Joshua Shrout Concurrent Associate Professor

Microbiology/Bacteriology: Community and motility behavior of bacteria
Joshua Shrout

Research Interests:

The Shrout Lab is interested to better understand how bacteria function in response to their environment. We are particularly interested in the "sociomicrobiology" and motility of bacteria where bacteria act at a community level. Bacterial community behavior is important to many different aspects of bacteria, including: survival, infection, symbiosis, elemental cycling, and pollutant degradation. We have relatively recently come to understand that surface-attached biofilms represent the dominant mode of bacterial growth. Thus, many studies of bacteria growing in test tubes cannot be translated to understand bacterial function in the “real world”. There are many biofilm-related global scale issues that pertain to 1) bacterial infections, 2) engineered water treatment, 3) corrosion of water distribution infrastructure, 4) hospital-acquired infections on medical devices (e.g., artificial joints, implants, catheters, etc.), and 5) biogeochemical cycling in nature. The Shrout Lab at Notre Dame seeks answers to these biofilm and bacterial community-associated problems by conducting fundamental research to understand cell-cell signaling and surface colonization of bacteria.

Most of this work is conducted using either Pseudomonas aeruginosa or Myxococcus xanthus. We use a variety of classic microbiology and molecular biology techniques in addition to microscopy and collaborate routinely with colleagues in Chemistry, Biology, Engineering, and Applied Mathematics to discern bacterial community behavior. Our research is currently funded by NIH and DOE.



  • Associate Professor, Department of Civil & Environmental Engineering and Earth Sciences, University of Notre Dame 2012-Present
  • Concurrent Appointment, Department of Biological Sciences, University of Notre Dame 2011-present
  • Member, Eck Institute for Global Health, University of Notre Dame 2008-present
  • Guest Scientist, Department of Ecophysiology-Lotte Søgaard-Andersen Group, Max Planck Institute for Terrestrial Microbiology 2015
  • Assistant Professor, Department of Civil Engineering and Geological Sciences, University of Notre Dame 2007-2012
  • Senior Fellow/Post-Doctoral Fellow, Department of Microbiology, University of Washington/University of Iowa 2003-2007
  • Ph.D., University of Iowa—Civil and Environmental Engineering 2002
  • M.S., Marquette University—Civil and Environmental Engineering 1998
  • B.S., Northwestern University—Environmental Engineering 1994


Seleted Professional Activities:

  • Editorial Board Member, Applied and Environmental Microbiology 2013-2021
  • Editorial Board Member, Journal of Bacteriology 2020-2022
  • Member, American Society of Microbiology
  • Member, American Association for the Advancement of Science