Method to Characterize Bacteria in Three-Dimensional Porous Media

Web Published:

Princeton Docket #19-3572

Researchers at Princeton University have developed a novel method to characterize bacteria motion, self-organization, structure, and biological behavior in three-dimensional (3D) porous media by injecting them into a jammed hydrogel matrix. The matrix is self-healing and supports the weight of the bacterial cells, enabling them to be injected to form any 3D structure and with any composition of bacteria. The matrix is also transparent, enabling the cellular positions, motions, and genetic processes to be visualized using fluorescence microscopy. Since the matrix is self-healing, individual cells can be targeted and removed for off-line biological assays without perturbing the rest of the bacterial community.



• To study microbial interactions, such as in gut microbiome, lung microbiome, microbial pathologies, environmental microbiology

• Fundamental microbiology studies



• Ability to target and recover bacteria for biological assaying

• Ability to simultaneously define bacterial communities of controlled 3D structures and compositions, visualize their structures and development, probe biological processes through fluorescence, and recover cells for off-line assays



• Tapomoy Bhattacharjee and Sujit S. Datta. “Bacterial Hopping and Trapping in Porous Media.” Nature Communications, Nature Publishing Group, 6 May 2019,


Intellectual Property

Patent protection is pending. Princeton is currently seeking commercial partners for further development and commercialization of this technology.


The Inventors


Sujit Datta

Sujit Datta is an Assistant Professor of Chemical and Biological Engineering at Princeton University. He is also an Associated Faculty at the Andlinger Center for Energy and the Environment and the Princeton Institute for the Science and Technology of Materials. He earned a BA in Mathematics and Physics and an MS in Physics in 2008 from the University of Pennsylvania, where he studied nanomaterials like graphene and carbon nanotubes with Charlie Johnson. He earned his PhD in Physics in 2013 from Harvard, where he studied fluid dynamics and instabilities in porous media and colloidal microcapsules with David Weitz. His postdoctoral training was in Chemical Engineering at Caltech, where he studied the biophysics of the gut with Rustem Ismagilov. He joined Princeton in 2017, where his lab seeks to understand and control the behavior of soft materials in complex settings, motivated by applications like oil/gas recovery, water remediation, carbon sequestration, and drug delivery. Prof. Datta is the recipient of the LeRoy Apker Award for outstanding achievements in Physics, the Andreas Acrivos Award in Fluid Dynamics from the American Physical Society, the Alfred Rheinstein Faculty Award, and the ACS Petroleum Research Fund New Investigator Award.


Tapomoy Bhattacharjee

Dr. Tapomoy Bhattacharjee is a distinguished postdoctoral research associate at the Andlinger Center for Energy and the Environment of the Princeton University. He received his B.S. degree in chemical engineering from the Jadavpur University in 2012. He earned an MS in chemical engineering in 2014 from the University of Florida. He earned his MS and PhD degree in mechanical engineering from the University of Florida in 2015 and 2018 respectively. During his doctoral research Dr. Bhattacharjee studied cells in jammed microgels with Prof. Thomas Angelini. He is currently working with Prof. Sujit Datta on understanding and controlling the behavior of bacterial colonies in porous media. Dr. Bhattacharjee is the recipient of the National Merit Scholarship by the Government of India, Outstanding International Student Award and Gator Engineering Creativity Award by University of Florida.



Prabhpreet Gill

Princeton University Office of Technology Licensing

(609) 258 – 3653 |


Patent Information:
For Information, Contact:
Prabhpreet Gill
Licensing Associate
Princeton University
Sujit Datta
Tapomoy Bhattacharjee