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"Exploring microbial phenotypic diversity with single-cell RNA sequencing

Dr. Anna Kuchina
Dr. Anna Kuchina
Department of Electrical & Computer Engineering
University of Washington
Online via Zoom
Special Information:
Please contact Nancy Perkins at for Zoom link and passcode
Type of Event:
Department Seminars


Bacterial gene expression is highly heterogeneous even in isogenic bacteria grown in the same conditions; bacteria differentiate into subpopulations that may assume different roles for the survival of community. Population-level gene expression measurements are insufficient to resolve such phenotypic states which have been only discovered through single-cell methods. Using quantitative single-cell time-lapse microscopy, we discovered a novel microbial gene regulatory strategy in the model organism Bacillus subtilis accomplished through chromosomal arrangement of key genes regulating the heterogeneous sporulation cell fate. Methods such as fluorescence microscopy, however, are typically based on reporters allowing to measure only a limited set of genes at a time and requiring tractable model organisms. To address these limitations, I developed microSPLiT, a scalable single-cell RNA sequencing method tailored for bacteria. MicroSPLiT revealed a plethora of gene expression states in >25,000 single B. subtilis cells, including rare and unexpected cell states that remained hidden at a population level. With high scalability and resolution, microSPLiT is an emergent technology for single-cell gene expression studies of complex natural and engineered microbial communities.

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