Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses

An integrated microbiome project for charactering microbial diversity in classroom based on virtual simulation experiments

Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6-week wet-lab and bioinformatics course for undergraduates was implemented through the project-based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step-by-step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.

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

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.

Analysis of Microbial Water Contamination, Soil Microbial Community Structure, and Soil Respiration in a Collaborative First-Year Students as Scholars Program (SAS)

The persistence of college students in STEM majors after their first-year of college is approximately 50%, with underrepresented populations displaying even higher rates of departure. For many undergraduates, their first-year in college is defined by large class sizes, poor access to research faculty, and minimal standing in communities of scholars. Pepperdine University and Whittier College, funded by a National Science Foundation award to Improve Undergraduate Stem Education (NSF IUSE), partnered in the development of first-year classes specifically geared to improve student persistence in STEM and academic success. This Students as Scholars Program (SAS) engaged first-year undergraduates in scholarly efforts during their first semester in college with a careful approach to original research design and mentoring by both faculty and upperclassmen experienced in research. Courses began by introducing hypothesis formulation and experimental design partnered with the scientific focus of each course (ecological, biochemical, microbiological). Students split into research teams, explored the primary literature, designed research projects, and executed experiments over a 6–7 week period, collecting, analyzing, and interpreting data. Microbiology-specific projects included partnerships with local park managers to assess water quality and microbial coliform contamination at specified locations in a coastal watershed. In addition, students explored the impact of soil salinity on microbial community structure. Analysis of these samples included next-generation sequencing and microbiome compositional analysis via collaboration with students from an upper division microbiology course. This cross-course collaboration facilitated additional student mentoring opportunities between upperclassmen and first-year students. This approach provided first-year students an introduction to the analysis of complex data sets using bioinformatics and statistically reliable gas-exchange replicates. Assessment of the impact of this program revealed students to view the research as challenging, but confidence building as they take their first steps as biology majors. In addition, the direct mentorship of first-year students by upperclassmen and faculty was viewed positively by students. Ongoing assessments have revealed SAS participants to display a 15% increased persistence rate in STEM fields when compared to non-SAS biology majors.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.

The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology

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.

Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations

Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.

Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course

Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. We aimed to improve scientific training by engaging students enrolled in an upper division elective course in a human microbiome CURE. The "Fiber Force" course is aimed at studying the effect of a wholesome high-fiber diet (40 to 50 g/day for two weeks) on the students' gut microbiomes. Enrolled students participated in a noninvasive diet intervention, designed health surveys, tested hypotheses on the effect of a diet intervention on the gut microbiome, and analyzed their own samples (as anonymized aggregates). The course involved learning laboratory techniques (e.g., DNA extraction, PCR, and 16S sequencing) and the incorporation of computational techniques to analyze microbiome data with QIIME2 and within the R software environment. In addition, the learning objectives focused on effective student performance in writing, data analysis, and oral communication. Enrolled students showed high performance grades on writing, data analysis and oral communication assignments. Pre- and post-course surveys indicate that the students found the experience favorable, increased their interest in science, and heightened awareness of their diet habits. Fiber Force constitutes a validated case of a research experience on microbiology with the capacity to improve research training and promote healthy dietary habits.

Primary Care Physicians' Knowledge, Attitudes, and Experience with Personal Genetic Testing

Primary care providers (PCPs) will play an important role in precision medicine. However, their lack of training and knowledge about genetics and genomics may limit their ability to advise patients or interpret or utilize test results. We evaluated PCPs’ awareness of the role of genetics/genomics in health, knowledge about key concepts in genomic medicine, perception/attitudes towards direct-to-consumer (DTC) genetic testing, and their level of confidence/comfort in discussing testing with patients prior to and after undergoing DTC testing through the 23andMe Health + Ancestry Service. A total of 130 PCPs completed the study. Sixty-three percent were board-certified in family practice, 32% graduated between 1991 and 2000, and 88% had heard of 23andMe prior to the study. Seventy-two percent decided to participate in the study to gain a better understanding about testing. At baseline, 23% of respondents indicated comfort discussing genetics as a risk factor for common diseases, increasing to 59% after undergoing personal genetic testing (PGT) (p < 0.01). In summary, we find that undergoing PGT augments physicians’ confidence, comfort, and interest in DTC testing.