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Related Experiment Video

Updated: Sep 10, 2025

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

Uncovering phenotypic inheritance from single cells with Microcolony-seq.

Raya Faigenbaum-Romm¹, Noam Yedidi², Orit Gefen¹

¹The Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.

|August 27, 2025

Summary

This summary is machine-generated.

Bacteria can remember their environment across generations, a trait erased by growth. Microcolony-seq reveals this bacterial memory, uncovering diverse inherited phenotypes in infections and suggesting new therapeutic targets.

Keywords:

EPEC S. aureus UPEC UTI adhesion factor bacterial differentiation bet-hedging bloodstream infection division of labor epigenetic inheritance pathogens single-cell single-cell heterogeneity virulence factors

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Area of Science:

Microbiology
Genomics
Epigenetics

Background:

Phenotypic heterogeneity is crucial for understanding bacterial development and stress responses.
Low mRNA abundance in single bacteria hinders the study of biologically relevant heterogeneity.

Purpose of the Study:

To develop a method for capturing and analyzing inherited heterogeneity in bacteria.
To investigate the long-term inheritance of host environment information by bacteria.
To identify distinct bacterial subpopulations and their fitness advantages.

Main Methods:

Microcolony-seq: analyzing microcolonies from single bacterial cells to capture inherited heterogeneity.
Integration of bulk RNA sequencing (RNA-seq), whole-genome sequencing, and phenotypic assays.
Application of the method to infected human samples.

Main Results:

Bacteria possess a ubiquitous ability to maintain long-term inheritance of the host environment.
Growth to stationary phase erases epigenetic inheritance, but memory persists within microcolonies.
Diverse inherited phenotypes were uncovered in infected human samples.
Bacterial memory appears widespread in both Gram-negative and Gram-positive bacteria.

Conclusions:

Microcolony-seq is a powerful tool for detecting distinct bacterial subpopulations and their fitness advantages.
Bacterial memory is a widespread phenomenon with implications for understanding infection dynamics.
The findings provide potential targets for therapies designed to address coexisting bacterial subpopulations.