Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNA

A Systematic Approach To Promote Environmental Engineering Students' Learning in Environmental Molecular Microbiology

Environmental Molecular Microbiology (EMM) is a core course cluster for students majoring in environmental engineering. To help students learn the EMM courses, we developed a three-stage teaching approach to deliver EMM courses in a systematic manner: prerequisite course and survey studies; course cluster teaching; and feedback and improvement.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

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

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.

Metagenomic Approaches to Identify Novel Organisms from the Soil Environment in a Classroom Setting

Molecular Microbial Metagenomics is a research-based undergraduate course developed at Georgia State University. This semester-long course provides hands-on research experience in the area of microbial diversity and introduces molecular approaches to study diversity. Students are part of an ongoing research project that uses metagenomic approaches to isolate clones containing 16S ribosomal ribonucleic acid (rRNA) genes from a soil metagenomic library. These approaches not only provide a measure of microbial diversity in the sample but may also allow discovery of novel organisms. Metagenomic approaches differ from the traditional culturing methods in that they use molecular analysis of community deoxyribonucleic acid (DNA) instead of culturing individual organisms. Groups of students select a batch of 100 clones from a metagenomic library. Using universal primers to amplify 16S rRNA genes from the pool of DNA isolated from 100 clones, and a stepwise process of elimination, each group isolates individual clones containing 16S rRNA genes within their batch of 100 clones. The amplified 16S rRNA genes are sequenced and analyzed using bioinformatics tools to determine whether the rRNA gene belongs to a novel organism. This course provides avenues for active learning and enhances students' conceptual understanding of microbial diversity. Average scores on six assessment methods used during field testing indicated that success in achieving different learning objectives varied between 84% and 95%, with 65% of the students demonstrating complete grasp of the project based on the end-of-project lab report. The authentic research experience obtained in this course is also expected to result in more undergraduates choosing research-based graduate programs or careers.

Practice makes pretty good: assessment of primary literature reading abilities across multiple large-enrollment biology laboratory courses

Primary literature is essential for scientific communication and is commonly utilized in undergraduate biology education. Despite this, there is often little time spent training our students how to critically analyze a paper. To address this, we introduced a primary literature module in multiple upper-division laboratory courses. In this module, instructors conduct classroom discussions that dissect a paper as researchers do. While previous work has identified classroom interventions that improve primary literature comprehension within a single course, our goal was to determine whether including a scientific paper module in our classes could produce long-term benefits. On the basis of performance in an assessment exam, we found that our module resulted in longitudinal gains, including increased comprehension and critical-thinking abilities in subsequent lab courses. These learning gains were specific to courses utilizing our module, as no longitudinal gains were seen in students who had taken other upper-division labs that lacked extensive primary literature discussion. In addition, we assessed whether performance on our assessment correlated with a variety of factors, including grade point average, course performance, research background, and self-reported confidence in understanding of the article. Furthermore, all of the study conclusions are independent of biology disciplines, as we observe similar trends within each course.