1887

Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome

    Authors: Jack T. H. Wang1,*, Joshua N. Daly1,2, Dana L. Willner1,2,4, Jayee Patil1, Roy A. Hall1,6, Mark A. Schembri6, Gene W. Tyson1,2,3, Philip Hugenholtz1,2,3,5
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; 2: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia; 3: Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia; 4: Diamantina Institute, The University of Queensland, Brisbane, Queensland 4072, Australia; 5: Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; 6: Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 01 May 2015
    • Supplemental materials available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Room 76-426, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia. Phone: +61 7 3365 4611. Fax: +61 7 3365 4699. E-mail: [email protected].
    • ©2015 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 50-60. doi:10.1128/jmbe.v16i1.816
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    Abstract:

    Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity—the oral microbiome—by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012–2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE ( < 0.05 using the Mann-Whitney U-test). Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.

Key Concept Ranking

16s rRNA Sequencing
0.6192874
Culture Methods
0.50647706
Gram-Positive Cocci
0.49696213
Bacterial Cell Structure
0.47839364
Chemicals
0.44164184
Streptococcus mitis
0.43644598
0.6192874

References & Citations

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3. Alcaraz LD, et al 2012 Identifying a healthy oral microbiome through metagenomics Clin Microbiol Infect 18 Suppl 4 54 57 10.1111/j.1469-0691.2012.03857.x 22647051 http://dx.doi.org/10.1111/j.1469-0691.2012.03857.x
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7. Bragg L, Stone G, Imelfort M, Hugenholtz P, Tyson GW 2012 Fast, accurate error-correction of amplicon pyrosequences using Acacia Nat Methods 9 425 426 10.1038/nmeth.1990 22543370 http://dx.doi.org/10.1038/nmeth.1990
8. Caporaso JG, et al 2010 QIIME allows analysis of high-throughput community sequencing data Nat Methods 7 335 336 10.1038/nmeth.f.303 20383131 3156573 http://dx.doi.org/10.1038/nmeth.f.303
9. Cullinan MP, Seymour GJ 2013 Periodontal disease and systemic illness: will the evidence ever be enough? Periodontology 2000 62 271 286 10.1111/prd.12007 http://dx.doi.org/10.1111/prd.12007
10. DeSantis TZ, et al 2006 Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB Appl Environ Microbiol 72 5069 5072 10.1128/AEM.03006-05 16820507 1489311 http://dx.doi.org/10.1128/AEM.03006-05
11. Drew JC, Triplett EW 2008 Whole genome sequencing in the undergraduate classroom: outcomes and lessons from a pilot course J Microbiol Biol Educ 9 3 11 10.1128/jmbe.v9.89 23653818 3577148 http://dx.doi.org/10.1128/jmbe.v9.89
12. Hanauer DI, Jacobs-Sera D, Pedulla ML, Cresawn SG, Hendrix RW, Hatfull GF 2006 Inquiry learning. Teaching scientific inquiry Science 314 1880 1881 10.1126/science.1136796 17185586 http://dx.doi.org/10.1126/science.1136796
13. Hyytia-Trees EK, Cooper K, Ribot EM, Gerner-Smidt P 2007 Recent developments and future prospects in subtyping of foodborne bacterial pathogens Future Microbiol 2 175 185 10.2217/17460913.2.2.175 17661654 http://dx.doi.org/10.2217/17460913.2.2.175
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15. Kazor CE, et al 2003 Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients J Clin Microbiol 41 558 563 10.1128/JCM.41.2.558-563.2003 12574246 149706 http://dx.doi.org/10.1128/JCM.41.2.558-563.2003
16. Keijser BJ, et al 2008 Pyrosequencing analysis of the oral microflora of healthy adults J Dental Res 87 1016 1020 10.1177/154405910808701104 http://dx.doi.org/10.1177/154405910808701104
17. Kroes I, Lepp PW, Relman DA 1999 Bacterial diversity within the human subgingival crevice Proc Natl Acad Sci USA 96 14547 14552 10.1073/pnas.96.25.14547 10588742 24473 http://dx.doi.org/10.1073/pnas.96.25.14547
18. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P 2010 Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates Environ Microbiol 12 118 123 10.1111/j.1462-2920.2009.02051.x http://dx.doi.org/10.1111/j.1462-2920.2009.02051.x
19. Lord T, Orkwiszewski T 2006 Moving from didactic to inquiry-based instruction in a science laboratory Am Biol Teach 68 342 345 10.1662/0002-7685(2006)68[342:DTIIIA]2.0.CO;2 http://dx.doi.org/10.1662/0002-7685(2006)68[342:DTIIIA]2.0.CO;2
20. Merkel S 2012 The development of curricular guidelines for introductory microbiology that focus on understanding J Microbiol Biol Educ 13 32 38 10.1128/jmbe.v13i1.363 23653779 3577306 http://dx.doi.org/10.1128/jmbe.v13i1.363
21. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J 2009 Metagenomic pyrosequencing and microbial identification Clin Chem 55 856 866 10.1373/clinchem.2008.107565 19264858 2892905 http://dx.doi.org/10.1373/clinchem.2008.107565
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2015-05-01
2019-10-23

