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Joe Sanfilippo

Assistant Professor of Biochemistry

Research Interests

Research Topics

Host-Pathogen Interactions, Microbial Physiology, Regulation of Gene Expression, Sensory Processing, Signal Transduction

Disease Research Interests

Infectious Diseases

Research Description

Exploring the intersection of bacteria and the physical world

In the Sanfilippo lab, we use an interdisciplinary strategy that combines approaches from biology, chemistry, physics, and engineering to probe how physical forces impact bacterial cells.

Bacteria sense shear flow and alter gene expression using rheosensing

Using a novel microfluidic-based transcriptomic approach, we were the first to discover that bacterial cells actively sense and respond to flow speed, through a process we named rheosensing (as rheo- is Greek for flow) (Sanfilippo et al, 2019, Nature Microbiology). A major focus of our research group is to discover the molecular and biophysical mechanisms that control rheosensing.

Using microfluidics to create realistic bacterial environments

Over the past 100 years, scientists have studied bacteria in simplified, static conditions. However, bacteria exist in complex, dynamic conditions in nature. Fluid flow is a fundamental driver of dynamic cellular systems, exemplified by the human urinary tract and bloodstream. In the Sanfilippo lab, we engineer custom microfluidic devices with a variety of heights, widths, and channel geometries to experimentally model realistic bacterial environments. 


B.S. (Genetics), University of Wisconsin, 2011
Ph.D. (Microbiology), Indiana University, 2016
Post-doc, Princeton University, 2016-2020

Additional Campus Affiliations

Assistant Professor, Biochemistry

Highlighted Publications

Sanfilippo, J.E., Lorestani, A, Koch, M.D., Bratton, B.P., Siryaporn, A., Stone, H.A., and Gitai, Z. Microfluidic-based transcriptomics reveal force-independent bacterial rheosensing. Nature Microbiology (2019).

Sanfilippo, J.E., Garczarek, L., Partensky, F. and Kehoe, D.M. Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis. Annual Review of Microbiology (2019).

Sanfilippo, J.E., Nguyen, A. A., Partensky, F., Karty, J. A., Strnat, J.A., Garczarek, L., Schluchter, W.M. and Kehoe, D.M. Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus. PNAS (2019).

Sanfilippo, J.E., Nguyen, A. A., Karty, J. A., Shukla, A., Schluchter, W.M., Garczarek, L., Partensky, F., and Kehoe, D.M. Self-regulating genomic island encoding tandem regulators confers chromatic acclimation to marine Synechococcus. PNAS (2016).

Recent Publications

Padron, G. C., Shuppara, A. M., Palalay, J. J. S., Sharma, A., & Sanfilippo, J. E. (2023). Bacteria in Fluid Flow. Journal of bacteriology, 205(4).

Padron, G. C., Shuppara, A. M., Sharma, A., Koch, M. D., Palalay, J. J. S., Radin, J. N., Kehl-Fie, T. E., Imlay, J. A., & Sanfilippo, J. E. (2023). Shear rate sensitizes bacterial pathogens to H2O2 stress. Proceedings of the National Academy of Sciences of the United States of America, 120(11), Article e2216774120.

Palalay, J. J. S., Simsek, A. N., Reed, J. L., Koch, M. D., Sabass, B., & Sanfilippo, J. E. (2023). Shear force enhances adhesion of Pseudomonas aeruginosa by counteracting pilus-driven surface departure. Proceedings of the National Academy of Sciences, 120(41), Article e2307718120.

Haney, A. M., Sanfilippo, J. E., Garczarek, L., Partensky, F., & Kehoe, D. M. (2022). Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation. mBio, 13(4).

Li, Y., Sanfilippo, J. E., Kearns, D., & Yang, J. Q. (2022). Corner Flows Induced by Surfactant-Producing Bacteria Bacillus subtilis and Pseudomonas fluorescens. Microbiology Spectrum, 10(5).

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