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June 3

​STEMCC:  National undergraduate research project participation
leads to discovery of novel virus 

Sean Matthews and fellow students in a lab show Pitri dishes with the CapTrips virus

Sean Mathews said his interest in science began in early childhood. He recalls competing with friends in elementary school over who knew the most animal facts. When the Ralston High School senior heard about an opportunity to participate in a microbiology research project at Metropolitan Community College last year, it didn’t take much convincing for him to sign up.

In addition to earning college credits in high school tuition free, the project offered Mathews the possibility of scientific discovery, an opportunity the science-minded student didn’t want to pass up.

“[In science,] everyone thinks about discovering animals, but they say there’s nothing left to be discovered anymore. I think microbiology is where all the hidden treasures are,” Mathews presciently said in November 2023, during the first quarter of the three-quarter research project sponsored by Howard Hughes Medical Institute (HHMI).

That turned out to be a good hypothesis. Mathews, 17, is among the first cohort of nine MCC students participating in the Science Education Alliance — Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) project.

Phages are viruses that infect bacteria. Found almost anywhere in the environment, they are among the most abundant biological agents on earth, however, their existence in science has been known for less than 100 years.

In the first stage of the SEA-PHAGES project, students took soil samples to find bacteriophages on the Fort Omaha Campus and around the Omaha metro area. One of Mathews’ samples from Hickory Hill Park in Papillion revealed a new virus when it was isolated in a petri dish and studied under a microscope.

In his lab notes, he jotted, “WE HAVE A VIRUS!!!”

That gave him the honor to name his discovery — something he actually thought about when he signed up for the study just in case it happened.

Science has a lot of laws, one being that a new virus can’t be named after another one. That nixed Mathews’ clever first choice to call his discovery “senioritis.” But there are no such rules against naming them after characters from Stephen King novels, so Mathews named the virus “CapTrips,” shorthand for the humanity-destroying virus named Captain in “The Stand.” The creatively named phage is now an entry in the HHMI bacteriophage database used by schools participating in the SEA-PHAGES project.

Studying phages is important because they have been shown to offer the same benefits as antibiotics, with the key differentiator being that they can be used to kill pathogenic bacteria without harming beneficial bacteria, said Bhaswati Manish, Ph.D., the MCC biology instructor who coordinated the College’s involvement in the project.

“Phages are like heat-seeking missiles that are able to target specific bacteria. It makes them a promising alternative to antibiotics, which can have a number of side effects and can lead to the development of antibiotic resistance,” Manish said. “Studying phages helps to understand the biology, structure, function and evolution of bacteria, as well as at the molecular level. This knowledge can be used to develop new strategies for preventing and treating bacterial infections and new biotechnology tools.”

MCC, a STEM learning destination

The purpose of the SEA-PHAGES project is to teach students the techniques and processes used in STEM (science, technology, engineering and math) research. Manish said the hands-on research is part of her department’s focus to bring innovative STEM learning opportunities to students. Participants who complete the program will receive up to nine credits.

Mike Flesch, MCC dean of math and natural sciences, said the HHMI partnership represents an important undergraduate research opportunity for community college students. MCC is the only community college in Nebraska to offer the SEA-PHAGES program. Fewer than 30 community colleges are participating nationally. More than 200 four-year schools and colleges throughout the country offer the program.

“Promoting STEM education is one of our goals at MCC because we need to be able to offer our students experiences that would be similar to what they may receive at a four-year institution,” Flesch said. “They’re learning research techniques that a lot of biotech companies are looking for in candidates for immediate employment, and they are also gaining valuable experience and credits for transfer degrees.”

There are two parts to the research — phage discovery and phage genomics. During phage discovery completed in the fall of 2023, phages were identified in soil samples, characterized and isolated from their natural environment, then purified and amplified in the laboratory. During the genomic phase of the research in the spring of 2024, students mapped and annotated the sequenced DNA of the phage and submitted them to the HHMI phage database. They were then submitted to GenBank under the National Center for Biotechnology Information.

Discoveries made in the program will be submitted as scientific reports to peer-reviewed science and biomedical journals for publication. Students will be involved in preparing the manuscripts and editing work as part of their course participation and research training. Two MCC students will participate in the HHMI SEA-Symposium, where they will gain the academic résumé-building opportunity to present their findings.

Mathews is already receiving good recognition for his work. At the Metropolitan Science and Engineering Fair in March, Mathews presented a poster on his phage research at Omaha’s Henry Doorly Zoo and Aquarium. His poster won an award that was presented at Lauritzen Gardens later that month. Mathews was also selected as one of the six top candidates in the Senior Division and participated at the Nebraska Junior Academy of Sciences (NJAS) meeting held at the University of Nebraska-Lincoln in April.

Six additional students from the SEA-PHAGES program made a joint presentation on two research posters at the NJAS event. Ye Ye Aye and Josephine McLean each received the Outstanding Research in Biology Award from University of Nebraska MedicalCenter for the work they presented at the annual Nebraska Academy of Sciences meeting.

