About
Bacteria are able to sense environmental changes in their surroundings and adapt themselves, both structurally and metabolically, in order to survive. These cells are able to switch between free-living states, sessile states in biofilms, and active infection of a host organism. Cells selectively express and employ distinct macromolecular machines according to specific growth conditions to interact with and manipulate their environment. Consequently, cells of the same species may have vastly different morphological and behavioral characteristics depending on the environment they occupy. The susceptibility to stressors such as antibiotics and phage infection may also dramatically impact cell morphology. More specifically, we recently begun studying bacteriophages and how these viruses infect their host (Ouyang et al., 2022). In collaboration with the Claessen lab (IBL), we discovered the reversible shedding of the bacterial cell wall as a widespread response to phage predation (Ongenae et al., 2021; Ongenae et al., 2022; Sidi Mabrouk et al., 2023). Due to the innate adaptability of bacteria, it is necessary to form a detailed understanding of how the cells sense diverse environments and how they structurally remodel to counter and thrive despite often dramatically changing conditions. This structural insight is a crucial prerequisite for designing novel drugs aiming to target the specific molecular machines during infection. To this end, we have recently begun studying pathogens in complex host environments, such as the structural behavior of Mycobacteria inside macrophages (M.marinum, M. avium and M.tuberculosis). Furthermore, we are investigating bacterial interactions inside mouse and human gut organoid systems using controlled bacterial communities, including commensal bacteria and pathogens such as P. aeruginosa and M. abscessus. To investigate these interactions at the nanoscale level with near-native sample preservation, we are developing novel workflows that will allow us extract tissue samples and process them for subsequent cryo-ET investigations. This workflow will be generally applicable to investigate microbial interactions in complex environments, such as inside microbiomes, or inside a host organism. To this end, we are also investigating a key microbe-host symbiosis system (luminescent Vibrio bacteria inside the light organ of the Hawaiian bobtail squid (funded by the Moore foundation).