Phage Discovery Program

The Phage Discovery Program is Tarleton State University's two-semester undergraduate research program in the HHMI SEA-PHAGES collaboration. Students isolate bacteriophages (viruses that infect bacteria) from soil, characterize them and annotate the genomes of the ones that are sequenced. The bench workflow the program follows is the SEA-PHAGES Phage Discovery Guide, currently the July 2025 edition, and this page links to it rather than restating it. Every phage the program has found is in the phage table, and the research side of the program, including the genome announcements students co-author, is on the science education page.

The program#

We are part of the SEA-PHAGES national collaboration in bacteriophage genomics, run by the Science Education Alliance of the Howard Hughes Medical Institute (HHMI) together with the University of Pittsburgh. Member schools follow a shared workflow and report every phage to PhagesDB. More about the national program is at seaphages.org. At Tarleton the program is two discovery-based research courses, both taught as Special Topics (BIOL 4090).

First semester (fall): Virus Isolation. Students find, purify and characterize a new phage from an environmental sample, and the best DNA goes to the Pittsburgh Bacteriophage Institute for whole-genome sequencing.

Second semester (spring): Phage Bioinformatics. Students annotate the whole genomes of the sequenced phages, and the finished annotations are submitted to GenBank. A class can then write a genome up as a short genome announcement.

How students join. Students enter the program through the fall Virus Isolation course and continue to Phage Bioinformatics in the spring. After both courses, students can keep characterizing their phages as independent research; how undergraduates join the lab for research is on the teaching page.

The discovery process#

In the program's words, phage discovery goes from a soil sample to a named, archived phage, and for some phages to an annotated genome in GenBank. Students collect a sample, look for phages that infect the host bacterium, purify one phage, grow it to a high titer, image it by electron microscopy, extract its DNA and archive it, and register it on PhagesDB. A phage whose DNA is unique and of high enough quality is sequenced, and the class annotates its genome the next semester.

The full procedure for every stage is the program's own document:

SEA-PHAGES Phage Discovery Guide (July 2025 edition). Genome annotation follows the separate SEA-PHAGES Phage Genomics Guide.

The lab's own bench methods are on the phage isolation protocol and phage DNA extraction protocol pages. For DNA, the lab uses a column-free ZnCl2/TES extraction in place of the Guide's resin column.

Host strains#

• Mycobacterium smegmatis mc²155 (ATCC 700084), used in the 2017 notebooks.
• Microbacterium foliorum NRRL B-24224, used from 2018 on.

Tarleton variants#

Where this lab does something differently from the July 2025 edition of the Guide, the difference is recorded here, with its reason as the lab notebooks give it.

• Restriction enzymes for Microbacterium foliorum phages (host M. foliorum NRRL B-24224). The lab screens DNA with HaeIII, NspI, SacII and SalI, with MseI added in 2023, because the Guide's enzyme lists are for other hosts' phages.
• Adopting a classmate's phage (host M. foliorum NRRL B-24224). After several negative isolations, a student or group adopts a phage from a classmate's positive plate or enrichment, gives it a new sample number and name, and carries it through purification as their own. This is a schedule fallback so every student has a phage to characterize within the semester, not a guarantee: an adopted isolate can also fail.
• A third archive tube kept at Tarleton. Two barcoded archive tubes go to Pittsburgh, and a third, unbarcoded tube stays in the Tarleton freezer so the lab keeps its own copy of each phage.
• Electron microscopy off site. Grids are prepared and stained in the lab, then taken or shipped to an outside EM facility for imaging.