Studying bacteria in the laboratory is powerful to identify molecular mechanisms which need to be connected to the organism’s lifestyle. This is obvious for bacterial pathogens which have evolved within a host and must also be studied in this context. We use all the traditional host models available but also alternative models such as moths.
We are also exploring the ecology of environmental bacteria and of their viruses. For this, we isolate new bacterial and virus species directly from the environment and in particular, the deep ocean floor, and attempt to grow them in the laboratory. Because bacteria generally do not live as single cell organisms but develop within spatially structured and sometimes multi-species communities, we are creating synthetic communities for in vitro studies. This allows us to observe collective predation, the dynamics of phage infections and the formation of complex biofilms directly under the microscope. We develop new analytical tools, recently using artificial intelligence. Finally, we also approach bacterial ecology from a genomics perspective, analyzing bacterial genome evolution and allowing bacteria to evolve in their ecological niches and in the laboratory under particular selection pressures. We support these studies via comparative genomics pipelines that we have installed at the Institute.
Keywords: soils, oceans, biofilms, imaging, genomics