Research team
Expertise
My research focuses on microbial genomics, bioinformatics, and microbial evolution. I study how bacteria, particularly lactic acid bacteria, adapt to their environment and exchange genetic material. These processes shape their characteristics, their role within microbial communities, and their classification. I work across a range of ecosystems, including fermented foods and the human microbiome. By analysing large-scale genomic and microbiome datasets, I aim to better understand how microbial diversity arises and how microorganisms evolve
Recombination dynamics in the evolution of Lactobacillaceae and Enterobacteriaceae
Abstract
Recombination is a major evolutionary force and signal in bacteria. However, its rate, origin, and impact remain underexplored across many taxa. This project addresses fundamental gaps in our understanding of recombination dynamics and their consequences for bacterial evolution, taxonomy, and functional diversity. Lactobacillaceae and Enterobacteriaceae will be studied as ecologically and phylogenetically distinct model families. Lactobacillaceae are widely used in probiotics and food fermentations, where accurate taxonomy is essential for safety and functionality. Enterobacteriaceae include clinically relevant pathogens, where strain-level resolution is critical for outbreak tracking and antimicrobial resistance monitoring. We will assess homologous and site-specific recombination within and between species, investigate recombination rates variation linked to species lifestyle, and evaluate the existence of intraspecies recombination barriers. Hereto, novel computational tools will be developed: a recombination-aware assembly error detector, enhanced phylogenetic methods, and a scalable species classifier. These tools will support the fundamental exploration of evolutionary processes and provide a framework for understanding how recombination contributes to microbial diversification. The project will advance core concepts in microbial evolution and taxonomy, with broad relevance across prokaryotic biodiversity.Researcher(s)
- Promoter: Lebeer Sarah
- Co-promoter: Van Puyvelde Sandra
- Co-promoter: Wittouck Stijn
- Fellow: Eilers Tom
Research team(s)
Funding
- FWO
Project type(s)
- Research Project