Three genomes, identified through research at Loomis Chaffee, are expected to be added to a database of viral genomes, contributing new, publicly available data to the scientific community. A genome is an organism’s complete set of genetic instructions, and its study can enable advances in personalized medicine, disease prevention, and evolutionary biology. 

The findings were made possible by the work of students in College-Level Microbiology, Science Department Head Neil Chaudhary '05, and the use of DNBSEQ-E25 — a portable sequencer platform from Complete Genomics — that Neil has described as a “game-changer.” 

The genetic sequencer, which helps scientists to read genetic code, came to the school in 2025 as part of a collaboration between Loomis and the sequencing company Complete Genomics, aimed at expanding access to advanced genomic technologies in educational settings. With the addition of the DNBSEQ-E25 system, Loomis became one of the first high schools in the United States — and the first to adopt the DNBSEQ platform — to bring next-generation sequencing capabilities in-house, enabling students to generate and analyze their own genomic data. 

The project, called SEA-PHAGES, a Howard Hughes Medical Institute-funded University of Pittsburgh program, started in 2025 with students engaging in “phage hunting,” which involves identifying and isolating bacteriophages from various environments, such as soil. When the students had extracted enough high-quality DNA, Neil prepared the DNA library for sequencing on the DNBSEQ-E25 instrument. “After much labor and more than a little ingenious troubleshooting by our intrepid students,” Neil said, “we were able to assemble and annotate the complete genomes of three soil-borne bacteriophage viruses.” 

Neil said the project “resulted in one of the first publications of novel scientific information by Loomis Chaffee students.” 

“It’s extremely rare,” he continued, “for high school students to have access to laboratories as well-equipped as ours. This new machine and the ability to sequence vast amounts of DNA in- house takes a stellar, well-resourced program and puts it in a class of its own.” 

Phage hunting is designed to increase undergraduate interest in the biological sciences, and the genetic sequencer has given students another tool that allows them to see themselves as scientists. In a report on the project written in March by Neil, the impact on students was evident in their comments. One student said, “The Phage Hunting Project really reinforced my ambition to become a real scientist in the future. It gave me an opportunity to have independence and agency over my work, carrying out steps in an organized fashion which scientists do in a lab.” Another noted that the “experience makes me more willing to join research programs in college.” 

Neil’s report noted that the school’s Microbiology and Molecular Biology courses have been lab-intensive for decades, back at least to when he took the courses himself as a junior at Loomis in 2003–04. “Always, an emphasis has been placed on extensive hands-on work,” he wrote. “I believe it is this emphasis, this willingness to trade textbook content for laboratory work, which has made this course so influential in the lives of its students. It was this course that made me want a life in life science, and I know there are many, many others like me.” 

Complete Genomics supported the deployment of the system as part of an effort to explore how next-generation sequencing technologies can be integrated into secondar education. In early 2025, Complete Genomics sent field engineer David Lambiase and field application scientist Devesh Patel to campus to install and validate the instrument. Mr. Patel then returned to train Neil and science teacher Amy Cornell on the use of the instrument. Now, a major achievement is completed: three accepted bacteriophage submissions to the SEA-PHAGES archives and the production of publicly available genomes on phagesdb.org.