Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes

ABSTRACT American Society for Microbiology Curriculum Guidelines highlight the importance of enabling students to think critically and learn by doing research. Moreover, information in biology, especially genetics and biotechnology, increases too rapidly for instructors to teach everything. To incre...

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Autores principales:	Chrystal Ho Pao, Sou-Cheng T. Choi, Shu Yun Lok, Storm Dorrough, Connie Abelseth, Joyce Shelton, Angelo Rentas
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	laboratory exercises genetics research module metagenomic study student oral microbes genetic databases bioinformatics Special aspects of education LC8-6691 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/663ab79919bd4f58b80922f2d617f46f
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spelling	oai:doaj.org-article:663ab79919bd4f58b80922f2d617f46f2021-11-15T15:04:52ZInquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes10.1128/jmbe.00136-211935-78851935-7877https://doaj.org/article/663ab79919bd4f58b80922f2d617f46f2021-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/jmbe.00136-21https://doaj.org/toc/1935-7877https://doaj.org/toc/1935-7885ABSTRACT American Society for Microbiology Curriculum Guidelines highlight the importance of enabling students to think critically and learn by doing research. Moreover, information in biology, especially genetics and biotechnology, increases too rapidly for instructors to teach everything. To increase students’ interest and comprehension of important core genetic concepts and to encourage students to practice scientific investigation, we designed a research module for upper-level biology/genetics students to examine oral bacteria. Students extracted their own oral microbial DNA and amplified and analyzed with general genus- and species-specific 16S rRNA PCR primers. The microbial DNA samples were also amplified with conserved bacteria 16S rRNA primers and the amplicons TOPO cloned (topoisomerase-based cloning) and Sanger sequenced. Lastly, the metagenomic microbial DNA samples were also sequenced by Illumina next-generation sequencing and analyzed with bioinformatics tools. We have implemented the module in three iterations of an undergraduate class at a small, liberal arts college. The project culminates in a poster presentation that the students on average performed in a high B range. Pre- and postsurvey analysis of student learning gains revealed significant student learning (P < 0.05 one-tailed, paired Wilcoxon signed ranked test, n = 23). Next, we surveyed student perceptions of the activity by a self-assessment. Significantly more than the medians, the students enjoyed the inquiry-driven module and considered it more effective in teaching about PCR and other molecular genetics concepts than the traditional prescribed laboratory exercises. We conclude that this microbe laboratory module induces research interest and is useful in teaching important genetics concepts.Chrystal Ho PaoSou-Cheng T. ChoiShu Yun LokStorm DorroughConnie AbelsethJoyce SheltonAngelo RentasAmerican Society for Microbiologyarticlelaboratory exercisesgenetics research modulemetagenomic studystudent oral microbesgenetic databasesbioinformaticsSpecial aspects of educationLC8-6691Biology (General)QH301-705.5ENJournal of Microbiology & Biology Education, Vol 22, Iss 2 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	laboratory exercises genetics research module metagenomic study student oral microbes genetic databases bioinformatics Special aspects of education LC8-6691 Biology (General) QH301-705.5
spellingShingle	laboratory exercises genetics research module metagenomic study student oral microbes genetic databases bioinformatics Special aspects of education LC8-6691 Biology (General) QH301-705.5 Chrystal Ho Pao Sou-Cheng T. Choi Shu Yun Lok Storm Dorrough Connie Abelseth Joyce Shelton Angelo Rentas Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
description	ABSTRACT American Society for Microbiology Curriculum Guidelines highlight the importance of enabling students to think critically and learn by doing research. Moreover, information in biology, especially genetics and biotechnology, increases too rapidly for instructors to teach everything. To increase students’ interest and comprehension of important core genetic concepts and to encourage students to practice scientific investigation, we designed a research module for upper-level biology/genetics students to examine oral bacteria. Students extracted their own oral microbial DNA and amplified and analyzed with general genus- and species-specific 16S rRNA PCR primers. The microbial DNA samples were also amplified with conserved bacteria 16S rRNA primers and the amplicons TOPO cloned (topoisomerase-based cloning) and Sanger sequenced. Lastly, the metagenomic microbial DNA samples were also sequenced by Illumina next-generation sequencing and analyzed with bioinformatics tools. We have implemented the module in three iterations of an undergraduate class at a small, liberal arts college. The project culminates in a poster presentation that the students on average performed in a high B range. Pre- and postsurvey analysis of student learning gains revealed significant student learning (P < 0.05 one-tailed, paired Wilcoxon signed ranked test, n = 23). Next, we surveyed student perceptions of the activity by a self-assessment. Significantly more than the medians, the students enjoyed the inquiry-driven module and considered it more effective in teaching about PCR and other molecular genetics concepts than the traditional prescribed laboratory exercises. We conclude that this microbe laboratory module induces research interest and is useful in teaching important genetics concepts.
format	article
author	Chrystal Ho Pao Sou-Cheng T. Choi Shu Yun Lok Storm Dorrough Connie Abelseth Joyce Shelton Angelo Rentas
author_facet	Chrystal Ho Pao Sou-Cheng T. Choi Shu Yun Lok Storm Dorrough Connie Abelseth Joyce Shelton Angelo Rentas
author_sort	Chrystal Ho Pao
title	Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
title_short	Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
title_full	Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
title_fullStr	Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
title_full_unstemmed	Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes
title_sort	inquiry-driven bioinformatics laboratory research module: metagenomic study of student oral microbes
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/663ab79919bd4f58b80922f2d617f46f
work_keys_str_mv	AT chrystalhopao inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT souchengtchoi inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT shuyunlok inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT stormdorrough inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT connieabelseth inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT joyceshelton inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes AT angelorentas inquirydrivenbioinformaticslaboratoryresearchmodulemetagenomicstudyofstudentoralmicrobes
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Inquiry-Driven Bioinformatics Laboratory Research Module: Metagenomic Study of Student Oral Microbes

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