An integrated microbiome project for charactering microbial diversity in classroom based on virtual simulation experiments

Abstract

Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6‐week wet‐lab and bioinformatics course for undergraduates was implemented through the project‐based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step‐by‐step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.

Scoping review methodology and its use to review online project-based learning in higher education, 2020-2023

“…Second, some studies also referred to discipline-related specific tools, software, and applications or generic tools that were used to implement the content of the projects. Examples of this type included visualizations tools such as Java, Tableau, D3 (Beyer et al, 2021), Internet of Things (IoT) technologies (Baudin et al, 2022;Hayashi et al, 2023); Azure Notebooks (used for remote programming; Sakamaki et al, 2022), a virtual desktop infrastructure enabled by Citrix machine creation system which enables instructors to take control of students' virtual machines (Sola-Guirado et al, 2022), making use of the online virtual simulation experiment websites, employing bioinformatics tools (VSEARCH and MicrobiomeAnalyst) in order to analyze data (Sun et al, 2023), and the use of online platforms for creating multimedia videos or multimodal content (Canva and Powtoon; Poonpon, 2021).…”

“…Online Class Sessions. A number of studies (i.e., Beyer et al, 2021;Arantes do Amaral & Fregni, 2021;Guo et al, 2021;Hayashi et al, 2023;Sola-Guirado et al, 2022, Sun et al, 2023 referred to the availability of the instructor(s)/researchers(s) during online sessions with the participants, organized chiefly during synchronous class time slots, to provide some theoretical insights, discuss related texts and the activities as well as steps related to the projects, clarify instructions, answer questions, and/or provide feedback. While some of the procedures involved a clear time limit dedicated to this activity, followed by students' group work (e.g., Sola-Guirado et al, 2022, referred to dedicating 30 minutes to going over different specifications related to the projects and allowing students time afterwards to work on their projects; Beyer et al, 2021, stated that the teaching staff remained available for questions and feedback during classes; Guo et al, 2021, referred to teachers' answering questions about subject matter as well as reminding students of practical matters to be considered), other studies referred to organizing meetings whose sole purpose was to discuss and solve challenges and provide feedback (e.g., Arantes do Amaral & Fregni, 2021; Peng et al, 2022).…”

“…In their summaries of the key findings, some of the authors of the articles reflected on various positive aspects of online PBL implementation. For example, a number of authors (e.g., Baudin et al, 2022;Chanpet et al, 2020;Peng et al, 2022;Sola-Guirado et al, 2022;Sun et al, 2023) emphasized that the students enjoyed the process of engaging in online PBL, and the activities helped to spark an increase in their interest in the topics in question. Moreover, Beyer et al (2021) stressed that not only the students, but also their instructors experienced PBL as more rewarding.…”