Human beings are made of more than just skin and bones — entire planets spin inside our bodies, each composed of thousands of different microbes. These microscopic worlds have been a subject of curiosity for years, and now a course at Kansas State University gives students the opportunity to discover these worlds from up close.
Phage Hunters is a biology course that teaches students to find, isolate and learn about a bacteriophage, a virus that kills bacteria.
Christopher Herren, biology professor, said the class gives younger students a chance to get hands-on lab experience early in their college careers.
“The idea was most people do research when they get to college and they’re like a junior or senior, let’s pull it all the way down to freshmen, and into community colleges, and even maybe into high schools — get people right into science,” Herren said.
The concept was born out of the Science Education Alliance at Howard Hughes Medical Institute. Graham Hatfull, a University of Pittsburgh professor who studies bacteriophage, spearheaded the idea. Hatfull wanted to get students involved in science while also creating a bank of phages found by students. HHMI formed a standardized educational program to aid in the project. The process begins with students finding dirt across campus.
“We take the dirt, we soak it in a liquid and then we filter that liquid and apply it to a bacterial culture, and we look to see if that bacterial culture dies,” Herren said. “If it does, there’s a virus in there, [and] we do further experiments to isolate the virus.”
Jordan Block, junior in microbiology and pre-medicine, took the course last year. Block said that while the new terminology was difficult to learn at first, the class provided an easy avenue for learning.
“It’s not something that’s just taught, you’re learning it as you go,” Block said. “You’re able to understand it more that way, like having an actual plate in front of you where you can see all the different formations [and] you can understand what it is, it’s easier to learn that way, I guess.”
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The students get to take a photo of their phage with an electron microscope, and later get the opportunity to name it. There are a few restrictions on the names students are allowed to choose. Herren said the names are run through Urban Dictionary to weed out any profanity — students are also prohibited from using any variation of Nicholas Cage in the name of their virus. Block named her own phage StillBlue.
Herren said the entire process is safe and most of the safety mechanisms they use — lab coats, gloves and eyewear — are actually used to keep the virus safe from human contamination.
“These are viruses that infect bacteria, and the bacteria we work with are dirt bacteria,” Herren said. “It’s the same bacteria in your garden, on the bottom of your shoes, or what are called BSL-1’s, which means there’s no safety precautions at all.”
Block said she enjoyed her experience working with the phages.
“I was never stressed in the lab,” Block said. “I was looking forward to every single day [in] that class to put on the lab coat and gloves and get to work with my phage and try to learn more about it through lab practices.”
The class is year-long — the first semester focuses on isolating the virus, while the second semester deals mostly with annotating the genome of a select few phages from the fall semester.
“The viruses we work with have anywhere from 50 to 120 genes — that’s not an unreasonable number for a dozen people,” Herren said. “We’ll go through each of those genes using software and be sure that the computer has annotated the genes properly. We’ll finally submit those to the National Archives. The students will then permanently have their name on a viral genome sequence that will live in the government repository forever.”
Research that saves lives
With antibiotics on the downslope, phages as a method of killing bacteria has gained interest as a way of clearing infections, Herren said. He said one of the more recent and famous cases involved Hatfull treating a young girl with cystic fibrosis who had contracted a bacterial infection after a double-lung transplant.
“She was dying. And so out of desperation, her parents just started Googling on the internet,” Herren said. “The name of the bacteria comes up in our research program, because it’s one of our hosts, [and] they contacted him.”
Herren said a mechanism in the federal government allowed an experimental treatment to be used on the girl because she was terminally ill.
“He screened all the phages that all the undergraduates have ever collected and found one or two of them that killed this particular strain of bacteria, prepared a bunch of it, flew it over to Britain, they injected her with it — cleared it right up,” he said.
While there have been multiple success stories regarding phage treatments, Herren said they still don’t fully understand exactly how it works. Researchers are beginning to look at it as a treatment, potentially in lieu of antibiotics.
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Building a future
Block said she applied for the course because she thought it would be a great experience that could introduce her to the lab work she wanted to be involved in. She also said the class gave her a lot of practical experience that she uses in her research lab now.
“I was lucky to be one of the first people to find a phage and continue on in the protocol faster than the others,” she said. “And so, I got to be a little bit of a guinea pig when it came to experimenting with protocols [and] trying to find a better way to do something for the rest of the class. It really helped me see how to evolve and change what the protocol is to better work for your situation.”
Herren said the course is exciting for students because as freshmen, they can have hands-on experience in working in a lab. This experience can help them when they go on to look for research jobs, he said.
“We put out 20 students a year that can walk right into undergraduate research and [are] ready to go,” Herren said. “We sort of feed into all the research labs, also to the vet center, also to the USDA and the Bioterrorism Institute.”
At the end of the spring semester, Block was chosen to attend a conference at HHMI and present a poster of a phage to students from across the country. The phage Block presented was called Faith5x5. Block said one of her favorite experiences from the class was having the opportunity to attend the conference and listen to the keynote speakers.
“It’s one of those situations that you always kind of dream of being in until you get there,” Block said. “And then it’s like, ‘Wow, I’m here — I’m a part of something bigger.’”