1887

Unique Down to Our Microbes—Assessment of an Inquiry-Based Metagenomics Activity

    Authors: Thomas B. Lentz1,‡, Laura E. Ott2,‡, Sabrina D. Robertson1,‡, Sarah C. Windsor3, Joshua B. Kelley4, Michael S. Wollenberg5, Robert R. Dunn6, Carlos C. Goller1,‡,*
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Biotechnology Program, North Carolina State University, Raleigh, NC 27695; 2: College of Natural and Mathematical Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250; 3: North Carolina Central University, Durham, NC 27707; 4: Washington and Lee University, Lexington, VA 24450; 5: Kalamazoo College, Kalamazoo, MI 49006; 6: Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 23 December 2016 Accepted 30 March 2017 Published 09 June 2017
    • ©2017 Author(s). Published by the American Society for Microbiology.
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: Jordan Hall 6102, Campus Box 7512, 2800 Faucette Drive, Raleigh, NC 27695. Phone: 919-513-4135. Fax: 919-513-4231. E-mail: ccgoller@ncsu.edu.
    • These authors contributed equally to the work.
    Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1284
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    Abstract:

    Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary. This activity was implemented in six introductory biology and biotechnology courses across five institutions. Attainment of student learning outcomes was assessed through completion of a quiz and students’ presentations of their findings. In presentations, students demonstrated their ability to develop novel hypotheses and analyze and interpret metagenomic data to evaluate their hypothesis. In quizzes, students demonstrated their ability to define key terms and describe the biological impact of the microbiota on human health. Student learning gains assessment also revealed that students perceived gains for all student learning outcomes. Collectively, our assessment demonstrates achievement of the learning outcomes and supports the utility of this inquiry-based activity to engage undergraduates in the scientific process via analyses of metagenomics datasets and associated exploration of a microbial community that lives on the human body.

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16s rRNA Sequencing
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References & Citations

1. Torsten TJG, Folker MA2015A 123 of metagenomics19 Nelson KEGenes, genomes and metagenomics: basics, methods, databases and toolsSpringerNew York, NY
2. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL2016Toward a predictive understanding of Earth’s microbiomes to address 21st century challengesmBio7e007141610.1128/mBio.00714-164895116 http://dx.doi.org/10.1128/mBio.00714-16
3. American Association for the Advancement of Science2011Vision and Change in Undergraduate Biology Education: A Call to Action: a summary of recommendations made at a national conference organized by the American Association for the Advancement of ScienceJuly 15–17, 2009Washington, DC
4. American Society for Microbiology2012Recommended curriculum guidelines for undergraduate microbiology educationAmerican Society for MicrobiologyWashington, DC
5. Handelsman J2016Announcing the national microbiome initiativeAvailable at: https://www.whitehouse.gov/blog/2016/05/13/announcing-national-microbiome-initiative
6. Rosenwald AG, Pauley MA, Welch L, Elgin SCR, Wright R, Blum J2016The CourseSource bioinformatics learning frameworkCBE Life Sci Educ15le210.1187/cbe.15-10-0217272907394803100 http://dx.doi.org/10.1187/cbe.15-10-0217
7. Gibbens BB, Scott CL, Hoff CD, Schottel JL2015Exploring metagenomics in the laboratory of an introductory biology courseJ Microbiol Biol Educ163410.1128/jmbe.v16i1.780259497554416502 http://dx.doi.org/10.1128/jmbe.v16i1.780
8. Muth TR, McEntee CM2014Undergraduate urban metagenomics research moduleJ Microbiol Biol Educ153810.1128/jmbe.v15i1.645248395174004741 http://dx.doi.org/10.1128/jmbe.v15i1.645
9. Robertson-Albertyn S, Hardee E, Stanley-Wall NR2016Microbe motels: an interactive method to introduce the human microbiomeJ Microbiol Biol Educ1728210.1128/jmbe.v17i2.966271583104858365 http://dx.doi.org/10.1128/jmbe.v17i2.966
10. Hulcr J, Latimer AM, Henley JB, Rountree NR, Fierer N, Lucky A, Lowman MD, Dunn RR2012A jungle in there: bacteria in belly buttons are highly diverse, but predictablePLOS One7e4771210.1371/journal.pone.0047712231448273492386 http://dx.doi.org/10.1371/journal.pone.0047712
11. Cracolice M2009Guided inquiry and the learning cycle2034 Pienta N, Cooper M, Greenbowe TChemists’ guide to effective teachingPrentice HallUpper Saddle River, NJ
12. Gormally C, Brickman P, Hallar B, Armstrong N2009Effects of inquiry-based learning on students’ scienceInt J Scholarsh Teach Learn3122
13. Kober N2015Designing instruction89120Reaching students: what research says about effective instruction in undergraduate science and engineeringThe National Academies PressWashington, DC
14. National Research Council2015Reaching students: what research says about effective instruction in undergraduate science and engineeringThe National Academies PressWashington, DC
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2017-06-09
2017-09-26

Abstract:

Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary. This activity was implemented in six introductory biology and biotechnology courses across five institutions. Attainment of student learning outcomes was assessed through completion of a quiz and students’ presentations of their findings. In presentations, students demonstrated their ability to develop novel hypotheses and analyze and interpret metagenomic data to evaluate their hypothesis. In quizzes, students demonstrated their ability to define key terms and describe the biological impact of the microbiota on human health. Student learning gains assessment also revealed that students perceived gains for all student learning outcomes. Collectively, our assessment demonstrates achievement of the learning outcomes and supports the utility of this inquiry-based activity to engage undergraduates in the scientific process via analyses of metagenomics datasets and associated exploration of a microbial community that lives on the human body.

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Figures

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FIGURE 1

Proposed timeline for implementation of the activity. The recommended allotment of time for each component of the activity is indicated. Activity components are divided based on which are suggested for in-class or out-of-class time.

Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1284
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FIGURE 2

Pre- and post-quiz scores assessing attainment of SLOs 1 and 2. Students were administered a quiz assessing SLOs 1 and 2 in a pre-/post-activity manner, with the average (±SD) scores for each cohort displayed. * < 0.05 using paired, two-tailed Student’s test. SLO = student learning outcome; UMBC = University of Maryland, Baltimore County; NCSU F’15 = North Carolina State University, Fall 2015; NCSU S’16 = North Carolina State University, Spring 2016; NCCU = North Carolina Central University; WLU = Washington and Lee University; KC = Kalamazoo College.

Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1284
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FIGURE 3

Post-activity assessment of student enjoyment. Students ( 83) were asked to respond to the indicated statement in the post-activity quiz. Bars indicate the total number of students who provided each response.

Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1284
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