Summer Workshop in Metagenomics: One Week Plus Eight Students Equals Gigabases of Cloned DNA

Rı́os-Velázquez, Carlos; Williamson, Lillie D.; Cloud-Hansen, Karen A.; Allen, Heather K.; McMahon, Mathew D.; Sabree, Zakee L.; Donato, Justin J.; Handelsman, Jo

doi:10.1128/jmbe.v12i2.177

Cited by 6 publications

(2 citation statements)

References 14 publications

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“…Ultimately, the goal of this discipline is to protect and preserve natural resources and human health by contributing to a sustainable environment. Environmental Molecular Microbiology (EMM) is a core course cluster for students majoring in environmental engineering which allows them to understand the molecular mechanisms underlying microbial processes in environmental engineering systems, e.g., wastewater treatment plants and in situ bioremediation sites (3)(4)(5). Courses in EMM cover fundamental principles, techniques, and applications of molecular microbiology in environmental engineering processes and help students gain insights into complex microbial processes at the molecular, cellular, community, and system levels.…”

Section: Introductionmentioning

confidence: 99%

A Systematic Approach to Promote Environmental Engineering Students’ Learning in Environmental Molecular Microbiology

Wang

Zhao

et al. 2021

J Microbiol Biol Educ.

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Section: Introductionmentioning

confidence: 99%

A Systematic Approach to Promote Environmental Engineering Students’ Learning in Environmental Molecular Microbiology

Wang

Zhao

et al. 2021

J Microbiol Biol Educ.

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“…Metagenomics-related laboratory modules are now being increasingly implemented in research-based and inquiry-based undergraduate instructional labs (5, 8, 12, 15, 17). An introductory biology course developed by Gibbens et al (8) consists of four 100-minute modules that include both sequence-based and function-based analyses of the metagenome prepared from environmental samples.…”

Section: Introductionmentioning

confidence: 99%

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

Rahman

Charles

Kaur

2016

J Microbiol Biol Educ.

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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.

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

Goller

Ott

2020

Biochem Molecular Bio Educ

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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.

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Summer Workshop in Metagenomics: One Week Plus Eight Students Equals Gigabases of Cloned DNA

Cited by 6 publications

References 14 publications

A Systematic Approach to Promote Environmental Engineering Students’ Learning in Environmental Molecular Microbiology

A Systematic Approach to Promote Environmental Engineering Students’ Learning in Environmental Molecular Microbiology

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

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

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