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.

Using undergraduate research to develop transferable skills for the modern workforce

“…Given the impact of engaging with undergraduate research on student retention within science programs 21,22 , the long-term value of exposure to research-based learning early in undergraduate education should not be underestimated 34 . focus-group interviews, the ALURE team consistently reported student-learning gains in scientific skills following the completion of ALURE modules 30,31 , with higher gains observed in critical thinking and problem-solving skills when compared to traditional practical modules 32 . Undergraduate research is a high-impact activity that can be of great benefit to students, and the ALURE project has demonstrated that it can be a valuable addition to the instructor's toolkit to bolster student-learning outcomes in transferable skills.…”

“…In second year, microbiome samples from 400-500 students are crowd-sourced each semester, and used in an ALURE project investigating microbial composition across different human body sites using culture dependent and independent identification methods 30 . Following on to third year coursework, students apply techniques in DNA analysis and protein expression in an In Focus laboratory and reporting assessment tasks as part of second and third year ALURE modules 30,31 .…”

“…Following on to third year coursework, students apply techniques in DNA analysis and protein expression in an In Focus laboratory and reporting assessment tasks as part of second and third year ALURE modules 30,31 . The range of learning gains observed following ALURE participation align with graduate attributes desired by STEM employers 8 -improvement in practical competencies for pathology and research laboratories, and generic transferable skills applicable to workplaces both in and out of science [30][31][32] .…”

Investigating introductory astronomy students’ perceived impacts from participation in course-based undergraduate research experiences

“…Promoting research experiences among all undergraduate students, both inside and outside the classroom, has been deemed important by the National Academies [1], the American Association for the Advancement of Science [2], and researchers of science teaching and learning [3][4][5][6][7][8]. Participation in scientific research experiences encourages cognitions related to scientific epistemology, such as uncertainty and global consistency, rather than the certainty and local consistency practiced in "simple" textbook experiments [9,10]. Such cognitions are important in learning how scientific knowledge is ascertained.…”

Personal microbiomes and next-generation sequencing for laboratory-based education

“…The study of microbiomes is naturally engaging to students because the topic is novel, has far-ranging implications and affects them on a personal level. In addition to these merits, the topic of microbiomes represents an excellent vehicle for bringing NGS into the classroom (Wang et al 2015). In this commentary, we discuss our experience in developing and implementing a 'Microbiome Portrait' laboratory module, which we have piloted through our NIH SEPA-funded program 'Bioinformatics Inquiry through Sequencing' (BioSeq 2016).…”