Abstract:

Clinical microbiology testing is crucial for the diagnosis and treatment of community and hospital-acquired infections. Laboratory scientists need to utilize technical and problem-solving skills to select from a wide array of microbial identification techniques. The inquiry-driven laboratory training required to prepare microbiology graduates for this professional environment can be difficult to replicate within undergraduate curricula, especially in courses that accommodate large student cohorts. We aimed to improve undergraduate scientific training by engaging hundreds of introductory microbiology students in an Authentic Large-Scale Undergraduate Research Experience (ALURE). The ALURE aimed to characterize the microorganisms that reside in the healthy human oral cavity—the oral microbiome—by analyzing hundreds of samples obtained from student volunteers within the course. Students were able to choose from selective and differential culture media, Gram-staining, microscopy, as well as polymerase chain reaction (PCR) and 16S rRNA gene sequencing techniques, in order to collect, analyze, and interpret novel data to determine the collective oral microbiome of the student cohort. Pre- and postsurvey analysis of student learning gains across two iterations of the course (2012–2013) revealed significantly higher student confidence in laboratory skills following the completion of the ALURE ( < 0.05 using the Mann-Whitney U-test). Learning objectives on effective scientific communication were also met through effective student performance in laboratory reports describing the research outcomes of the project. The integration of undergraduate research in clinical microbiology has the capacity to deliver authentic research experiences and improve scientific training for large cohorts of undergraduate students.

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Figures

Image of FIGURE 2.

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FIGURE 2.

Sample student gel electrophoresis results. Polymerase chain reactions (PCRs) from student oral samples were mixed with loading dye (Fermentas) before running out at 120 V for 30 minutes in 0.8% agarose gels. Expected PCR band sizes were compared against standard bands from 100 bp DNA ladder (New England Biolabs). A subset of the total samples collected is shown.

Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 50-60. doi:10.1128/jmbe.v16i1.816
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Image of FIGURE 1.

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FIGURE 1.

Sample student data for identification of oral bacteria via culture-dependent and culture-independent techniques. Culture-dependent identification of oral swabs was carried out as previously described in Appendix 1 . Culture-independent identification involved oral swabbing and genomic DNA extraction of student participants using an Epicentre DNA extraction kit. This was followed by polymerase chain reaction (PCR) amplification of the V5–V8 portions of the 16S rRNA gene, which was then sequenced for bacterial identification.

Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 50-60. doi:10.1128/jmbe.v16i1.816
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Image of FIGURE 3.

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FIGURE 3.

Student performance across project report criteria (as per Table 1 ) in 2012 and 2013. The proportion of students within the course cohorts who achieved a Fail (<49% – black), Pass (50–74% – grey), or a High Pass (75–100% – white) within each of the criteria is depicted.

Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 50-60. doi:10.1128/jmbe.v16i1.816
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Image of FIGURE 4.

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FIGURE 4.

Student perspectives on laboratory skill proficiency following the microbiome ALURE. Student confidence was measured through responses to survey questions in 2012 (n = 130) and 2013 (n = 197) on a 0–4 scale (0 = Do not know how to do; 1 = Not competent; 2 = Need practice; 3 = Competent; 4 = Highly competent). The mean survey response ± SEM is plotted above. * denotes a statistically significant difference between student survey responses before and after the laboratory experience as determined by the Mann-Whitney U-test ( < 0.05). ALURE = authentic large-scale undergraduate research experience; SEM = standard error of the mean.

Source: J. Microbiol. Biol. Educ. May 2015 vol. 16 no. 1 50-60. doi:10.1128/jmbe.v16i1.816
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