Discovery of 42 novel Microbacterium phages

Ansh Abbaraju, Anaya Abney, Midhat Adnan, Ankith Alluri, Gen Baldomero, Praneeta Bandi, Lindsey Bellis, Kirsten Benes, McKenzie Betts, Rae Boateng, Mark Boktor, India Brooks, Ashleigh Browne, Zach Buchler, Rohan Chandraghatgi, Rahul Chowdhury, Abby Dech, Emely Del Orbe, Pari Desai, Toni DeSalvo, Anna Desch, Pearl Diabene, Giselle Dickinson, Kanai Dismus, Shehab Farrag, Josh Franco, Ruthi Gandhi, Jaitri Gangula, Kacy Gao, Braden Garcia, Yerobi Garcia, Millin Gulati, Mathew Habib, Sophia Hoch, Humza Imam, Margarita Jaya, Bayanne Kakhia, Deshna Karra, Medha Kasina, Milanpreet Kaur, Laiba Khan, Abigail King, Riya Kumar, Liliya Loda, Tanya Lulla, Nia Lynn, Deana Mancuso, Kushi Manjegowda, Jessica Martinez, Rilee Martzloff, Iyana McEachern, Pelumi Ojo, Tofunmi Olatubosun, Baruni Palayam, Jinal Patel, Kiah Patel, Siddharth Patel, Marilyn Paul, Francesca Pavluk, Grace Rabago, Simrit Rajan, Colston Raroha, Darshan Reddy, Natalie Richards, Dior Rodgers, Hannah Rogers, Kushal Shah, Haris Shareef, Alec Shonk, Jennine Shuti, Tasneem Siddique, Nikki Simonyan, Sammey Soliman, Shreyas Soma, Bianca Sosa, Will Stanley, Idalys Suin, Nawal Syed, Sean Vanson, Jessica Vasserman, Nick Yancy, Laura Duwel, Brett Condon

This year students at Drexel University discovered 42 novel bacteriophages using Microbacterium foliorum NRRL B-24224 as a host. These phages were isolated and purified from soil samples collected largely near Drexel’s campus in Philadelphia, but also included samples from rural Pennsylvania and New Jersey. Five of these novel Microbacterium phages were sequenced by the Pittsburgh Bacteriophage Institute: two from the EA1 subcluster (Phireproof and PhredFlintston), two from the EC cluster (CrazyRich and Phorgeous), and one from the EE cluster (BinkBonk). All five produced lytic plaques and are expected to exhibit siphoviridae morphology. Bioinformatics analysis of these five genomes revealed high similarity to previously characterized phages in their respective clusters, with no distinguishing features identified to-date. Each of our four student sections annotated two genomes: one unique to their section, and one that was subsequently annotated by all four sections. BinkBonk was annotated by all four sections and was the object of our second annual “Phage Cup” competition, where each section competes with one another to produce the most accurate annotation. Students are guided and mentored through the bioinformatics process for their section’s first genome, after which they apply the skills they have practiced, and self-organize to direct their section’s efforts during the Phage Cup. Student demonstrated a remarkable increase in both efficiency and accuracy in genome annotating during the Phage Cup, due, perhaps, to their practice, motivation, and self-organized quality-control activities. Students have now submitted research proposals for their Spring projects to further characterize the five sequenced genomes discovered this year. These projects will test the impact of a wide range of experimental factors on phage life cycle and lytic efficiency. These factors include various antibiotics, UV light, pH, pressure, temperature, nutrient composition, salinity, bacterial cell wall precursors, toxins, mutagens, tail length, host density, fertilizer components, directed evolution, location, organic origins, and ethanol. Our students’ Spring projects will generate significant insight into the nature and behavior of the phages we discovered this year, and perhaps—due to the high degree of genome similarity—other EA1, EC, and EE cluster phages.