Mechanically resolved imaging of bacteria using expansion microscopy.
2019; 17 (10): e3000268
Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (muExM) in which bacterial cells are physically expanded prior to imaging. We find that expansion patterns depend on the structural and mechanical properties of the cell wall, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of muExM to distinguish species through an in vitro defined community of human gut commensals and in vivo imaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.
View details for DOI 10.1371/journal.pbio.3000268
View details for PubMedID 31622337
- Phase transitions in mutualistic communities under invasion PHYSICAL BIOLOGY 2019; 16 (4)
Phase transitions in mutualistic communities under invasion.
Predicting the outcome of species invasion in ecosystems is challenging due to the non-equilibrium nature of the transitions that occur during invasion events. This limits the accuracy of classical ecological models that are typically fit to equilibrium conditions. Here, we address this limitation by solving for the transition dynamics of a cross-feeding community along an analytically tractable manifold defined by the system carrying capacity. We find that continuous changes in invader characteristics and environmental conditions induce discontinuous transitions in the invasion outcomes, resembling phase transitions in physical systems. These sharp transitions are emergent properties of species-resource interactions and relate directly to the extent of overlap in the growth strategy of competing species, with first and second order transitions resulting from complete and partial overlap, respectively. Moreover, we demonstrate that these phase transitions can be modulated by environmental variations to organize species in space.
View details for PubMedID 30790772
Locked Expansion Microscopy to in Situ Analyze Microbial Communities
CELL PRESS. 2018: 532A
View details for Web of Science ID 000430563200415