SEA-PHAGES: Making Discoveries to Fight Bacteria

By Tiffany King

Experiential learning has long been an important part of a College of Coastal Georgia education. Today, students in two new courses are experiencing what it is like to work on research with the potential to save lives.

The School of Arts and Sciences recently launched two research courses, SEA-PHAGES Laboratory Research I and II, in which students have discovered novel bacteriophages—viruses that infect bacteria—which could one day save lives.

The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program is a two-semester, discovery-based, undergraduate research course. Students can participate in one or both of the courses. The program is administered by Ebery Family Professor of Biotechnology Graham Hatfull at the University of Pittsburgh in conjunction with the Howard Hughes Medical Institute’s Science Education division. More than 100 universities in the United States and abroad are participating in the program.

Bacteriophages, “phages”, are viruses that infect and replicate within bacteria and archaea, ultimately killing their host bacteria. Phages are target-specific and can attack host bacteria without harming the human body. The use of phages can be an effective tool to combat bacteria that are resistant to antibiotics. Bacteriophage exists abundantly in the soil, which is where students start in the first part of the course.

Dr. Gerard White, associate professor of biology, applied and received an invitation to join the SEA-PHAGES program and now instructs SEA-PHAGES Laboratory Research I at the College. He said students hunting for phage have collected soil samples from various locations—including in backyards, a compost heap, the marsh, and mud. To isolate phage, students used two different host bacteria—Microbacterium foliorum and Arthrobacter globiformis. Students learned new lab techniques to isolate phage from their samples and employed other techniques from previous courses. Out of the 13 students in the course, seven found their own phages, while others used peers’ phages for analysis. Students also had the opportunity to name their phages. Coastal student Madison Lee named her phage “Persistence” because she collected and attempted to isolate phage from 20 different soil samples before she was successful. Her last soil sample was collected on the College’s campus. Like Lee, many students became genuinely invested in isolating and learning about their phage. White described how amazed he was with seeing students attend additional lab hours on Fridays to work on their phages, catch up, or get ahead in the course.

Coastal students Jamie Richardson and Ashley Steverson use laboratory techniques to hunt for phage. (Photo by Dr. Gerard White)

After isolating phages, students’ samples were sent to Augusta University for transmission electron microscopy (TEM)—a technique in which a beam of elections is transmitted through a specimen to form an image. Most of the student’s phages, including Lee’s Phage Persistence and Krystal Riner’s Phage Moe, yielded great TEM images.

A TEM (transmission electron microscope) image of Kristel Riner’s Phage Moe. (TEM image by Brendan Marshall of Augusta University)

Coastal students extracted and analyzed phage DNA, and two of the DNA samples that looked the most promising were Benjamin Fountain’s Phage Karate, which infected M. foliorum, and Lee’s Phage Persistence, which infected A. globiformis. Their samples were sent to the University of Pittsburgh for genome sequencing.

“When we received the Phage Karate and Phage Persistence genome sequences, we were very excited to be informed that these were both novel bacteriophages which nobody had isolated before,” White said.

Student Madison Lee works to isolate phage from her soil samples. She collected 20 soil samples until she was successful in finding phage. (Photo by Dr. Gerard White)

All discovered phages were also sent for archiving at the University of Pittsburgh, where they could possibly be used for research purposes and/or for medical treatments.

Bacteriophage is being regarded by many scientists as an effective treatment for infections. As reported in Nature Medicine Journal in May 2019, one group of scientists used an experimental bacteriophage therapy to fight the infection of a 15-year-old girl in London. She suffered from cystic fibrosis and had been taking antibiotics for eight years to control two bacterial strains. After receiving a double lung transplant, doctors noticed signs of an infection resistant to antibiotics. University of Pittsburgh’s Hatfull was contacted by a colleague at the hospital about the case and the possibility of doing a phage treatment. Hatfull turned to the vast collection of phages housed at the University of Pittsburgh and after testing, a mixture of three phages were used for her treatment. All three phages were discovered by different college students over the span of six years—one from Durban, South Africa in 2010; another from the University of Pittsburgh in 2010; and the third from Providence College in 2012. Through the treatment, the patient’s wounds began to heal and she showed much improvement.

“It’s pretty exciting when you think that a student could find something and it could be useful,” White said. “There’s other potential uses for bacteriophage as well, such as phage therapy, or we could just find genes in the bacteriophage that could be useful for humankind in general. When you think of the far reaching possibilities, it’s just very exciting.”

Many students have continued onto the second phase of the course which is being taught by Dr. Holly Nance, assistant professor of biology. Her students are annotating the genome sequences of Phage Karate to better understand its genetic makeup. Phage Persistence will also be annotated at a future time.

At the end of the SEA-PHAGES Laboratory Research I and II courses, a professor and one Coastal student will have the opportunity to attend the Howard Hughes Medical Institute’s annual SEA Symposium that focuses on SEA-PHAGES research from students and faculty members around the country. The selected student will present a poster about what the research classes discovered about the Phage Karate genome. White said he’s been amazed by the quality of SEA-PHAGES presented by students at the symposium. Coastal will have the opportunity to join those ranks and, through SEA-PHAGES, continue to positively impact the world.

Part two of this article will focus on the discoveries from SEA-PHAGES Laboratory Research II, instructed by Dr. Holly Nance.