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-Theme 1: microbiota and BPO occurrence (invasion, resistance, resilience): this theme involves in situ analyses with massive data acquisition defining the environments colonized (including humans and observation sites in natural environments such as those of the Lyon urban hydrology field observatory) by BPOs, and also the analysis of environmental DNA sequences using DNA meta-barcoding and metagenomic approaches. These approaches make it possible to identify human or agricultural activities and certain factors, such as the occurrence of pollutants or drugs, that explain the occurrence of BPO in certain biotopes and clinical cases. These approaches help explain the distribution of BPO species and epidemic or environmental outbreaks. This highly interdisciplinary theme involves collaboration with the humanities and social sciences, medicine, agri-food, hydrology, geography, environmental chemistry and civil engineering.

-Theme 2: BPO adaptation to environmental constraints. This theme involves laboratory studies on pure BPO cultures or in interaction with other biotic components of the colonized systems, such as lung or intestinal epithelial cells, and aims to clarify the processes of BPO colonization and growth in the contexts studied in theme 1. The emergence of new properties or genomic innovations in these contexts is also analyzed. Comparative analyses of BPO genomes and transcriptomic profiling are carried out, supported by large-scale phenotyping. This theme also involves the search for nature-based solutions to prevent BPO installation in colonized environments, such as the use of sugar-based biomimetics blocking BPO adhesins and preventing epithelial cell colonization.

Expression of lateral flagella following genomic island acquisition in Burkholderia ambifaria