Overview

• Hebrew University researchers introduced Microcolony-seq to profile RNA, genomes, and phenotypes from microcolonies derived from single cells, distinguishing genetic mutations from inherited phenotypic states.
• The study shows bacterial descendants can retain a record of past environments for roughly 20 generations before the memory is erased when cultures enter stationary phase.
• In Escherichia coli and Staphylococcus aureus, the method identified stable subpopulations that prioritize distinct programs such as virulence, motility, or stress survival.
• Patient samples from urinary tract and bloodstream infections contained co-existing groups with differing antibiotic susceptibility or virulence, demonstrating that picking one colony can misguide treatment choices.
• The authors recommend testing multiple colonies and note the heterogeneity may help explain past S. aureus drug and vaccine trial failures, with potential applications extending to fungal pathogens, the microbiome, and fermentation.