“In addition to the scientific processes they are learning, the phases of the research also help our students work in teams and develop their verbal and written communication skills when they present and explain their work,” Flesch said. “Through participation, they expand their knowledge, learn hands-on lab techniques, learn about basic research protocols and expand their horizons on potential careers.”

Flesch said special learning opportunities like these are key to growing the College’s academic programs and preparing people in its four-county service area for their future, which could be immediate employment or working toward transfer to one of the College’s four-year university partners.

“Dr. Manish has been instrumental, along with her colleagues, in bringing this opportunity to our students,” Flesch said.

In addition to the biology department’s HHMI research project, physics instructor Kendra Sibbernsen helped secure a STEM research opportunity sponsored by NASA that took college students from MCC, UNO and UNL to Roswell, New Mexico, to study an annular eclipse using high-altitude balloons to collect data. The same group traveled to Carbondale, Illinois, in April to do follow-up research on the total solar eclipse while situated in its path of totality.

“You’ve got to have dreamers with the spirit and drive to put these kinds of projects into operation — people who are looking at opportunities to bring undergraduate research opportunities to our students,” Flesch said.

Manish and fellow MCC biology instructor, Carla Delucchi, Ph.D., have been leading laboratory-driven learning during the SEA-PHAGES project on the Fort Omaha Campus. The first cohort ranges from current high school students like Mathews to adult learners who are returning to college, with a mix of male and female students from different demographic groups.

Manish said it can be nerve-wracking to bring a new project into the College’s academic offerings, but it is rewarding to create access to this kind of undergraduate research for postsecondary students. Participating in undergraduate research at four-year institutions can be cost-prohibitive. Manish said providing the offering at MCC for $68 per credit hour — along with scholarships the MCC Foundation has made available for this project — can help reach talented students in underrepresented groups.

“HHMI wants this research to be accessible to a diverse group of students and we all agreed that community colleges can be a great way to accomplish that,” Manish said.

Manish’s research background is in neuroscience and cancer biology topics. She has more than 20 years of experience working in laboratories. She said students participating in the SEA-PHAGES project at MCC can create competitive advantages for themselves, whether their goal is to continue their studies at a four-year university, graduate school or enter the workforce.

Graduate schools are looking for students with bacteriophage research experience. Having this research background can also make students more competitive for jobs in academia or with biotech companies involved in developing new treatments for bacterial infections and other biotechnological applications, Manish said.

Flesch said the project is an example of what he believes MCC does best — meet students where they are now.

“We have students coming in with different needs. Some people need to be able to get a good job in the next 90 days to support their families. And some people are 18 years old and have their whole life in front of them. You need to be able to onboard and get people into the system wherever they are, and that’s what we do really well at MCC. This program fits so well into the development of a STEM workforce and is one of those great opportunities we’re incorporating into our curriculum,” Flesch said.

Amelia LaDue, a 35-year-old student participating in the study, took a different route to the same laboratory table as Mathews. She was three courses away from completing her nursing degree at a four-year college when her interests shifted to virology and microbiology. Attending MCC to begin a new career path made the most sense financially, she said. The way education is delivered at MCC has also clicked.

“I’m a mother and a wife. I can’t afford to spend thousands of dollars on student loans right now. Being able to have this opportunity at a community college has been a godsend to me,” LaDue said. “The instructors are amazing. I’ve learned more in this classroom setting than all of the others combined. They really let you get your hands dirty and let you make mistakes and help you through them. It's a very hands-on approach to learning that you don't see a lot."

From the slide of a microscope to a big-picture view

Overall, phages are helping create a better understanding of the trillions of microbial cells living in each person and their role in health and disease. Manish said the applications of the research have the potential to address several critical issues in the fields of health care, climate change, food and agriculture and STEM education. Phage therapy is being used to treat a variety of bacterial infections, including cystic fibrosis, wound infections and urinary tract infections. They are being used to develop new vaccines that protect against bacterial diseases. Phages can aid in engineering bacteria for use in the production of biofuels and pharmaceuticals. New studies are showing promising results for phages to treat diseases found in plants. Manish said it has been exciting to see the students see the bigger picture as they progress through each phase of the research.

“They are understanding that they are serving a bigger purpose than the experience they are developing for their own careers. These phages could be the reason that we are one day able to cure someone from cystic fibrosis,” Manish said. LaDue said participating in SEA-PHAGES has been an “amazing opportunity” that is affirming her choice to change career paths.

“This is the kind of research I want to go into. This is something that could ultimately save lives and help people thrive in ways that they wouldn’t have been able to before,” LaDue said.

Students interested in undergraduate research opportunities in the SEA-PHAGES program may contact Bhaswati Manish ( For more information on the College’s participation> in the Nationwide Eclipse Ballooning Project, email Kendra Sibbernsen (