Undergraduate Microbiology Research Articles

Synthesizing a Berberine Derivative and Evaluating Antimicrobial Activity To Reinforce with Students the Potential Significance of Small Chemical Structure Changes for Biological Systems

The convenient synthesis of dihydroberberine by the reduction of berberine is described as an experiment for an upper-division undergraduate organic chemistry laboratory course. Students obtained up to 74% yield of the desired pure product without the use of chromatographic techniques. The antimicrobial activities of both compounds against Staphylococcus aureus and Candida albicans were then assessed and compared in an upper-division undergraduate microbiology laboratory course. The students verified that berberine shows higher antimicrobial activity than its derivative dihydroberberine, demonstrating that small changes in a chemical structure can result in great biological differences.

Makgeolli: Rapid Production of an Alcoholic Beverage from the Fermentation of Rice.

Undergraduate microbiology courses offer a perfect opportunity to introduce students to historical food preservation processes that are still in use today. Specifically, food fermentation exercises encourage students to consider other cultures and their food and beverage traditions, in addition to teaching students techniques that can be performed in their own kitchens. In previous semesters of an undergraduate microbiology course we have taught a variety of fermentations through the production of yogurt, sauerkraut, kimchi, and cheese. Student enthusiasm for these food labs led us to explore new fermentations, especially those from other cultures. To this end, a laboratory procedure and worksheets for producing the Korean rice wine makgeolli from fermented rice in the presence of amylase enzyme was developed. Students ferment the rice, bottle the ferment, and those of legal drinking age test the product while completing exercises that challenge them to explore the microbiological concepts of fermentation. Underlying themes of this laboratory activity also include basic concepts of food safety and kitchen cleanliness. The laboratory experiment can be completed in less than two weeks and can be modified easily for students of varying scientific backgrounds. Overall, the intersection of metabolism, food science, cultural diversity, and history excited students and enhanced their understanding of the microbial processes at work in fermentation.

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology.

Misconceptions, or alternative conceptions, are incorrect understandings that students have incorporated into their prior knowledge. The goal of this study was the identification of misconceptions in microbiology held by undergraduate students upon entry into an introductory, general microbiology course. This work was the first step in developing a microbiology concept inventory based on the American Society for Microbiology’s Recommended Curriculum Guidelines for Undergraduate Microbiology. Responses to true/false (T/F) questions accompanied by written explanations by undergraduate students at a diverse set of institutions were used to reveal misconceptions for fundamental microbiology concepts. These data were analyzed to identify the most difficult core concepts, misalignment between explanations and answer choices, and the most common misconceptions for each core concept. From across the core concepts, nineteen misconception themes found in at least 5% of the coded answers for a given question were identified. The top five misconceptions, with coded responses ranging from 19% to 43% of the explanations, are described, along with suggested classroom interventions. Identification of student misconceptions in microbiology provides a foundation upon which to understand students’ prior knowledge and to design appropriate tools for improving instruction in microbiology.

Modeling and Visualizing Bacterial Colony Purification Without the Use of Bacteria or Laboratory Equipment.

Microorganisms typically exist in diverse and heterogeneous communities within their various environmental niches. The isolation of an individual species from these communities is an essential laboratory skill to study of the properties and behaviors of that organism. To achieve this separation, the “quadrant streak” for single colony purification is often included in undergraduate microbiology laboratory curricula. To aid student mastery of this technique, I have developed a simulated culture purification activity that allows students to immediately visualize the dilution and separation of an artificial microbial community with the goal of isolating purified colonies. This tool uses readily available, inexpensive, art supplies to simulate a mixed bacterial culture. The “mixed culture” consists of craft glitter of at least two distinct colors, held together with water-soluble, highly pigmented watercolor or gouache paint. Students practice aseptic technique by using a paintbrush to mimic an inoculating loop to streak and dilute the culture on a piece of cardstock. Sterilization of the “loop” is simulated by rinsing the brush. Students will immediately self-assess whether they are correctly performing the quadrant streak, rather than having to wait until the next laboratory session for bacteria to grow, which may allow them to master the technique sooner.

