Using population dynamics to decipher phage infection

Bacteriophage infection outcomes are shaped by dynamic interactions between virus, host, and environment. Understanding how these factors govern the phage life cycle requires integrated experimental and theoretical approaches. This dissertation presents a framework for decoding phage developmental strategies through high-throughput measurements and mechanistic modeling of the population dynamics of phage-infected bacteria. In Chapter 2, I present a high-throughput assay that uses optical density (OD) measurements in a microplate reader to monitor the growth dynamics of infected bacterial cultures. This method enables quantification of phage titer, lysogeny frequency, and the lytic growth rate of phages. Applying this method to E. coli and phage lambda reveals that as bacterial growth slows, the lytic growth rate decreases and the propensity for lysogeny increases, demonstrating the influence of host physiology on phage decision-making. In Chapter 3, I introduce the preliminary efforts to extend this framework to additional systems. I apply the OD-based assay to study how phage phi3T uses its own quorum-sensing peptide to regulate lysogeny in B. subtilis. I also examine how B. subtilis defends against phi3T infection and use a mathematical model to suggest that resistance emerges in a cell density-dependent manner. Finally, I use optimality theory to interpret lambda’s lysogeny strategy. Together, this work provides a unified experimental and theoretical toolkit for probing phage-host-environment interactions.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Quant Biology

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Geng, Yuncong

Contributors dc:contributor

• Golding, Ido
• Maslov, Sergei
• Kim, Sangjin
• Whitaker, Rachel J.

• Phage
• Population Dynamics

Statement dc:rights

• Copyright 2025 Yuncong Geng

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/129840

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F129840