Evolutionary genomics of Klebsiella pneumoniae’s temperate phages
About us
Our group studies genetic innovation in the context of co-evolution between bacteria and their viruses – phages. Specifically, we are fascinated by the extraordinary diversity of receptor-binding proteins (RBPs). Our research is clustered around three main areas:
- What is the genetic and structural diversity of RBPs?
- How that diversity translates into function of RBPs?
- How novel RBPs evolve and can we understand the rules governing their innovation?
Our model system is Klebsiella pneumoniae, whose extraordinary capsular diversity makes it one of the richest arenas available for studying the evolution of phage host range. Klebsiella’s phages use diverse RBPs – including those with enzymatic domains like depolymerases – to recognise their hosts and commence infection.
We are a dry lab combining large-scale comparative genomics, phylogenetics and structural bioinformatics. Our goal is to understand how RBPs innovate, diversify and specialise as phages adapt to the shifting landscape of bacterial surface polysaccharides — and how bacterial populations respond in turn.
Our analyses aid fundamental understanding of evolution as well as provide specific predictions that can be tested in the laboratory, often together with our collaborators.
The project
You will be a part of a collaborative NCN SONATA BIS project with the group of Zuzanna Drulis-Kawa at University of Wroclaw, the purpose of which is to study the genetic diversity of prophages in Klebsiella pneumoniae to better understand viral host range.
Our research has already:
- built a framework to predict genetic determinants of capsule specificity in K. pneumoniae1,
- created a major resource for studying the genetic, structural and functional diversity of depolymerase carrying RBPs2,
- built a genetic and structural RBP Atlas in Klebsiella, linking RBP modularity with phage host range3.
By joining the project during the most exciting and productive phase, you will have the capacity to use these data to advance our understanding of how temperate phages evolve and how their RBPs adapt to novel hosts.
Your role
The postdoc will focus on a new and emerging question from the project: how do prophage-encoded enzymes that modify or degrade capsules shape phage host range?
One of our most important and recent discoveries is that Klebsiella prophages carry a far broader repertoire of capsule-interacting enzymes than previously appreciated: alongside the classical depolymerases that degrade the capsule, many carry SGNH-domain esterases that instead modify it, by removing O-acetyl groups4. Some prophages rely on one strategy, some on the other, and some appear to carry both, raising questions we haven’t yet been able to ask:
- What determines the specificity of a deacetylase-carrying phage, and how does it depend on the genetic context of the host (incl. K-locus and other prophages)?
- How do these different host-recognition strategies (depolymerase, deacetylase) gain and lose out over evolutionary time, and what happens to a prophage’s enzyme repertoire when its host’s capsule type changes?
You will use our expanding collections of K. pneumoniae genomes to address questions like these — situating the acetylation/deacetylation axis within the broader picture of prophage host-range evolution and RBP diversification, rather than treating it in isolation.
Collaboration
The lab works closely with experimental collaborators, including the phage biology group of Zuzanna Drulis-Kawa (University of Wroclaw). While the position is primarily computational, the project includes an active experimental component focused on prophage induction, phage isolation and functional characterisation of phage-encoded enzymes, offering opportunities for interested candidates to contribute to interdisciplinary work.
Who we’re looking for
- A background in bioinformatics, computational biology, or evolutionary/microbial genomics (PhD obtained max. 7 years prior)
- Experience with comparative genomics and/or phylogenetics; comfort working with large bacterial genome datasets
- Solid programming and data analysis skills (Python and/or R)
- Genuine curiosity about microbial evolution and host-pathogen interactions
- Evidence of intellectual maturity with at least one first-author publication (preprints will be considered).
- Prior experience with phage biology, glycobiology or protein structure is welcome but not required.
What we offer
- An initial 1-year, fully funded postdoctoral position at MCB, Jagiellonian University in Krakow, funded via NCN — with a strong possibility of extension to 2 years.
- A collaborative environment linking computational genomics (Krakow) with experimental phage biology (Wroclaw).
- Access to large, near-complete genome collections and in-house pipelines (GWAS-based capsule–phage association, AlphaFold3 structural annotation).
- All benefits of full-time employment at the Jagiellonian University (health insurance, 35 days of annual leave, access to beneficial sports membership programme).
- Freedom to shape the computational direction of the project and develop independent ideas within its broader scope.
Get in touch
This is a preliminary, informal call, not yet the official position advertisement — a full formal ad, with confirmed salary and application procedure, will follow once NCN funding details are settled. If you’re interested, please contact Rafal Mostowy directly at rafal.mostowy@uj.edu.pl, ideally by 21 July 2026, and share your CV and a short description of why you’re applying for this position in particular.
Footnotes
Otwinowska* A, Koszucki* J, Panicker VR, et al., Drulis-Kawa Z & Mostowy RJ (2026). Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes. PLOS Biology. https://doi.org/10.1371/journal.pbio.3003716↩︎
Otwinowska* A, Olejniczak* S, Latka A, et al., Mostowy RJ & Drulis-Kawa Z (2026). DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases. Nature Communications. https://doi.org/10.1038/s41467-026-73570-7↩︎
Panicker VR, Smug BJ, Klein-Sousa V, Enright MC, Taylor NMI, Drulis-Kawa Z & Mostowy RJ (2026). Structural modularity of receptor-binding proteins underlies host-range strategy diversification in Klebsiella pneumoniae phages. bioRxiv 2026.05.12.724579. https://doi.org/10.64898/2026.05.12.724579↩︎
Otwinowska* A, Koszucki* J, Panicker VR, et al., Drulis-Kawa Z & Mostowy RJ (2026). Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes. PLOS Biology. https://doi.org/10.1371/journal.pbio.3003716↩︎