Partnering with Students in Iceland and Continental Europe to Develop a New Undergraduate Microbiology Research Journal

Partnering with Students in Iceland and Continental Europe to Develop a New Undergraduate Microbiology Research Journal

Video Lecture Capture Technology Helps Students Study without Affecting Attendance in Large Microbiology Lecture Courses

Recording lectures using video lecture capture software and making them available for students to watch anytime, from anywhere, has become a common practice in many universities across many disciplines. The software has become increasingly easy to use and is commonly provided and maintained by higher education institutions. Several studies have reported that students use lecture capture to enhance their learning and study for assessments, as well as to catch up on material they miss when they cannot attend class due to extenuating circumstances. Furthermore, students with disabilities and students from non-English Speaking Backgrounds (NESB) may benefit from being able to watch the video lecture captures at their own pace. Yet, the effect of this technology on class attendance remains a controversial topic and largely unexplored in undergraduate microbiology education. Here, we show that when video lecture captures were available in our large enrollment general microbiology courses, attendance did not decrease. In fact, the majority of students reported that having the videos available did not encourage them to skip class, but rather they used them as a study tool. When we surveyed NESB students and nontraditional students about their attitudes toward this technology, they found it helpful for their learning and for keeping up with the material.

The Necessity of Prerequisite Undergraduate Microbiology Courses for Pre-Allied Health Professionals.

WA letter to the editor addressing recent concerns about the necessity of microbiology as a prerequisite for pre-nursing and pre-allied health programs.

Undergraduate Laboratory Exercises Specific to Food Spoilage Microbiology

AbstractFood spoilage has an enormous economic impact, and microbial food spoilage plays a significant role in food waste and loss; subsequently, an equally significant portion of undergraduate food microbiology instruction should be dedicated to spoilage microbiology. Here, we describe a set of undergraduate microbiology laboratory exercises that focus specifically on food spoilage which were taught in 2 lab periods as part of the undergraduate food microbiology lab curriculum at Cornell University. The lab was broken down into 3 exercises. Two exercises lead students to determine the likely source of contamination in a canned salsa through (exercise 1a) plating and observation of colony morphology and (exercise 1b) determination of the thermal resistance for those isolates. The final exercise (2) involved detection of the spoilage bacterium Alicyclobacillus in apple juice. Spoiled juice demonstrations were also prepared in this exercise for students to observe sensorial changes resulting from spoilage, emphasizing that spoilage is not always visually detectable. Students were able to successfully determine the source of contamination based on the results of their laboratory findings, which they used to make recommendations for production to reduce microbial food spoilage in the canned salsa product. Based on student answers to discussion questions provided following lab exercises, participants were able to (a) identify the significance of microbial spoilage and how spoilage is principally different from food safety, (b) describe varying sensorial changes associated with microbial spoilage, and (c) employ methods and analysis to evaluate sources and type of contamination. Downloadable handouts and stepwise instructions are available as supporting information.

Development of a Lac Operon Concept Inventory (LOCI).

Concept inventories (CIs) are valuable tools for educators that assess student achievement and identify misconceptions held by students. Results of student responses can be used to adjust or develop new instructional methods for a given topic. The regulation of gene expression in both prokaryotes and eukaryotes is an important concept in genetics and one that is particularly challenging for undergraduate students. As part of a larger study examining instructional methods related to gene regulation, the authors developed a 12-item CI assessing student knowledge of the lac operon. Using an established protocol, the authors wrote open-ended questions and conducted in-class testing with undergraduate microbiology and genetics students to discover common errors made by students about the lac operon and to determine aspects of item validity. Using these results, we constructed a 12-item multiple-choice lac operon CI called the Lac Operon Concept Inventory (LOCI), The LOCI was reviewed by two experts in the field for content validity. The LOCI underwent item analysis and was assessed for reliability with a sample of undergraduate genetics students (n = 115). The data obtained were found to be valid and reliable (coefficient alpha = 0.994) with adequate discriminatory power and item difficulty.

Use of Shadowing-Based Learning in an Allied Health Microbiology Course.

Students in an undergraduate microbiology course for health professions majors perform a shadowing-based learning exercise for their course project. Students accomplish this by shadowing a health care professional of their choice, specifically incorporating basic microbiological concept themes into their observations. These concept themes include the biological nature, health effects, detection, and control of microorganisms. Upon completion of the shadowing experience, students present a concise report, which is graded on how well the students connect course scientific concepts with actual clinical practice.

