Metagenomics module project

Metagenomics is the study of all of the DNA in a given environmental sample. It can be used to determine what species are present in the sample, what they are doing, and how they are doing it. Metagenomics has a huge number of applications including drug/enzyme discovery, microbial ecology, biofuel production, and forensic science. As a multidisciplinary field that generates vast amounts of data, metagenomics is absolutely ideal for student projects. Classroom metagenomics activities are cheap, easy to learn, and can be used to teach a large variety of biological topics including genetics, genomics, microbiology, DNA science, experimental design, experimental technique, hypothesis generation, and the process of science. Importantly, metagenomics provides students with the ability to perform authentic research to test their own hypotheses.

Minnesota Mississippi Metagenomics Project (M3P Project)

The metagenomics lab modules described below make use of materials and data obtained from The Minnesota Mississippi Metagenomics Project.  Run by Dr. Michael Sadowsky, the M3P is designed to catalog the microbial populations in the Minnesota portion of the Mississippi river and learn more about how human activities may be influencing these microbial ecosystems. more information >>

Description of the project

In order to bring metagenomics into the classroom, four metagenomics modules were developed for BIOL 1009 General Biology. These labs allowed students to visualize microbes, extract metagenomes, setup a PCR reaction, and perform gel-electrophoresis. Students also performed functional metagenomics screens to uncover antibiotic resistance, and used bioinformatics programs to analyze sequence data from Mississippi River microbes. Each of these labs had clear learning goals designed to engage students in critical thinking and discovery-based science (see below). While these labs are all robust and user friendly, they are not “cookbook labs”. Instead, students are given the chance to create and test multiple hypotheses which makes each learning experience unique and exciting.

Learning outcomes

Lab Module

Module-specific Learning Objectives/Outcomes

Skills/Methods
  1. The Microbial World
  1. Explain the risks and benefits of living with microbes
  2. Define metagenomics and explain its applications
  3. Postulate how the surrounding landscape influences the microbial populations in the Mississippi river
  4. Outline the importance of microbes to river ecosystems
  5. List three potential benefits of using metagenomics to study river microbes
  1. Sample collection
  2. Light microscopy
  3. Microbe sizing
  4. Microbe filtering
  1. Extracting the Microbial Metagenome
  1. Explain how and why the 16S rDNA differs among organisms
  2. Draw and label a rarefaction curve and explain how it can be used to estimate sampling completeness
  3. Explain how DNA storage and handling techniques minimize damage caused by metal ions and enzymes
  4. Illustrate the concept of an Operational Taxonomic Unit (OTU)
  5. Predict antibiotic resistance profiles of Mississippi microbes
  6. Diagram how PCR works at the molecular level
  1. Extract genomic DNA
  2. Learn to use micropipettes and centrifuges
  3. Set-up a PCR reaction
  4. Formulate a hypothesis

 
  1. Sequence and Function Based Analysis
  1. Compare and contrast sequence-based & function-based metagenomics and list the strengths and weaknesses of each
  2. Plan a functional metagenomics screen and explain how this technique can be used to uncover novel proteins
  3. Explain how 16S rDNA analysis can classify microbe populations
  4. Define an ‘E. coli fosmid library’ and explain how it can be used to identify proteins of interest
  5. Describe the principle behind gel electrophoresis
  1. Perform gel electrophoresis
  2. Analyze/interpret gel data
  3. Use sterile technique to plate E. coli clones
  1. 4. Bioinformatic Analysis
  1. Define Bioinformatics
  2. Explain how organisms are classified
  3. Interpret a phylogenetic tree
  4. Identify homologous genes

 
  1. Analyze results of functional screen
  2. Explore and use IMG
  3. Perform comparative genomics
  4. Interpret a phylogenetic tree
  5. Identify homologs to commercially useful genes

Results

Student learning gains were quantified using a pre-/post test system with questions to assess student knowledge of metagenomics, experimental techniques, and data analysis. Identical assessments were administered at the beginning and end of the semester. The results clearly indicated that students made significant learning gains for nearly all topics tested. Students also indicated that they were very enthusiastic about these modules, and several even said that these modules made them consider new career plans in the fields of metagenomics and bioinformatics. This result was especially surprising and exciting as students in this class typically adopt majors in Dance, Economics, Mathematics, Architecture or other non-biology disciplines.

Research relating to these metagenomics modules was recently accepted for a JMBE curriculum publication entitled “Exploring Metagenomics in the Laboratory of an Introductory Biology Course” to be published in May 2015.