Student-Driven Course-Based Undergraduate Research Experience (CUREs) Projects in Identifying Vaginal Microorganism Species Communities to Promote Scientific Literacy Skills

Abstract

Objectives: We aim to build a students' own engagement in original microbiological course-based undergraduate research experience (CUREs) model served two research and teaching scientific purposes including students' scientific literacy skills and instructors' role, which could further be applied as contribution to broader scientific knowledge and conduct novel research in their future research experience and careers.

Methods: We describe a student-driven CUREs model on the microorganism species in female vaginal using general bacterial culture techniques and high-throughput 16S rRNA gene amplicon sequencing to enable students to center experimental research method under the direction of instructors. A total of 8 undergraduate students and 5 instructors from Shanghai Jiao Tong University School of Medicine participated in the project. The CUREs were divided in four operating scopes: project planning, implementation, summarizing and feedback phases. Instructors help students to develop learning research goals.

Results: This project helped students to gain "hard skills" experiences in scientific theoretical research process and technical practices. Students reached the conclusion that Lactobacillus species dominated the primary vaginal microbiota in reproductive-age women, 16S rRNA sequencing is a method widely applied for microbiology detection. CUREs also increased students' engagement in scientific experiments and promote 3 learning goals in "soft skills": (1) Develop students' self-study and efficacy ability, expression capability and professional research communication skills; (2) Strengthen students' motivation and ownership in science research, overcoming failure, benefitting persistence and patience, building professional science identity, competence, and confidence in collaboration, implement spirit of rigorous and carefulness; (3) Obtain authorship, independent and logical thinking capability, summarizing ability and confidence enhancement. Instructors proposed guiding research question for the students and determine evidence in achieving pedagogical goals in CUREs.

Conclusions: Our microbiological CUREs project served two scientific purposes: research and teaching, which increase students' engagement in promoting learning gains in scientific research skills, ownership, identity development, and spirit of motivation, self-efficacy, persistence, collaboration, communication, as well as opportunities to make relevant scientific discoveries. These abilities equipped them with essential foundation for the subsequent collaborative experiments and future scientific study.

Keywords: 16S rRNA gene amplicon sequencing; course-based undergraduate research experiences; scientific literacy skills; student-driven; vaginal microorganisms.

Figure 1

CUREs project served two research and teaching scientific purposes including students' scientific literacy skills and instructors' role.

Figure 2

Framework in target, obstacle, solution, and goal of CUREs students reach.

Figure 3

Steps of flow chart for 16S rRNA gene amplicon sequencing.

Figure 4

Distribution of vaginal microorganisms in premenopausal and postmenopausal women using general bacterial culture techniques. (A,B) Vaginal secretion triple test: Candida albicans, the dominant bacterial population related to a higher positive rate of leukocyte esterase (A) and poorer cleanliness (B). Staphylococcus epidermidis, the main bacterial population, was related to decreased hydrogen peroxide content (C), a higher sialidase content existed in the Enterococcus faecalis population (D). Women carrying Lactobacillus as the primary bacterial population were less susceptible to certain pathogens, such as Candida albicans (E). There was no significant difference in lactobacillus as the dominant bacteria between the premenopausal and postmenopausal groups (F). There was also no significant difference in Lactobacillus, as the dominant bacteria, distribution in different phases of the menstrual cycle (G). Among them, Lactobacillus dominated 65.9% (27/41) in pregnant women and 55.22% (307/556) of non-pregnant women (H).

Figure 5

Community taxonomy system at the genus level and COG-based functional structure distribution. (A) Taxonomic composition distribution graph showing the relative sample microorganism classification abundance. The horizontal or vertical axis is the sample number or relative abundance ratio. The width of different colors indicates the relative abundance ratio of different species at the taxonomic level. Left panel: Bray-Curtis-based sample clustering tree diagram; middle panel part: Histogram of species abundance of clustering order; right panel: Illustration of the species. (B) A functional abundance heat map based on COG was drawn using the functional abundance matrix. Each column represents a sample, the row represents the function, and the color block represents the functional abundance value. The redder the color is, the higher the abundance, and the more blue the color is, and the lower the distance. Samples from the same group have the same color. Sample distance is represented by the length of the branches. The more similar the samples are, the closer the branches of the same color in the figure are from the same group. (A) RNA processing and modification; (B) Chromatin structure and dynamics; (C) Energy production and conversion; (D) Cell cycle control, cell division, chromosome partitioning; (E) Amino acid transport and metabolism; (F) Nucleotide transport and metabolism; (G) Carbohydrate transport and metabolism; (H) Coenzyme transport and metabolism; (I) Lipid transport and metabolism; (J) Translation, ribosomal structure and biogenesis; (K) Translation, ribosomal structure and biogenesis; (L) Transcription; (M) Replication, recombination and repair; (N) Cell wall/membrane/envelope biogenesis; (O) Cell motility; (P) Post-translational modification, protein turnover, and chaperones; (Q) Secondary metabolites biosynthesis, transport, and catabolism; (R) General function prediction only; (S) Function unknown; (T) Signal transduction mechanisms; (U) Intracellular trafficking, secretion, and vesicular transport; (V) Defense mechanisms; (W) Extracellular structures; (Y) Nuclear structure; (Z) Cytoskeleton; (C) Distribution bar plot.

Figure 6

The dominant flora and heatmap of genera from the tree diagram. The dominant flora in premenopausal (A) and postmenopausal (B) groups. The difference in abundance in samples on a branch is compared using a colored pie chart. Different colors represent different samples, and the larger the fan area of the color, the higher the abundance of the sample on the branch. The semicircle on the right indicates the species abundance composition of the sample, while the left semicircle indicates the proportion of different samples in the dominant species. The length and width represent the abundance and distribution ratio of species in the sample. Heat map of the top 50 species classifications at the genus-level species abundance matrix from a tree diagram. The distribution of flora in different phases of the menstrual cycle and postmenopausal women is shown in premenopausal women (C), postmenopausal (D) and both (E) groups. The same sample group has the same color. Each column in the figure represents a sample, and the row represents the community structure. The color blocks represent relative species abundance values. The redder the color, the higher the relative abundance, while the bluer the color, the lower the relative abundance. The color shade reflects the abundance of the community distribution, and clustering reflects community similarities and different distributions at each classification level.