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Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

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 (p < 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.

SUBMITTER: Wang JT

PROVIDER: S-EPMC4416505 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

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Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

Wang Jack T H JT Daly Joshua N JN Willner Dana L DL Patil Jayee J Hall Roy A RA Schembri Mark A MA Tyson Gene W GW Hugenholtz Philip P

Journal of microbiology & biology education 20150501 1

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 cohort ...[more]

PMID: 25949757

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Project description:Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

Project description:The benefits of mentored undergraduate research to student success, retention, and persistence in science, technology, engineering, and mathematics (STEM) have long been identified. However, many students miss out on the opportunity to engage in research often due to unfamiliarity of various research opportunities or how to approach potential research mentors. To address this, we developed a scalable online badge, Introduction to Research, that draws on aspects of the Entering Research curriculum (Branchaw, Pfund, & Rediske, 2010) to help students explore and prepare for undergraduate research in the biomedical and behavioral sciences. Students in the BUILD Training Program, part of the larger STEM BUILD at UMBC Initiative, completed the badge in conjunction with a 3-week classroom-based undergraduate research experience (CURE) before the start of their second year of undergraduate study at the University of Maryland, Baltimore County (UMBC). We were interested in investigating how this intervention, online badge plus CURE, correlated to students engaging in undergraduate research before the end of their second year at UMBC. We did this through student self-report, comparing students who had participated in the online badge plus CURE (BTP) to those who participated in neither (Control). Our data demonstrate that students who participated in the Introduction to Research Badge and CURE entered into mentored research at a significantly higher rate than students who were exposed to neither. Further, previously validated instruments of students 'research self-efficacy and science identity were used to compare how the Introduction to Research Badge and CURE may impact these two psycho-social variables. Students who participated in the Introduction to Research Badge and CURE had significantly higher gains in research self-efficacy compared to the control group. However, no change was observed in science identity for either group. Collectively, our results suggest that students who engage in the Introduction to Research Badge in combination with a CURE engage in mentored research within a year of completion at higher levels than students who engage in neither.

Dataset Information

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

Publications

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

Similar Datasets

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