Fitness of bacteriophage across environments - PI: james gurney project summary bacteriophages (phages) are central players in microbial ecology, shaping bacterial populations in natural and…

The National Institute of General Medical Sciences awarded Georgia State University Research Foundation Inc. $434,729 on September 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to support research on bacteriophage gene essentiality and infection dynamics across environmental contexts.

The award funds research to map phage gene function and track infection dynamics using complementary molecular approaches. The work will exploit DNA mismatch-repair deficient hosts to create full mutant libraries of bacteriophages, generating near-saturated mutational landscapes to identify differentially essential versus non-essential phage genes and determine how gene essentiality varies across bacterial strains and environments. The research will also adapt single-cell RNA sequencing to capture transcriptional programs of both bacteria and phages within individual infected cells, revealing how bacterial physiological state influences susceptibility to phage infection and how phages retune their transcription to exploit different host environments. Integration of these tools will define how environmental and host factors shape phage gene function and how bacterial heterogeneity alters infection outcomes, addressing knowledge gaps in phage-host interactions and bacterial transcriptional heterogeneity.

The award is classified as a Project Grant. Period of performance extends from September 1, 2026, through August 31, 2031. Work is performed in Atlanta, Georgia. Principal investigator is James Gurney.

Fitness of bacteriophage across environments - PI: james gurney project summary bacteriophages (phages) are central players in microbial ecology, shaping bacterial populations in natural and clinical environments. Despite their ubiquity and importance, our understanding of phage gene essentiality and infection dynamics remains limited. Unlike bacteria, phages lack genetic tools such as knockout libraries, and we know little about which phage genes are essential for infecting bacteria across different environmental and host contexts. At the same time, bacterial populations exhibit striking transcriptional heterogeneity at the single- cell level, generating subpopulations that may resist phage infection without genetic mutation. These two knowledge gaps (1) context-dependent phage gene essentiality (2) bacterial transcriptional heterogeneity limit our ability to explain and predict phage-host interactions. This mira application seeks to bridge these gaps by using and developing new approaches to map phage gene function and track infection dynamics at unprecedented resolution. First, we will exploit DNA mismatch-repair deficient hosts to create full mutant libraries (fmls) of phages. These libraries generate near-saturated mutational landscapes, allowing US to identify differentially essential versus non-essential phage genes and to determine how gene essentiality changes across bacterial strains and environments. Second, we will adapt and extend our single-cell RNA sequencing (scrna-SEQ/petri-SEQ) to capture the transcriptional programs of both bacteria and phages within individual infected cells. This approach will reveal how bacterial state influences susceptibility to phage, and how phages retune their transcription to exploit different host environments. By integrating these complementary tools, the proposed research will define how environmental and host factors shape phage gene function, and how bacterial heterogeneity alters infection outcomes. This work is innovative because IT brings high-throughput mutational mapping and single-cell transcriptomics into phage biology for the first time, creating an essential gene and differentially expressed transcriptomic approach to phage biology. The research will provide fundamental insights into the principles of phage-bacteria interactions, addressing long- standing gaps in evolutionary microbiology, gene regulation, and microbial ecology. The expected outcome is a mechanistic understanding of how phage genomes encode infection strategies and how bacterial states constrain or enable those strategies. This knowledge will broadly impact the fields of microbiology, systems biology, and evolutionary genetics, while laying the foundation for rational approaches to manipulating phages in both environmental and therapeutic contexts.