OpenStax: Microbiology Provides a Cost-Effective and Accessible Resource for Undergraduate Microbiology StudentsReview of: OpenStax: Microbiology . Nina Parker, Mark Schneegurt, and Anh-Hue Tu; (2016). OpenStax and ASM. 1100 pages. (Note: At time of journal printing, this book was not yet published. Certain publication details may change slightly.)

This is a review of Openstax: Microbiology, a textbook that has been put together by a collaborative effort between Openstax College and the American Society for Microbiology. The text will be offered in a variety of formats including web-based, PDF, and hardcopy, and is set for publication Spring 2016. Review of: OpenStax: Microbiology. Nina Parker, Mark Schneegurt, and Anh-Hue Tu; (2016). OpenStax and ASM. 1100 pages. (Note: At time of journal printing, this book was not yet published. Certain publication details may change slightly.)

Learning through Teaching: A Microbiology Service-Learning Experience.

Service learning is defined as a strategy in which students apply what they have learned in the classroom to a community service project. Many educators would agree that students often learn best through teaching others. This premise was the motivation for a new service-learning project in which undergraduate microbiology students developed and taught hands-on microbiology lessons to local elementary school children. The lessons included teaching basic information about microbes, disease transmission, antibiotics, vaccines, and methods of disease prevention. This service-learning project benefitted the college students by enforcing their knowledge of microbiology and provided them an opportunity to reach out to children within their community. This project also benefitted the local schools by teaching the younger students about microbes, infections, and handwashing. In this paper, I discuss the development and implementation of this new microbiology service-learning project, as well as the observed impact it had on everyone involved.

Western Faculty Profile: Dr. Kelly Summers

Dr. Kelly Summers is an Assistant Professor in the Department of Microbiology and Immunology at the University of Western Ontario in London, Ontario. Having completed multiple degrees in London (Including her Senior Postdoc), she holds multiple research positions there and is one of Western’s most highly acclaimed individuals. Her research revolves around immunology and contains, but is not limited to the topics of diabetes, cardiopulmonary bypass surgery. She has her own lab called the Screening Lab for Immune Disorders (SLID), located at the Lawson Health Research Institute in London. In addition to her research, she teaches several undergraduate Microbiology and Immunology courses and is widely respected by her students. Andrew Wang, a second year representative for WURJ interviewed Dr. Summers about her background, and experiences as both a professor and researcher.

Threshold learning outcomes for a microbiology major

The concept of National Guidelines for Microbiology Curricula was workshopped at the inaugural meeting of EduCon (the ASM Microbiology Educators’ Conference) in 2014. Subsequently, an ad hoc special working group was formed at the 2015 EduCon to formulate National Guidelines for the threshold learning outcomes of Australian undergraduate microbiology curricula. The group, through discussion and several iterations, developed draft threshold learning outcomes for microbiology majors based on the Science Learning and Teaching Academic Standards Statement and informed by the curricular guidelines of the American Society for Microbiology. In this context, microbiology is taken to mean study of any or all microorganisms. Collectively, the group agreed that a major in microbiology should demonstrate significant learning of the key concepts of microbiology (see Merkel et al .) at an advanced undergraduate level and recognised that there are diverse course structures that could enable this outcome. Commonly, the course structure would require completion of four units of microbiology at years 3 (single degree) or 3 and 4 (double degree) depending on the degree undertaken; however, one of these units could be replaced with a complementary science unit. A capstone unit of microbiology in which students demonstrate critical evaluation and synthesis of a microbiological topic should be included. These standards would necessitate that assessment tasks be linked to each of the learning outcomes and should show progressive development throughout the major. To help Australian academics validate that their students have reached these threshold learning outcomes, each subcategory will be progressively linked to curriculum learning resources that will be available with these guidelines at an EdSIG website hosted by the ASM. Additionally, a list of some current microbiology majors at Australian universities will provide examples of what subjects might be included in a microbiology major. The draft threshold learning outcomes were discussed and supported by the National Examinations and Qualifications Board of the ASM at their December, 2015 meeting and subsequently by National Council in February 2016. The draft threshold learning outcomes were then circulated to the state branches and to all members of EdSIG for comment. The threshold learning outcomes for a microbiology major presented here are the outcomes from these discussions. It is not the intent of EdSIG that ASM would accredit microbiology majors nor to exactly define curricula, but rather to give guidance to Australian academics on what ASM considers that a microbiology graduate should able to do whilst working professionally as a microbiologist.

