities also focus on novice learners and may not be appropriate for an upper-level undergraduate Human Anatomy and Physiology course ( Estes, 2015 ; Robertson-Albertyn et al, 2016 ; Coil et al, 2017 ; Rabelo-Fernandez and Rios-Velazquez, 2021 ).…”