Research Projects

Research Organisation Partners

• Biotechnical faculty, UL
•  Bacteriology Department, Universtiy of Wisconsin, Madison 

Abstract

Phages are bacterial Mobile Genetic Elements (MGEs) that have been detected wherever their host bacteria exist, usually outnumbering the bacteria by 10-fold. Lysogenic (or temperate) phages, next to killing the bacteria, are able to integrate into the bacterial chromosome and multiply within it as a prophage. Prophages, present in nearly 70% of all bacteria, are implicated in influencing diverse bacterial adaptive traits through lysogeny. The phenomenon known as prophage conversion, wherein a prophage modifies the host phenotype, is mediated by accessory genes that can be gained or lost by the phage without disrupting its functional lytic cycle. Specific temperate phages, such as those of Firmicutes, exhibit notably high rates of gene gain and loss through recombination or gene shuffling, occurring between co-infecting phages or functional and defective prophages. Despite evidence from comparative genomics, experimental studies on phage recombination and its impact on the fitness and adaptation of bacterial hosts are limited. The broader implications of lysogeny on bacterial hosts over extended evolutionary timescales, particularly in non-pathogenic bacterial models, remain poorly understood. The primary objective of this project is to investigate the influence of temperate phage recombination on the adaptation of bacterial hosts. The project is organized into three research work packages: WP1) Selection and isolation of recombining phages with unique sets of accessory genes; WP2) Experimental evolution of bacteria with phage cocktails; and WP3) Phenotypic and genotypic characterization of evolved bacteria and phages.  The PHEVO research hypothesis states that the presence of temperate phages will accelerate host adaptation. This positive phage effect is anticipated to be most pronounced in environments characterized by high phage diversity, facilitating recombination and the exchange of beneficial genes, and in complex selection regimes demanding a diverse set of adaptive traits. Although currently in its foundational experimental stage, this research has the potential to emerge as an innovative strategy for the rapid optimization of beneficial bacteria. In essence, the project stands as a milestone in advancing our fundamental understanding of the intricate relationship between temperate phage evolution through recombination and the adaptation of bacterial hosts.

External link to Researchers Open in new window

• External link to Anna Dragoš Open in new window
• External link to Virginie Marie-Aline Grosboillot  Open in new window
• External link to Valentina A. Floccari  Open in new window
• External link to Nina Vesel  Open in new window
• External link to Polonca Štefanič Open in new window 
• External link to Eva Stare Open in new window 
• External link to Maja Popović  Open in new window
• External link to Ines Mandić-Mulec  Open in new window
• External link to Eli Podnar Open in new window 
• External link to Hannah Rose Bonham Open in new window
• External link to Jaka Jakin Lazar Open in new window 

The phases of the project and their realization

• WP 1. Selection and isolation of recombining phages with unique sets of accessory genes.

Milestone 1: Phage cocktails for experimental evolution designed and prepared.
Deliverables: Upgraded Synphage software for phage genome comparison and visualization (freely available on Github platform), Conservation map of SPbetaviruse genomes, List and conservation level of accessory genes of SPbetaviruses, Host range of selected SPbetaviruses, Collection of purified SPbetaviruses (likely including new genus members), Phage cocktails for evolution experiment.

• WP 2: Experimental evolution of bacteria with phage cocktails.

Milestone 2: Evolution completed, evolved host populations compared with ancestors using basic fitness assays, single isolates for detailed phenotypic studies selected. Deliverables: Evolved populations of bacteria and phages (including frozen record from subsequent evolutionary timepoints); adaptive trajectories incl. CFU, sporulation and germination dynamics; selected strains for further phenotypic and genomic characterization.

• WP 3: Phenotypic and genotypic characterization of evolved bacteria and phages. Milestone 3: Evolved strains and phages sequenced. Effect of selected evolved phages and genetic modules on host fitness verified.

Deliverables: Sequenced genomes of selected evolved bacteria and phages. Map of recombination events and recombination hotspots along with annotated corresponding genomic regions. Collection of chimeric phages and expression vectors containing selected chimeric phage modules and recombinant strains carrying these phages/vectors and their effect on fitness directly tested.