Research Areas

Microbial communities are the engines of Earth's biogeochemical cycles and the hidden drivers of both resilience and vulnerability in the environments they inhabit. We study them not as static genetic inventories, but as dynamic, spatially organized systems whose behavior emerges from how individual cells interact with each other and with their physical surroundings. We build imaging and computational tools that enable visualization of these interactions across scales.

Our long-term goal is to understand how bacteria acquire and pass on antibiotic resistance in the complex environments they actually live: sewers, soils, the human gut, and to build the tools that make that process visible.

Unraveling the Multiscale Mechanisms Driving the Emergence and Spread of Antibiotic Resistance in Complex Microbiomes

Environmental antimicrobial resistance (AMR) reservoirs are chemically and biologically complex, major gaps remain in resolving how ARGs spread within these microbial communities. This level of resolution is essential for characterizing wastewater samples and their highly heterogeneous genetic and metabolic contributions. Spatial context is also crucial, as the emergence of resistance mutations can be associated with the physical structure of the community (i.e. biofilms). The overarching goals are to establish the quantitative and imaging foundation for probing how antibiotic resistance is acquired and propagated in complex microbiomes, from single cells to whole communities.

While metagenomics has catalogued the breadth of ARGs in wastewater and gut, three fundamental questions remain: which bacterial hosts carry these genes, what mechanisms enable their transfer, and are they actively conferring resistance?

We aim to integrate these complementary modalities into a unified view of AMR in natural microbiomes such as the human gut and wastewater. To this end we are developing integrated computational and spatial-Raman microspectroscopy pipelines to quantify in-situ HGT with imaging modalities that enables direct visualization of host-MGE interactions at the single-cell level.

Natural microbial consortia for rare earth element bioaccumulation in geothermal waters