Shifting the Focus from the Organism to the Community of Pathogens: A Systems Biology Analysis of the Pathobiome. COMBAT

Microbial ecology has witnessed tremendous progress over the last decade empowered by new sequencing technologies. These innovations in DNA sequencing resulted in a paradigm shift concerning our understanding of pathogenic processes and gave birth to a new scientific concept, namely the “pathobiome”. In the pathobiome concept, the microbial community containing a pathogenic agent exerts a major influence on the persistence, transmission and evolution of the pathogen. It is therefore mandatory to identify those species that contribute, either as partners or antagonists, to pathogen’s survival, extinction or dispersal by applying concepts and approaches of systems biology. Developing multi-meta-omic systems biology frameworks would allow us to go beyond the identification of mere statistical co-occurrence patterns and instead develop computational models that describe the spatio-temporal dynamics of the pathogen and the functional interactions with its biotic environment. To demonstrate the power of our approach, we will use systems level analysis and modelling to investigate the contribution of the biotic environment to the colonization and dissemination of Candida albicans.