PhD defence
Bacterial Lifestyle Studies in the Genomics Era
- G. Guerrero
- Date
- Wednesday 11 November 2026
- Time
- Location
-
Academy Building
Rapenburg 73
2311 GJ Leiden
Supervisor(s)
- Prof.dr. D. Claessen
- Prof.dr. M. H. Medema
Summary
Understanding the genetic drivers of bacterial adaptation to free-living or host-associated environments remains a critical challenge due to the growing gap between abundant genomic data and functional analysis. To address this bottleneck, this research introduces bacLIFE, an automated, user-friendly computational workflow that combines large-scale comparative genomics with machine learning. This tool accurately predicts bacterial lifestyles and identifies lifestyle-associated genes (LAGs) across diverse datasets. By applying bacLIFE to over 16,000 Burkholderia and Pseudomonas genomes, the workflow successfully pinpointed hundreds of putative genes tied to plant pathogenicity. Crucially, these computational predictions were experimentally validated via site-directed mutagenesis and in vivo plant bioassays.
These experiments confirmed the virulence roles of six novel LAGs, including a newly discovered NRPS-PKS gene cluster, during rice and bean infections. Finally, this predictive framework was extended by integrating transcriptomics and adapting the methodology to analyze fungal lifestyles (funLIFE). This workflow successfully translates large-scale genomic data into testable laboratory hypotheses, providing a scalable approach for future genomic and functional discoveries.
PhD dissertations
Approximately one week after the defence, PhD dissertations by Leiden PhD students are available digitally through the Leiden Repository, that offers free access to these PhD dissertations. Please note that in some cases a dissertation may be under embargo temporarily and access to its full-text version will only be granted later.
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