biosampling

Lyndsi Powell and Dan Liu swab the Biopond as a part of a metagenomics lab in Introductory Biology. 

Photo: Marcus Katz

Ever wondered what kinds of microbes grow on the Ben Franklin bench? Introductory Biology students are set to find out.

Five different labs in Introductory Biology courses have been replaced with a metagenomics “module,” divided into five parts. After swabbing different locations around campus and taking soil samples, students will identify their samples from the DNA they extracted.

“The landscape in higher education is changing quite a bit to be more student inquiry-driven, and to bring authentic research into the classroom,” lab coordinator Karen Hogan said of the new lab program.

With students able to take samples from practically anywhere on campus, they are finding out real information about their environment, which has a direct impact on their health. The only places students couldn’t swab were on non-University private property and at dining halls.

Lab coordinators were worried about students “finding pathogenic organisms” in the dining halls, lab coordinator Linda Robinson said, so they decided to keep them off-limits. Exposing students to potentially harmful bacteria was a risk in general, and Robinson emphasized that at no point would students be culturing live bacteria. They froze their samples immediately to kill anything potentially disease-causing.

The program’s scale sets Penn apart from other universities. Between the two courses, over 500 students are participating in the lab. Labs like this at other universities are usually conducted on a very small scale, and in past years they have been small-scale at Penn as well. Often only upperclassmen or graduate students would participate, and only in specific areas of research. Hogan said that one of the reasons the lab is being implemented at the freshman level is to make students aware of this field of biology before they need to pick a major.

“In biology and research, genomics is huge right now,” she said. “We want to expose students to it in the early stages.”

In addition to swabbing, extracting DNA, amplifying identification genes and analyzing molecules, students will also act as computational biologists in the latter part of the semester.

“You generate massive amounts of sequencing data with these platforms we use to sequence the DNA,” Hogan said.

Students completed a bioinformatics tutorial to prepare them for handling the sequencing data they will get back from a lab in Illinois, which will tell them what kinds of microorganisms they found around campus. Though the class is introductory, the tutorial was far from simple.

“Students would be incredibly frustrated at times,” Hogan said. “But they stuck it out and troubleshooted and helped each other.”

Bioinformatics plays a major role in labs today, which makes exposing students to the field especially important.

In terms of careers, “Students don’t even know that it’s an option,” Hogan said.

The metagenomics lab will likely be offered for at least the next few years, Hogan said. Students were surveyed at the beginning of the semester and will be surveyed again at the end to give lab coordinators like Robinson and Hogan ideas for any modifications they’ll make to the lab process.

“In the last week of the semester each group will give oral presentations of their findings,” Robinson said. “That will be a good time to look at what we’re going to change.”

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