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Discovering Antibiotics: A Microbiology Lab Where Students Take the Lead

Dr. Lauren Klabonski’s Microbiology lab gives undergraduates a chance to drive research with lifesaving potential.


Lauren Klabonski, PhD

Visiting Assistant Professor of Biology, Gettysburg College, Pennsylvania

PhD in Biology/Biological Sciences, BS in Biology

Penicillin has, thankfully, been around for many decades now: It was 1928 when Scottish scientist Alexander Fleming first extracted it from mold growing in a petri dish of Staphylococcus bacteria in his laboratory at St. Mary’s Hospital in London. Today, Dr. Lauren Klabonski has undergraduate students in her Microbiology course at Gettysburg College doing something very similar: They cultivate bacteria from soil samples, and then they isolate, name, identify, and test the bacteria’s potential for production of new types of lifesaving antibiotics.

Klabonski says that she and a colleague originally developed the course (then called Bio 232 Discovering Antibiotics) during her graduate work at Drexel University. They got funding from the Howard Hughes Medical Institute in support of the Small World Initiative, a program that focuses on crowdsourcing antibiotic discovery.

The potential public health benefits of such a course are obvious, but Klabonski is also focused on ensuring that the students each get something out of the experience individually: Namely, she wants them to become more confident in their ability as scientists. This means giving them as much responsibility as possible throughout the entire 16-week period.

“At the beginning, students are like deer in headlights,” Klabonski says. “But when the first time they see something grow from their plated soil samples, they feel more confident, and as they go on [and begin running tests], that trying-and-succeeding becomes a huge boost for them and keeps them interested.”

Below, she shares an overview of the project—and how she lets students run the show.

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“While students are learning about microbes and techniques in Microbiology lecture, in the lab I am able to teach them how to ask questions, how to set up an experiment, and how to troubleshoot when things don’t go right. I try to give them as realistic a research experience as possible in the lab portion of the course.”

— Lauren Klabonski, PhD

Course: Bio 230 Microbiology

Course description: Bio 230 is a general microbiology course, which means we have the opportunity to discuss microbiology as it relates to cell and molecular biology, evolution, ecology, biotechnology, and medicine. In Bio 230 Laboratory, you will learn classical and modern microbiological techniques. You will also conduct a semester-long independent research project aimed at isolating and characterizing antibiotic-producing microbes from the soil; this project is designed to improve your skills in experimental design, data analysis and interpretation, and communicating results. At the end of Bio 230, I hope you have an appreciation for the ubiquity, diversity, complexity, and utility of microbes.

Klabonski’s tips for letting undergraduates lead their own lab

Klabonski believes in providing her students with less formal instruction and giving them space to make their own decisions.

She begins the lab experience by giving every student the choice of where to find and harvest soil for their experiment. “From the very beginning, it gives students a sense of ownership over the experiment, down to where they will sample the dirt from,” she says.

Her respect for individual autonomy continues throughout the course. Students decide, for example, which growth conditions (temperature, oxygen levels, growth media, etc.) to use to help the bacteria in their soil samples flourish.

As the microbes grow, students decide which of them seem to be emerging as the most powerful producers of antibiotics, both against their natural competitors in the soil and against bacteria that cause infections and are commonly antibiotic resistant. (On average, she says, students are able to isolate at least two microbes they can identify and test.)

Students finally choose which tests to use to identify their antibiotic-producing microbes. Some tests are considered traditional microbiological techniques, such as staining, using microscopes to examine cell structure, and biochemical tests; others, like DNA sequencing of the bacteria, are more modern. This approach gives students an appreciation for the pros and cons of both “old school” and “new school” techniques in microbiology.

Here are a few specific examples of how she gives students autonomy over their work:

Treat them more like peers

A lot of labs are very “canned,” says Klabonski. There is a specific recipe to follow to get the “right” answer, and it is always the same. Not so in the Microbiology lab. The professor is sure to tell students that she cannot predict the outcome of their experiments.

“In a way, I feel that the fact that I don’t know the outcome is helpful to the students,” she says. “It makes them rethink how science works. Science is not, ‘Hey, there’s always a right answer and somebody always knows it.’ If we already know the answer, what is the point of doing research? Science is a learning process, and it helps the students to know we are all going through it together over the course of the semester.”

Let them name their discoveries

After isolating one or more strains of bacteria, Klabonski has students name their candidates. Some students have chosen human names (Todd and Daisy), while others have taken a more whimsical turn. For example, when observing a bacterial strain that turned yellow, the group named it Pikachu, after the Pokémon mascot of the same color. “It feels powerful to be able to name something whatever you want, even if it doesn’t really have any consequence to it,” she says.

Show them that science is not a solo sport

In a research lab, unanticipated test results occur more often than not, Klabonski notes. So when they happen in her class, she and her Peer Learning Associate (PLA) use them as teachable moments. “Sometimes a student doesn’t see any bacteria growing, or their samples get contaminated, or their results don’t make sense,” she says. “I find ways to help students see value in failed experiments and point out the importance of persistence in getting results in the lab. I try to encourage them, reminding them that in a real research environment, sometimes your stuff just doesn’t work, and it’s not a good day for science.”

For this reason, Klabonski encourages data-sharing and group discussion in the frequent lab meetings she conducts with the whole class. Professional and research scientists rarely work in a vacuum, she reminds students. More often they are on a team where, even if their own experiment goes awry, they can share their insights and opinions on their colleagues’ data. Having students share their data and troubleshoot together also makes them feel that they are not alone in experiencing difficulties, reduces frustration, and helps normalize the struggles associated with doing research.

Require them to write like scientists

Throughout the semester, Klabonski’s students must keep track of their progress in lab notebooks, which she assesses every few weeks. In the notebooks, they justify experiments, report on results, and discuss conclusions. Klabonski also asks students to write a final paper—structured like a grant proposal—in which they make the case for why their particular microbes should be funded for further study.

Remember the educational goal

“We have all seen the data to support that undergraduate research experiences help increase retention of students in STEM, particularly for underrepresented groups,” Klabonski says. “The unfortunate thing is there are often not enough true research experiences in laboratories to go around, especially at smaller institutions. By conducting a lab like this as part of a traditional microbiology course, it was my goal to give as many students access to an authentic research experience as possible.”

She says several students have applied for summer jobs in microbiology labs after taking her course, and others have told her they never felt as confident in a lab as they did in hers, because they were invested in the project and felt as though they had a say in the outcome. “For me, both of these would be considered success stories—the lab helped foster an interest in microbiology research and it increased my students’ confidence in their scientific abilities,” Klabonski adds. “That resilience and confidence is something that extends far beyond the lab and can help these students in all their future endeavors, whether in science or in life.”

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