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Viral micro-epidemics and evolutionary dynamics in bacterial biofilms


Bacteria build microscopic communities, termed biofilms, and much like human communities, biofilms provide bacteria with stability and increased resilience. Biofilms can be beneficial, for instance in industrial wastewater treatment systems, or as part of a healthy gut microbiota. However, biofilms can also cause damage to various industrial and health systems, even resulting in potentially lethal drug-resistant infections. An important new approach in the control of biofilm populations is the prescriptive use of viral parasites, called phages, to attack harmful bacteria within the biofilms. Though biofilms and phages are ubiquitous in nature, little is known about biofilm-phage interactions. In this project, investigators will develop new techniques to spatio-temporally track the real-time spread of phage infections within biofilm colonies. Using an integrated computational simulation and experimental platform, researchers will investigate mechanisms by which phages infect biofilms, the existence and evolution of infection-resistance within biofilm-dwelling bacteria, and explore the possibility of leveraging the knowledge gained in the control of microbial community composition. In addition, as part of the educational broader impacts of the project, the PI will develop hands-on teaching modules for K-12 students in surrounding rural communities. <br/><br/>Biofilms are stress-tolerant bacterial communities composed of cells embedded in a secreted matrix of extracellular adhesives. The biofilm mode of growth is commonplace, existing within the microbiomes of living surfaces of plants and animals. Another ubiquitous feature of bacterial biofilms is exposure to bacteriophages. While biofilm-dwelling bacteria presumably encounter phages often, very little is known about bacteria-phage interactions within biofilms on the cellular scales that are crucial for understanding microbial evolution. This gap in understanding is due in part to the absence of appropriate theoretical and experimental techniques for interrogating phage-biofilm interactions. To address this gap, the PI proposes to develop and use techniques from individual-based modeling to simulate biofilm-phage interactions. Investigators will also develop a new experimental system to mimic biofilm-phage infection. The system will consist of Escherichia coli and phage T7 co-cultured in a microfluidic platform to enable direct visualization of the phage infection process using high-throughput confocal microscopy. Investigators will leverage their novel, integrated theoretical and experimental platform to study (1) the influence of phage exposure on the evolution of biofilm formation, and (2) the influence of biofilm architecture on the evolution of phage resistance. Anticipated outcomes from this research will lead to an increased understanding of the relatively unquantified bacteria-phage interaction dynamics within biofilms.<br/><br/>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Carey Nadell
Dartmouth College
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