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Students discovering ‘new knowledge’ through phage-hunting course

Barry McNamara
Sarah Poirier '22 of Lombard, Ill., works with a sample during a lab session on the day that phage was successfully isolated at Monmouth.
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MONMOUTH, Ill. – Let the record show that Sept. 18, 2018, was the day that phage was found at Monmouth College.

“We have liftoff,” said biology professor Eric Engstrom, who teaches the College’s phage-hunting course with department colleague Tim Tibbetts. “Our students found phage the world’s never seen before. Tim and I are walking around the ceiling today.”

Phage is a virus that infects bacteria. It’s “a biological entity,” said Engstrom, stopping short of calling it an organism.

“They’re fascinating things,” said Engstrom. “They’re everywhere that bacteria are found, but we don’t know how to think about phage. We’re trying to broaden our understanding. Most of its genes, we have no idea what they do. This opens up a lot of questions, such as are they phage-specific? We just don’t know until we have lots of samples.”

‘A good virus’

Research was conducted in the 1950s on using phage to treat infection, but that information was pushed to the back burner because of the rise of antibiotics. Phage has become relevant again because some diseases, such as tuberculosis, are resisting antibiotics.

“We’re becoming interested in this again,” said Engstrom. “We let it rust. Can we clean it up and put it back to use?”

Engstrom said phage is now being used to “treat patients for whom no other cure is available. It’s not a scientific study. It’s really a Hail Mary to try to save a life. ... When phage have bacteria hosting them, they inject their genome into the host. The bacteria ‘pops.’”

An article titled “Phage find clever ways to infiltrate resistant bacteria and shuttle DNA between strains” described lysins, which are cell-popping phage proteins released by dying infected bacteria. The lysins also killed resistant bacteria.

“I was super excited,” said freshman Piper Miller of Virden, Ill., one of the students to find phage. “Some diseases are resistant to a lot of antibiotics, but they’re not resistant to a virus. Phage is a good virus. It can’t harm humans at all.”

“You get phage from the soil, and then we help it live longer, eventually getting it to patients who need it,” said her classmate, Nya Hernandez of Chicago.

A nationwide initiative

Monmouth students aren’t the only ones hunting for phage. The College is part of a five-year, nationwide discovery-based undergraduate research initiative. Other schools participating include community colleges to larger research institutions such as Johns Hopkins University.

Some funding for the initiative is provided by the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program. Also known, appropriately, as PHAGES, it is administered by the Howard Hughes Medical Institute. Under the program, biology students participate in wet lab and bioinformatics research as they discover and investigate new phages.

The odds of finding phage are fairly high, said Engstrom. It can be found wherever bacteria are present. “There are more bacteria in a teaspoon of dirt than there are stars in the sky,” he said. Engstrom said there are an estimated 10 to the 31st power – or 10 nonillion – phage on Earth.

The challenge for students is isolating that phage in the lab and finding exactly what type of phage they have.

Freshman Sarah Poirier of Lombard, Ill., said only about 1,000 phages have had their genomes sequenced prior to the PHAGES program.

“We’re playing our small part in adding to the genomes that are out there,” she said. “The more we learn about viruses down the road, the better we can help.”

Authentic research, by freshmen

Engstrom said he is excited that first-year college students are part of the research because of what it could mean later to them, including several students in the class who hope to attend medical school.

“The very first thing they encounter is real, functional science,” he said. “This is an authentic research lab. It’s different from the typical lab experience. We’re getting new knowledge and learning about the world.”

The students also learn how to think critically and solve problems.

“Students have to work through this,” said Engstrom. “For example, the first time we went out, no one got phage. We tell them, ‘Don’t be discouraged. That’s the nature of research.’”

“This relates a lot to medical school and what we’re hoping to do in the future,” said Poirier.

The phases of PHAGES

Now that the students have isolated phage, the next steps are: purify, amplify, characterize and microscopy. Then the phage will be sent to the University of Pittsburgh for genome sequencing. Students enrolled in the fall semester class will continue to work with phage in the spring in Monmouth’s bioinformatics lab, annotating their samples.