(7e) Microbiome Engineering for Human Health and Agricultural Productivity

Microbial communities are ubiquitous in nature and contribute to human health, agricultural productivity, and industrial and environmental processes. Organisms within these communities exchange metabolites, actively inhibit or enhance growth of each other, and have direct and indirect interactions with their environment. Despite the impact these communities can have on our lives, we do not yet know how to control their behavior. To enable the engineering of microbial community function, my research program will use experimental data from natural and model microbiomes to develop predictive models to engineer complex emergent behavior of microbial communities.

Human Microbiome: My current research is focused on microbes that colonize the human skin, and how they impact wound healing, attraction/repulsion of biting insects, and interaction with the immediate environments. Microbiome representatives from the human skin have diverse activities including secretion of host-responsive metabolites, UV resistance, production of volatile organic compounds, and secretion of pigments such as melanin. In this work we focus on developing systems to study model communities of skin microbiota and determine how their diverse functions are combined to impact human health. Our overarching goals it to modulate the microbiome in situ to promote positive outcomes in wound healing and interaction with the environment.

Microbiomes in Agriculture: In agricultural systems, plant-associated microbes contribute to disease resistance, drought tolerance, and nutrient uptake. Plant systems are amenable to microbiome engineering research, as germ-free plants are easily generated and induced phenotypes are easily measured. My research group will interface with agricultural sciences to solve current and emerging problems in agricultural productivity, including the rapidly approaching peak phosphorous, inefficient fertilizer uptake, and the spread of emerging plant pathogens.

My research group will build on the above research by using engineering principles to design communities of genome-sequenced bacterial isolates using individual phenotypes, phylogenetic relationships, and predicted genomic content and test the ability of the community to mimic the natural microbiome response to stress. Models of bacterial growth kinetics, metabolism, and interactions in culture conditions will be used to predict behavior in a community. Integrating quantitative experimental data with predictive models will help us understand how the microbiome assembles in nature, ultimately leading to the ability to engineer constructed communities of bacteria with specific and predictable functions.

PhD Dissertation: Kinetics of vesicular stomatitis virus mRNA and genomes during infection

Mentor:John Yin, University of Wisconsin-Madison, Department of Chemical and Biological Engineering

Research Career

My research career began as an undergraduate where I studied gas hydrate formation at the Colorado School of Mines. I helped develop software for predicting hydrate formation in gas pipelines and tested predictions using a novel reactor in the laboratory. This valuable experience familiarized me with quantitative experiments and laboratory techniques, but more importantly convinced me to go to graduate school to continue my academic career. In graduate school I changed my focus to biological engineering, where I learned how to design experiments and control biological systems to make quantitative measurements of viral replication. I used the data I collected to build kinetic models of viral infection, and showed that viral mRNA production is independent from host environment and only depends on viral genome number. This suggests that transcription is robust and insensitive and helps to identify targets for anti-viral strategies for RNA viruses. While studying interactions between two organisms (viruses and cells), I became interested in complex ecological systems with multi-member interactions. I was fortunate to find a post-doctoral position as a part of the Plant-Microbe Interfaces project at Oak Ridge National Laboratory studying the microbiome of Populus trees. At ORNL I learned about the contribution of the plant microbiome to host growth and productivity. I am currently at the Johns Hopkins University Applied Physics Laboratory, where our goal is to engineer biological systems to meet the needs of the Department of Defense. At APL I am studying the microbiome of the human skin and how it contributes to wound healing and interaction with the immediate environment of the host. In my postdoctoral studies, I have focused specifically on understanding bacterial genetic and phenotypic diversity in the system to help determine how interactions between microbiome members and the host lead to overall system function.

Teaching Interests:

As I have moved through my academic career I have become more active in my role as a teacher and mentor. During my undergraduate studies I worked closely with many of my peers, and began to appreciate the different learning and teaching styles present in the group. I had the opportunity to informally tutor younger students in heat and mass transfer classes; in both cases their grades improved after we began working together. In graduate school I got my first opportunity to formally teach classes to students. As a teaching assistant for the introductory transport course, I enjoyed spending time developing lectures and example problems for students, and focused on how I could engage the entire class in a single topic. I also worked as a TA for the process control laboratory where I helped students run experiments and taught them to present their results in concise reports. As a post-doc I have worked with undergraduate summer students and new graduate students from chemistry, biochemistry, biological systems engineering and chemical engineering. Their unique backgrounds have helped me generalize my teaching methods. I have helped them learn how to work in the laboratory, analyze data, and present results. The students helped identify metabolic pathways, isolated bacteria that grow on Populus metabolites, identified genes that affect plant growth, and developed methods for studying root growth in microfluidic devices. Watching students succeed with my input has been extremely important to my development and has helped me appreciate the commitment of my teachers and mentors throughout my academic career.