Integration of metagenomics data and predictive approaches to order phage genome diversity

• Applicants: Professor Dr. Bas E. Dutilh; Dr. Johannes Söding
• Subject Area: Microbial Ecology and Applied Microbiology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 569109015

The bacterial world is becoming increasingly well understood thanks to collaborations between experts in ecology, metagenomics, and computational science. However, the study of bacteriophages lags behind, as they are more numerous and more diverse than their bacterial hosts, and their community dynamics are even more complex. Phage analysis requires specialized tools due to their smaller genomes, ancient origins, rapid evolution, and distinct selection pressures, which weaken genomic signals and confound conventional analysis tools. Given their significant impact on bacterial communities, it is crucial to classify this vast diversity to predict host interactions and ecological roles. This project addresses a major roadblock in modern phage ecology: the challenge of high-level classification. While alignment-based methods suffice for identifying genera and subfamilies, they fail at the family level, where only 52 families have been described to date. We propose that decomposing phage genomes into co-evolving gene or genomic modules (PGMs) will be key to an effective classification system. We will use PGMs to improve functional annotation based on structure-based interactions. Additionally, by combining amino acid sequence information, structural conservation, and module composition in phylogenetic analysis, we will provide an innovative solution capable of inferring multiple taxonomic ranks. Finally, by identifying and sharing phage modules and developing innovative classification approaches, we aim to advance phage research, improve taxonomy, and understand their ecological impact.

• DFG Programme: Research Grants
• International Connection: France
• Cooperation Partners: Dr. Jessica Andreani; Professorin Dr. Marie-Agnès Petit