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Applied Microbiology Laboratory

Joshua Shrout


The Shrout Lab investigates bacterial community development processes, namely the development of bacterial biofilms.

Problems we are working on

Biofilms are surface-associated communities of bacteria encased in a self-generated matrix of polysaccharides, proteins, and nucleic acids. These biofilms are encountered in almost every imaginable environment and are important to environmental, industrial, and clinical scenarios. Biofilms are thus central to a myriad of scientific studies as we seek to understand bacterial colonization and function. Because many bacteria use self-driven motility during biofilm development, there is great importance associated with understanding how bacterial groups expand over surfaces and colonize them.


The Applied Microbiology Laboratory at Notre Dame is fully equipped to study bacteria using standard microbiological and molecular techniques. We also maintain a state-of-the-art confocal microscope used for spatial and temporal imaging of these complex bacterial communities.


a) Single-cell motility behavior of the bacterium Pseudomonas aeruginosa. In collaboration with Gerard Wong at UCLA, we recently identified that the bacterium Pseudomonas aeruginosa can stand upright and "walk". We are now working to determine the environmental conditions necessary to promote walking and how it is regulated at the cell level.
b) Group cell-cell signaling and swarming behavior of Pseudomonas aeruginosa. We recently showed that specific surfaces impair the ability of Pseudomonas aeruginosa to use chemical signal communication called quorum sensing. We are working to understand why bacteria show varied behavior when growing differing surfaces.
c) Single-cell and coordinated motility behavior of Myxococcus xanthus. The soil bacterium Myxococcus xanthus is an important soil bacterium that degrades complex organic material. This bacterium coordinates its movement using at least two mechanisms but it remains to be understood how the actions of these two mechanisms are coordinated amongst large groups of bacteria moving together.

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