(4kv) Collective Bacterial Responses in Complex Environments

Introduction:

Bacterial communities affect human health, particularly as infectious pathogens, and our understanding of these dynamic populations needs to consider both their complex natural environments and growth across scales. Microbiological research has begun to address single cell dynamics or spatially fixed biofilm communities, but these studies largely focused on traditional approaches using test tubes or plates. We still lack understanding of bacterial behaviors at the microcolony scale between single cells and large biofilms, as well as their responses in complex physiological environments – such as fluid flow, nutrient gradients, competitor invasion – that cannot be recapitulated in a test tube. It is necessary to develop tractable, controllable experimental systems that mimic physiological conditions to elucidate collective bacterial microcolony behaviors.

As an experimental researcher interested in bacterial populations, my work lies in the currently unfulfilled niche between bioengineering, microbiology, and collective systems. My PhD training as an experimental biophysicist studying mixed populations of antibiotic resistant and sensitive bacterial communities, combined with complex systems classes to develop my computational expertise, began my focus on collective systems. As a Fellow in the Center for the Physics of Biological Function at Princeton University, I continued studying collective systems across scales, from neural processing in the nematode C. elegans to bacterial populations in flow.

Current Research:

My current research focuses on bacterial populations in fluid flow, utilizing microfluidics, microscopy, and simulations. Reports of clinical endocarditis (heart infections) present counter-intuitive bacterial dynamics: bacterial vegetations preferentially colonize heart valves, areas with the narrowest cross sections in the heart and subsequently the highest shear rates. Given the high shear conditions, how do bacterial populations colonize heart valves?

To address this paradox, I created a tractable microfluidic system to study the effects of flow on bacteria microcolonies, examining Staphylococcus aureus and Enterococcus faecalis, two species implicated in endocarditis. My studies recapitulated the paradoxical increase in colonization in high flow, with these behaviors driven by mechanisms at the microcolony scale. S. aureus clustered microcolony dynamics are driven by signaling molecule transport: S. aureus quorum sensing molecules, called Autoinducing Peptides (AIPs), accumulate in low flow and drive a transcriptional response leading to cellular dispersal. However, in high flow, AIP is transported away by flow, leading to increased colonization. Unlike S. aureus, E. faecalis colonization is driven by mechanical effects on the chained microcolonies. The linear chains of E. faecalis are pushed towards the surface due to the torque from fluid flow. In higher flow conditions, this larger torque increases chain adherence and surface attachment following a chain breakage. For both species, I created mechanistic models to fully elucidate the dynamics driving bacterial microcolony behavior. Beyond specific mechanisms, my work further introduces the concept of microcolony morphologies (clusters or chains) and the direct impact these morphologies have in driving responses in complex fluid environments.

Future Research:

My interdisciplinary lab will continue my focus on bacterial communities in complex environments, beginning with flow environments. Given the success of my microfluidic studies, my first focus is to create host-mimicking microfluidic experiments: adding host-surface factors and introducing pulsatile flow or quake valves to mimic the heart beating. With tunable experimental designs, my lab will be able to precisely control the different environmental components and develop our understanding of the factors driving bacterial dynamics. Utilizing microscopy, transcriptional profiling, and computational modeling, our studies will monitor the mechanical and genetic dynamics. Continued study examining other pathogenic species and infectious conditions (urinary tract infections, lung infections), will provide new avenues of exploration where my lab can once again build our conceptual model of bacterial responses to flow as we increase the complexity of our microfluidic channels. In these studies, we will further consider the microcolony morphologies: do other species in flow environments form chains, clusters, or other distinct shapes, providing advantages in flow?

Beyond flow environments, our work will further expand to other environmental factors like nutrient gradients, antibiotics or phages, or competitor invasion. These studies will not only elucidate the bacteria’s mechanical or genetic responses, but will broadly focus on bacterial microcolony morphologies. Do bacteria with similar behaviors have similar morphologies, and what advantages (or disadvantages) arise from their morphologies? Furthermore, variability between species, or within the same species through morphology mutants, will provide opportunities to study community behaviors and how those behaviors respond in different environmental contexts. With the experimental techniques, analysis, and computational approaches from our earlier studies, we will be well positioned to extend our understanding of collective bacterial dynamics. Are there classes of morphologies that drive molecular and physical responses to flow, antibiotic or phage interaction, competitor invasion, or nutrient gradients? And will our knowledge of the interplay between microcolony morphologies and physiological environments help us modulate those behaviors to improve human health through novel diagnostics and treatments?

Teaching Interests:

As an interdisciplinary scientist, I experienced a range of teaching styles, finding the most beneficial experiences to be those where the professor engaged with the students, allowing student curiosity to shape our discussion. In my own teaching, I created an active learning style classroom environment, utilizing demos and promoting student led discussions. I look forward to teaching bioengineering and biophysical courses from introductory to graduate level. Furthermore, fluid dynamic, complex systems, and programming classes would be exciting courses to teach given my research and teaching expertise.

Teaching Experiences

I was a lecturer for the Princeton Physics department for two semesters, teaching Introductory Physics, which focused on mechanics. As a lecturer, I was responsible for three weekly lectures, holding office hours, creating weekly quizzes, and developing review materials. After discussing the main topics and equations, I had students work through problems both as a class and in small groups while I assisted and answered questions. Furthermore, I stressed commonalities across questions, helping students develop generalizable rules, instead of a rigid case-by-case approach. Additionally, none of my students were physics majors, with most being biology majors. I drew on my own biophysical background to connect the topics we were learning about (i.e. flow in different sized tubing) to relevant biological questions. I solicited questions for review, getting to know my students and which learning approaches (i.e. drawing diagrams, using demos) helped different students grasp particularly challenging concepts. In my future classes, I will continue these active learning strategies and connect with my students based on their interests and learning styles.

As a graduate student instructor, I taught two programming in the sciences courses, focused on MATLAB (graduate) and Python (undergraduate). I not only had to explain the scientific analysis, but further help students translate that analysis into a working program. Without those two crucial components- analysis and syntax- the students’ overall understanding would be lacking. As an educator, I have experience teaching multiple, related topics and the ability to link those pivotal concepts together, helping my students to become successful scientists.

Mentorship and Service

Beyond the classroom, I mentored students both inside and outside of the lab. Throughout my PhD, I mentored five undergraduates, teaching them lab techniques and analysis, as well as answering their questions about graduate school and research. As a postdoc, I mentored an undergraduate through Princeton ReMatch, a program designed to introduce first year students to research. I also mentored graduate students in lab as a senior graduate student and postdoc. I additionally volunteered as a mentor through women and minority in physics groups during my PhD and postdoc.

As a woman in STEM, I further dedicated time to service-oriented projects, focused on increasing minority access to STEM. As co-Chair of the 2023 Princeton Local Organizing Committee for the APS Conference for Undergraduate Women in Physics, I organized sessions geared towards learning about the subfields of physics as well as opportunities and resources for underrepresented students. I also recruited students from national diversity conferences (SACNAS, NSBP, ABRCMS) and organized outreach events with different women in physics and diversity focused groups, expanding my reach to K-12 schools.

I value my time as an educator, and I look forward my students’ excitement when they learn a new concept or solve a tough question. As an educator and mentor, it is necessary to not only be knowledgeable about the subject, but further be inclusive, engaging, and enthusiastic. These are all components I look to bring to my future classroom and lab.