Name your phage: virus discovery brings science to undergraduates

Quick, what organism is the most numerous form of biological life? If you say bacteria, you are partly right. The correct answer is bacteriophages – viruses that infect bacteria. Bacteriophages, also called phages, are more numerous than the bacteria they infect. Of an estimated 1031 viral particles in the biosphere, the overwhelming number are bacteriophages – more than all other biological entities combined.

In the face of these daunting figures, how to identify and analyze bacteriophages? Pitt biologist Graham Hatfull explores one approach – recruit thousands of undergraduates around the nation and beyond to discover, identify, and sequence phages.

Bacteriophages armed for battle. Image by Travis Mavrich at the Hatfull Lab

The sequences  become part of the PhagesDB database maintained by Hatfull, Eberly Family Professor at Pitt, and Howard Hughes Medical Institute (HHMI) professor. While presenting students with valuable educational and research experience, Hatfull essentially crowd-sources the sequencing of thousands of phages.

The program is known as SEA-PHAGES – Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science. It is funded by HHMI and administered by Hatfull and his colleagues.

Students in the two-semester SEA-PHAGES course are guided all the way from sampling soil and water to preparing lab samples and eventually sequencing phages using instructional and software tools made available by the program. Since 2008, students in SEA-PHAGES have isolated roughly 13,000 phages collected in ponds, puddles, streams, and even in a flower pot; 2,600 of their genomes have been completely sequenced. Students name their viruses – Buggaboo, Grizzly, Olga and Waterdiva being among recent choices.

Electron micrograph of multiple bacteriophages attached
to a bacterial cell wall; magnified approximately 200,000 times.
Image: Wiki Commons

Many of the students attend small institutions without advanced laboratory facilities or experienced instructors. Virus discovery may not be uncommon in Pitt’s advanced research environment, but a freshman discovering a virus at Texas’ Le Tourneau University rates a story in the Houston Chronicle.

Pitt Center for Research Computing enables Hatfull’s lab to analyze the thousands of resulting sequences, which often cluster in closely-related families. Hatfull’s lab uses Pitt CRC’s
high-throughput computing (HTC) resources for high-speed next-generation RNA sequencing analysis. Fangping Mu, Pitt CRC research assistant professor and lead HTC consultant,
oversees the sequencing workflow and analysis software.

“CRC is plugged into the SEA-PHAGE infrastructure. We need the RNA sequence analysis available at the CRC to make sense of the data,” Hatfull says. “Without it we can’t compare which genes are responsible for which particular gene expression.”

It is impossible to keep pace with phages, no matter how many student scientists work in SEA-PHAGES. Endless adaptation has created a genetically diverse population that endlessly adapts. Bacteria are constantly infected by phages (globally an estimated 1023 infections per second). Bacteria  continually evolve new defenses against phages. Phages continually evolve new ways to attack bacteria and develop resistance to bacterial defenses. Phages also attack other phages and develop defenses against those attacks, along with new ways to attack.

“Bacteria and phages are locked in a 3-billion year war,” Hatfull says simply. “Dynamic populations have been evolving for a long time, and they keep evolving.”

Pitt students Aishwarya Mukundan and Daniel Zipfel
in the SEA-PHAGES lab.


Electron microscope image of an individual phage.
Image: Wiki Commons, Hans-Wolfgang Ackermann
First published in PLoS Biology


















Brian Connelly
Pitt Center for Research Computing

Friday, September 4, 2020