The Use of Stuffed Microbes in an Undergraduate Microbiology Course Increases Engagement and Student Learning.

Student engagement, attention, and attendance during a microbiology lecture are crucial for student learning. In addition, it is challenging to cover a large number of infectious diseases during a one-semester introductory microbiology course. The use of visual aids helps students retain the information presented during a lecture. Here, I discuss the use of stuffed, plush microbes as visual aids during an introductory microbiology course. The incorporation of these stuffed microbes during a microbiology lecture results in an increase in engagement, interest, attendance, and retention of material.

Brewing for Students: An Inquiry-Based Microbiology Lab.

In an effort to improve and assess student learning, there has been a push to increase the incorporation of discovery-driven modules and those that contain real-world relevance into laboratory curricula. To further this effort, we have developed, implemented, and assessed an undergraduate microbiology laboratory experiment that requires students to use the scientific method while brewing beer. The experiment allows students to brew their own beer and characterize it based on taste, alcohol content, calorie content, pH, and standard reference method. In addition, we assessed whether students were capable of achieving the module learning objectives through a pre-/posttest, student self-evaluation, exam-embedded questions, and an associated worksheet. These objectives included describing the role of the brewing ingredients and predicting how altering the ingredients would affect the characteristics of the beer, amongst others. By completing this experimental module, students accomplished the module objectives, had greater interest in brewing, and were more likely to view beer in scientific terms. Journal of Microbiology & Biology Education.

Developing Research-Based Undergraduate Microbiology Curricula

Despite being an important part of the mission for colleges and universities, teaching is often given short shrift. Designing courses is particularly challenging for new faculty members, who often get little training as graduate students or postdoctoral fellows on how to design or teach courses. Increasing diversity in classrooms, large class sizes, and the fast pace of scientific discoveries serve to make teaching even more challenging. In addition, academic rewards, including promotions, salary increases, and tenure, tend not to credit faculty members for their effective and innovative teaching skills, putting further time constraints on them as they balance research, teaching, and service demands.

The ASM Curriculum Guidelines for Undergraduate Microbiology: A Case Study of the Advocacy Role of Societies in Reform Efforts.

A number of national reports, including Vision and Change in Undergraduate Biology Education: A Call to Action, have called for drastic changes in how undergraduate biology is taught. To that end, the American Society for Microbiology (ASM) has developed new Curriculum Guidelines for undergraduate microbiology that outline a comprehensive curriculum for any undergraduate introductory microbiology course or program of study. Designed to foster enduring understanding of core microbiology concepts, the Guidelines work synergistically with backwards course design to focus teaching on student-centered goals and priorities. In order to qualitatively assess how the ASM Curriculum Guidelines are used by educators and learn more about the needs of microbiology educators, the ASM Education Board distributed two surveys to the ASM education community. In this report, we discuss the results of these surveys (353 responses). We found that the ASM Curriculum Guidelines are being implemented in many different types of courses at all undergraduate levels. Educators indicated that the ASM Curriculum Guidelines were very helpful when planning courses and assessments. We discuss some specific ways in which the ASM Curriculum Guidelines have been used in undergraduate classrooms. The survey identified some barriers that microbiology educators faced when trying to adopt the ASM Curriculum Guidelines, including lack of time, lack of financial resources, and lack of supporting resources. Given the self-reported challenges to implementing the ASM Curriculum Guidelines in undergraduate classrooms, we identify here some activities related to the ASM Curriculum Guidelines that the ASM Education Board has initiated to assist educators in the implementation process.

Kimchi: spicy science for the undergraduate microbiology laboratory.

Undergraduate microbiology courses offer a perfect opportunity to introduce students to historical food preservation processes that are still in use today. The fermentation of vegetables, as occurs in the preparation of sauerkraut and kimchi, uses an enrichment step to select for the growth of naturally occurring lactic acid bacteria (LAB). This is an active learning exercise in which students learn a food preparation skill and basic microbiological terms such as selection and enrichment. When performed in conjunction with cultured fermentations, such as yogurt making, students can see the difference between fermentations by naturally occurring microorganisms versus inoculated microorganisms. Additionally, this exercise introduces students to concepts of food safety, intrinsic factors influencing microbial growth such as pH, and cultural uses of fermentation to preserve locally available foods.

16S rRNA gene survey of microbial communities in Winogradsky columns.

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.