Basing a Curriculum on Discovery-Based Research

Dec. 5, 2016

The Small World Initiative (SWI) aims to change student engagement with science by incorporating discovery-based research into the laboratory classroom. If you are currently a microbiologist, chances are your introductory microbiology lab course syllabus had changed little in decades (my own lab manual still referred to glass tubes closed with ‘cotton stoppers,’ which had been replaced with plastic caps years before my arrival on campus). Your own intro lab course likely culminated in each student receiving an unknown bacterial sample, the identity of which was uncovered by applying techniques learned during the semester. While such tasks allow students to apply their critical thinking skills, they fail to engage students in the discovery process that is one of the foundations of scientific practice. 

SWI Project design
The SWI project design incorporates many microbiology-based concepts. Source

SWI is a program that applies microbiology-based techniques to addressing the serious problem of a diminishing world supply of effective antibiotics. During the semester, students isolate microbes from soil samples using different growth media to identify potential antibiotic-producing microbes. Their goal is to identify a true unknown sample: one without a correct answer in the instructor’s manual. Through the identification process, students learn many of the techniques taught routinely in traditional microbiology lab courses: sterile technique, streaking for isolates, selective and differential media tests, and biochemical assays. Depending on time and resources, students may also practice DNA isolation and sequencing analysis, antibiotic compound purification and identification protocols, and interaction of identified compounds with eukaryotic cells (see figure, left).

Dr. Mary Miller has taught at Baton Rouge Community College for four years, after previously teaching at a nearby research university. At BRCC, Miller had access to interested students, but limited resources for research. Bringing in SWI to the introductory microbiology course “was a breath of fresh air,” she says. Miller was in the 2013-14 cohort with 30 other instructors implementing the course and is now in her fourth semester using SWI. Her school was the first school in Louisiana and one of the first community colleges in the United States to institute the program.

The first step is for students to collect soil samples from a location of their choosing, allowing students to direct their own project from the beginning. The soil samples are homogenized, diluted, and plated for growth on a rich medium. Isolates are screened for their ability to inhibit growth of an ESKAPE pathogen, and isolates that show zones of inhibition are identified using traditional techniques such as the Gram stain. This learn-by-doing method encourages students to search the literature to find novel ways to identify their unknowns. For example, one of Miller’s recent students couldn’t Gram stain her organism despite multiple attempts.

“I told her, why don’t you see if there’s a different staining technique,” says Miller. “She came back and said there’s this acid-fast stain. I said there sure is, would you like to do that?” Sure enough, the student’s organism was an acid-fast organism, a concept that the student had investigated and applied to solve her research question.

With emphasis on the discovery aspect of the course, Miller emphasizes to students that research is necessary to prepare for experimentation: “You can’t come to lab unprepared. There has to be a literature-based reason for what you’re going to do, and you have to have that reason prepared ahead of class.” Students are encouraged to research assays that may help them better identify their isolates. “I always encourage students to find a confirmative test. If we can do that test, we will.”

BRCC has a diverse student population and many nontraditional students who are working or have children. Many students begin the course without having seen a research lab or understanding how research is conducted. In addition to hours spent at the bench, Miller is conscious to encourage students to explore outside of the lab as well: this past fall, she and her class collected specimens from along the Gulf coast, showing students the field work necessary outside of the lab that is an important part of the scientific process. Miller finds that the exposure real-time research can change student perception of what they want to be when they finish school.

Student Response

Dr. Mary Miller uses SWI as part of her introductory microbiology lab course
Dr. Mary Miller uses SWI as part of her introductory microbiology lab course.

Student response to real-time research has been overwhelmingly positive, Miller reports. Given the multiple decision students make in sample selection and media choices, many students feel ownership of their research projects in a way different from those in traditional microbiology lab courses. “My class is three hours long and often times I have to ask them to leave. If I can stay, they’re happy to stay an hour later,” says Miller. The excitement to spend more time in lab than the class period allows is one of the biggest differences between students in the SWI-based course and Miller’s previous experience teaching traditional microbiology lab skills.

“The student response is why I keep doing it. Their reaction is just amazing.”

Student excitement leads them to form collaborative networks, usually including the entire class. Students call across the classroom, excited about classmates’ results. But the uncertain nature of research can also lead to discouragement when students fail to find new antibiotic producers. “Disappointment from students that didn’t find antibiotic producers” was a challenge Miller faced in maintaining student interest for those students.

“I’ve learned to remind them that this is research. This is not your traditional lab where X + Y = Z. A negative result is as important as a positive result in learning about your organism.” Miller’s class concludes with 16S rRNA sequencing to confirm isolate taxonomy. These sequences help students resolve their observed microbial characteristics, such as fastidious growth or fermentation status, with the organism’s identity.

The real-time research experience inspires some students to continue along an academic path. Whenever a student has a particularly strong interest sparked, Miller finds a way to encourage further growth. This may occur through student recommendation to the BRCC Bridges-to-Baccalaureate program or student presentation at research conferences like ABRCMS. BRCC students also travel to ASM Microbe and regional ASM meetings, where SWI holds poster presentation sessions for programs from all universities or colleges using the program. This allows students from various SWI to see how other students approach problems, giving students further access to research opportunities and network building.

Communication Skills

Each semester of Miller’s course includes a poster session but there are many opportunities for students to share what they’ve learned about the dearth of antibiotics. “Some instructors of SWI have brought their poster presentations to museums to get the community involved. Our goal at BRCC is to bring campus-wide awareness.” As part of that goal, students at BRCC this semester have planned an awareness campaign to teach non-science students about the growing risk of antibiotic resistance. Enthusiasm gained from research experience leads students to be ideal science ambassadors to their surrounding community. 

The involvement with both research and science communication gives students the feeling of contributing to society through their coursework. Though called Small World Initiative, Millers students have told her: ‘we’re doing something big.” That sense of purpose motivates some students to work long hours and perform extra literature reviews toward the goal of discovering new antibiotic-producing microbes.

Incorporating and Expanding SWI

Incorporating SWI “can be ideal for the very motivated instructor,” says Miller, emphasizing the time commitment needed on behalf of the instructors in using SWI. “Imagine the work it takes to guide a single research student. Now multiply that by 25 students, who may or may not be going in the same direction.” Miller requires students to keep well-annotated notebook to help students stay on organized and help her follow the course of each student over the semester.

What’s next for Miller? Her students have requested an upper-level research course for those who want to continue research, which poses a challenge at the community college level: student financial aid is often limited and ideally credit for BRCC courses would transfer to a four-year school if a student transfers. While students may take the course for ‘fun’ to expand their research skills, Miller is working to encourage student interest in research as well as give them a course that meets these requirements. Working with organic chemistry may provide a way to continue studies while applying techniques from chemistry classes, like nuclear magnetic resonance (NMR).

Additionally, Miller provides guidance to instructors in the United Kingdom who wish to implement SWI and other active learning exercises into their classrooms. Through the London-based Microbiology Society, Miller has traveled to the University of Reading for the past two summers to train instructors on incorporating SWI. Institutions in Ireland, Scotland, and London have begun using SWI as part of their coursework. Miller recently presented her experiences to a room full of microbiology instructors at the 2016 ABRCMS meeting. With testimonials from experienced instructors like Miller, a revolution in research-based science education seems a certainty.

Are you inspired by Miller’s experience? Do you want to initiate the SWI as part of your course curriculum? You can fill out an application to be a SWI partner instructor and take part in the next instructor training. 

Author: Julie Wolf

Julie Wolf
Dr. Julie Wolf is in science communications at Indie Bio, and was a former ASM employee. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.