Visualizing microbial societies

Phenotypic heterogeneity, a form of microbial “individuality” that underlies clonal population survival and sociality, has so far been reported primarily through serendipity. Our lab now seeks to make the study of phenotypic variation systematic and to use this new perspective to gain fundamental insights into its core principles and functional roles. We are employing state-of-the-art single-cell and spatial transcriptomics approaches to realize this goal and shed light on how phenotypic heterogeneity manifests in environmental and host contexts.

Spatial transcriptomics

Dynamic compartmentalization is a central part of all living systems. In eukaryotes, subcellular mRNA targeting regulates expression levels and enables localized protein synthesis. By contrast, it was long assumed that bacteria lack such RNA-based spatial regulation due to their “minimalistic” cellular architectures. However, strong evidence for RNA localization has accumulated over the last several years in various bacterial species suggesting spatial regulation may be a widespread feature in prokaryotes. Our lab is using high-throughput single-molecule imaging to study this newly described mode of organization.


Bacteria are remarkably skilled at doing more with less, utilizing clever regulatory mechanisms to increase their adaptability despite limited genomic realty. Our lab studies cis-acting riboregulators: 5’UTR-encoded RNA elements that sense intracellular metabolites and in response turn gene expression “ON” or “OFF.” This mode of regulation allows an mRNA to autonomously regulate its own expression as a function of metabolite concentration via premature transcription termination or by modulating its translation efficiency. Our lab applies (meta-)transcriptomics and functional genomics approaches to study riboregulation across bacteria, with the ultimate goal of developing new solutions for environmental and sustainability technologies.