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Assistant Professor
6201 Marsico Hall


Uncovering the role of cell-cell heterogeneity in infection

During infection individual cells of a bacterial pathogen can co-occur in distinct physiological states. Such phenotypic heterogeneity has been recently reported in landmark virulence processes including expression of toxin genes, sporulation, genetic exchange, cell-attachment, and resistance and persistence to antibiotics and can provide community benefit to the pathogen. The focus of our research is to understand the extent and role of phenotypic heterogeneity in infection and the genetic programs that control differentiation and switching dynamics between cellular states. This understanding can then be used to devise therapeutic interventions that specifically target virulent cells.


Traditional “bulk-level” measurements of bacterial pathogens average the signal of specialized cells in the population and therefore mask their individual physiological role. Therefore, high-throughput single cell studies of pathogenic heterogeneity are needed to understand how a community of bacterial cells collectively organize infection and coordinate virulence. However, despite the importance of cellular heterogeneity in infection, there is a lack of high-throughput methods to assess genome-wide heterogeneity in bacteria at the single-cell level.

To address these challenges, we recently developed the first microfluidic technique that achieves high quality bacterial single-cell transcriptomics. This technique overcomes many technical difficulties inherent to bacterial single cell RNA-seq including the lack of mRNA polyadenylation, the presence of diverse microbial cell walls, and the high rRNA loads and short mRNA half-life of bacterial mRNA. Using this tool and other methods there are fundamental questions our lab will address: What are the mechanisms and signals that activate cells in a benign state to transform into a virulent phenotype? Which particular virulence programs and metabolic physiologies are expressed in specialized cells, and can we use this knowledge to predict perturbations that reduce toxicity? Can we uncover the dynamics and mechanisms that regulate the differentiation of particular cells into the pathogenic states? Can we learn how single-bacterial cells interact with other bacterial species in the microbiome and with the host, especially the host immune system?



McNulty R, Sritharan D, Liu S, Hormoz S, Rosenthal AZ. Droplet-based single cell RNA sequencing of bacteria identifies known and previously unseen cellular states. bioRxiv. 2021. p. 2021.03.10.434868. doi:10.1101/2021.03.10.434868

Brennan MA, Rosenthal AZ. Single-Cell RNA Sequencing Elucidates the Structure and Organization of Microbial Communities. Front Microbiol. 2021;12: 713128.

Kimmel JC, Penland L, Rubinstein ND, Hendrickson DG, Kelley DR, Rosenthal AZ. Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome Res. 2019;29: 2088–2103.

Rosenthal AZ, Qi Y, Hormoz S, Park J, Li SH-J, Elowitz MB. Metabolic interactions between dynamic bacterial subpopulations. Elife. 2018;7. doi:10.7554/eLife.33099

Choi HMT, Calvert CR, Husain N, Huss D, Barsi JC, Deverman BE, Hunter MC, Kato M, Lee SM, Abelin AC, Rosenthal AZ et al. Mapping a multiplexed zoo of mRNA expression. Development. 2016;143: 3632–3637.

Rosenthal AZ, Zhang X, Lucey KS, Ottesen EA, Trivedi V, Choi HMT, et al. Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proc Natl Acad Sci U S A. 2013;110: 16163–16168.

Matson EG, Rosenthal AZ, Zhang X, Leadbetter JR. Genome-wide effects of selenium and translational uncoupling on transcription in the termite gut symbiont Treponema primitia. MBio. 2013;4: e00869-13.

Rosenthal AZ, Matson EG, Eldar A, Leadbetter JR. RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture. ISME J. 2011;5: 1133–1142.

Rosenthal AZ, Elowitz MB. Following evolution of bacterial antibiotic resistance in real time. Nat Genet. 2011;44: 11–13.

Rosenthal AZ, Matson EG, Eldar A, Leadbetter JR. RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture. ISME J. 2011;5: 1133–1142.

Altendorf K, Booth IR, Gralla JD, Greie JC, Rosenthal AZ, Wood JM. Osmotic stress. EcoSal. 2009. Available:

Rosenthal AZ, Kim Y, Gralla JD. Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons. Mol Microbiol. 2008;68: 907–917.

Rosenthal AZ, Kim Y, Gralla JD. Poising of Escherichia coli RNA polymerase and its release from the σ38 C-terminal tail for osmY transcription. J Mol Biol. 2008. Available:

Huo Y-X, Rosenthal AZ, Gralla JD. General stress response signalling: unwrapping transcription complexes by DNA relaxation via the sigma38 C-terminal domain. Mol Microbiol. 2008;70: 369–378.

Rosenthal AZ, Hu M, Gralla JD. Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS). Mol Microbiol. 2006;59: 1052–1061. 

Sørensen OE, Thapa DR, Rosenthal A, Liu L, Roberts AA, Ganz T. Differential regulation of beta-defensin expression in human skin by microbial stimuli. J Immunol. 2005;174: 4870–4879.