Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Genetic Determinants of Klebsiella Phage Infection


Marissa R. Gittrich1* ([email protected]), Courtney M. Sanderson1, Cara M. Noel1, Jonathan E. Leopold1, Erica Babusci1, Olivia R. Farinas1, Aghiad Abadoul1, Steven Grabski1, Paul Hyman2, Vivek K. Mutalik3, Matthew B. Sullivan1


1The Ohio State University; 2Ashland University; and 3Lawrence Berkeley National Laboratory



The overarching goal of this project is to establish ecological paradigms for how viruses alter soil microbiomes and nutrient cycles by developing foundational (eco)systems biology approaches for soil viruses. Here the team seeks to understand how phages infect bacteria, specifically, what bacterial genes are required for infection to (1) see if researchers scan predict the bacterial genes required for phage infection based on phage sequences, and (2) use these data to generate models to understand how phages and bacteria interact in an ecological setting.


Novel bacteriophages (phages) are being cataloged at unprecedented rates, and current research broadly credits them with driving nutrient and energy cycling across many of Earth’s ecosystems. However, little is known about the bacterial genes required for infection beyond a few model phage-host systems. Such data are critical for modeling phage-host interactions in complex communities. Here, the team mapped bacterial genetic determinants of phage infection using a randomly barcoded, genome-wide loss-of-function transposon mutant library (RB-TnSeq) of a plant growth-promoting rhizobacterium (Klebsiella sp. M5a1). This library was individually challenged by 25 diverse, double-stranded DNA phages spanning four known phage families at three multiplicities of infection (0.1, 1, and 10). The genetic screen uncovered a multitude of bacterial factors involved in phage infection, such as genes involved in receptor formation, transcription regulation, electron transport, and genes with unknown functions. When disrupted, some bacterial genes, such as those encoding putative glycosyltransferases involved in LPS biogenesis, conferred resistance to up to 50% of the phages across multiple phage families, potentially due to preventing phage adsorption. Other bacterial genes involved in intracellular functions, such as the electron transport chain and transcriptional regulation, were phage-specific, indicating that such cellular processes are differentially required across the diverse phage set. This supports previous findings in Escherichia coli that genes involved in intracellular functions are phage-specific, while genes encoding for receptors required for phage adsorption are more broadly required across phages. Additionally, the team found that some phages, although highly related, required a unique set of bacterial genes for phage infection. Together these findings provide a foundation to develop predictive models of phage infection that can be applied to environmental systems.

Funding Information

This research is based upon work supported by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0020173 and DE-SC0023307 to The Ohio State University. Marissa R. Gittrich was supported in part by the NIH T32 GM086252.