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: [email protected].
    • These authors contributed equally to the work.
    Source: J. Microbiol. Biol. Educ. June 2017 vol. 18 no. 2 doi:10.1128/jmbe.v18i2.1284
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • HTML
    51.99 Kb
  • PDF
    668.30 Kb
  • XML
    60.75 Kb

    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.

Key Concept Ranking

16s rRNA Sequencing
0.5154701
0.5154701

References & Citations

1. Torsten TJG, Folker MA 2015 A 123 of metagenomics 1 9 Nelson KE Genes, genomes and metagenomics: basics, methods, databases and tools Springer New York, NY
2. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL 2016 Toward a predictive understanding of Earth’s microbiomes to address 21 st century challenges mBio 7 e00714 16 10.1128/mBio.00714-16 4895116 http://dx.doi.org/10.1128/mBio.00714-16
3. American Association for the Advancement of Science 2011 Vision 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 Science July 15–17, 2009 Washington, DC
4. American Society for Microbiology 2012 Recommended curriculum guidelines for undergraduate microbiology education American Society for Microbiology Washington, DC
5. Handelsman J 2016 Announcing the national microbiome initiative Available 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 J 2016 The CourseSource bioinformatics learning framework CBE Life Sci Educ 15 le2 10.1187/cbe.15-10-0217 27290739 4803100 http://dx.doi.org/10.1187/cbe.15-10-0217
7. Gibbens BB, Scott CL, Hoff CD, Schottel JL 2015 Exploring metagenomics in the laboratory of an introductory biology course J Microbiol Biol Educ 16 34 10.1128/jmbe.v16i1.780 25949755 4416502 http://dx.doi.org/10.1128/jmbe.v16i1.780
8. Muth TR, McEntee CM 2014 Undergraduate urban metagenomics research module J Microbiol Biol Educ 15 38 10.1128/jmbe.v15i1.645 24839517 4004741 http://dx.doi.org/10.1128/jmbe.v15i1.645
9. Robertson-Albertyn S, Hardee E, Stanley-Wall NR 2016 Microbe motels: an interactive method to introduce the human microbiome J Microbiol Biol Educ 17 282 10.1128/jmbe.v17i2.966 27158310 4858365 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 RR 2012 A jungle in there: bacteria in belly buttons are highly diverse, but predictable PLOS One 7 e47712 10.1371/journal.pone.0047712 23144827 3492386 http://dx.doi.org/10.1371/journal.pone.0047712
11. Cracolice M 2009 Guided inquiry and the learning cycle 20 34 Pienta N, Cooper M, Greenbowe T Chemists’ guide to effective teaching Prentice Hall Upper Saddle River, NJ
12. Gormally C, Brickman P, Hallar B, Armstrong N 2009 Effects of inquiry-based learning on students’ science Int J Scholarsh Teach Learn 3 1 22
13. Kober N 2015 Designing instruction 89 120 Reaching students: what research says about effective instruction in undergraduate science and engineering The National Academies Press Washington, DC
14. National Research Council 2015 Reaching students: what research says about effective instruction in undergraduate science and engineering The National Academies Press Washington, DC

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v18i2.1284
2017-06-09
2019-10-19

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.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/jmbe/18/2/jmbe-18-33.html?itemId=/content/journal/jmbe/10.1128/jmbe.v18i2.1284&mimeType=html&fmt=ahah

Figures

Image of FIGURE 1

Click to view

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
Download as Powerpoint
Image of FIGURE 2

Click to view

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
Download as Powerpoint
Image of FIGURE 3

Click to view

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
Download as Powerpoint

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error