Poonam Phalak

Poonam Phalak, 2nd Year
Program: Chemical Engineering
Advisor: Michael Henson
Education: Institute Of Chemical Technology (Formerly UDCT) Mumbai, India
Bachelor of Chemical Engineering (2005-2009)


Phalak, P., Chen, J., Carlson, R. P., & Henson, M. A. (2016). Metabolic Modeling of a Chronic Wound Biofilm Consortium Predicts Spatial Partitioning of Bacterial Species. BMC Systems Biology, 10(1), 90.

Chen, J., Gomez, J. A., Höffner, K., Phalak, P., Barton, P. I., & Henson, M. A. (2016). Spatiotemporal Modeling of Microbial Metabolism. BMC Systems Biology, 10(1), 1.

Henson, M. A. & Phalak, P. (2016). In silico Analysis of Clostridium difficile Biofilm Metabolism and Treatment,” Proc. Foundations of Systems Biology in Engineering, in press.

Research Summary

Biofilm Metabolic Modeling with Genome-scale Time and Spatial Resolution

I am participating in an interdisciplinary, NIH funded project on multiscale modeling of chronic wound biofilms. The goal of the project is to utilize a novel combination of biofilm reactor experiments, spatial metabolomics and transcriptomics, and computational modeling to better understand and treat chronic wound infections. My work focused on multiscale biofilm modeling is an essential component of the project. We have developed a general methodology for biofilm consortia modeling based on combining genome-scale metabolic reconstructions with fundamental transport equations that capture the relevant biofilm diffusional processes. Application of the method to a P. aeruginosa/S. aureus biofilm system generated exciting predictions concerning the impacts of biofilm thickness, spatial location of nutrient sources, metabolite cross-feeding, P. aeruginosa motility and P. aeruginosa mediated lysis of S. aureus on biofilm physiology. We recently published a paper on these findings in BMC Systems Biology.

I am currently building a genome-scale metabolic reconstruction of the chronic wound isolate Clostridium perfringens in collaboration with project team members from the Center for Biofilm Engineering (CBE) at Montana State University. The availability of this reconstruction will allow a biofilm model for the P. aeruginosa/S. aureus/C. perfringens system to be developed. We applying our modeling methodology to gut related diseases and cystic fibrosis where antibiotic treatment may be ineffective due to biofilm formation. We will publish a conference paper on Clostridium difficile biofilm formation/treatment in the proceedings of Foundations of Systems Biology in Engineering (FOSBE).