With the Researcher Spotlight, the Microbial Systems Initiative aims to introduce you to the breadth and diversity of research interests and potential growth opportunities on the University of Illinois at Urbana-Champaign campus. We hope that by highlighting both the researchers and their research, we can help you to learn more about and connect with your colleagues to enhance multidisciplinary research and education in microbial sciences here at Illinois.
Shannon Sirk, PhD, is an assistant professor in the Department of Bioengineering, the Institute for Genomic Biology, and the Carle Illinois College of Medicine. Her research focuses on engineering beneficial traits into commensal microorganisms for therapeutic applications.
What is your research in microbial systems about?
We are trying to take some of the “beneficial microbes” that live in your gut and engineer them to be even more beneficial. Specifically, we are working to generate strains of human gut bacterial species that can produce disease-fighting compounds in the intestinal tract. Our goal is to address some of the key limitations with current therapeutic approaches for important diseases such as recurrent gastrointestinal infections and colorectal cancer. By delivering the therapeutic compound directly to the site of disease, rather than administering it intravenously as is currently done, we should be able to increase efficacy and decrease adverse side effects while also decreasing the costs associated with production and administration of conventionally manufactured biological therapeutics.
How are you conducting your research?
We use synthetic biology approaches to build and interrogate our microbial systems. Since we are working with largely uncharacterized gut bacterial species, we don’t have a lot of the tools that are available for standard, well-studied lab strains like E. coli. We therefore spend a lot of time identifying, replicating, and testing the genetic parts and cellular components that the bacteria need to produce our therapeutic compounds. Ultimately, we are building bacterial drug factories, and we use a systems approach to study how the parts function together to create functional living machines. As we begin to implement our technology and introduce the engineered strains into the natural microbial communities of the gastrointestinal tract, we will further explore the integration of the strains into, as well as their impact on, the existing host-microbial system.
How does being a part of the Illinois community support and enhance your research?
The environment here is strongly collaborative and hugely supportive of the research we do in my group. The recent establishment of the Microbial Systems Initiative on campus has really brought microbial systems biology research and microbiome research to the forefront and has brought together dozens of researchers from multiple disciplines that has resulted in a situation in which the whole is greater than the sum of its parts. As a bioengineer with a background in molecular biology, having access to the depth and breadth of expertise in microbiology and other areas has enhanced my ability to formulate and evaluate research strategies as well as carry out experiments that would otherwise be out of reach.
How will your research or work improve society or reach people?
Our overarching goal is to increase access to disease treatments; by “access” we mean delivering drugs to normally inaccessible body sites (such as the gut) as well as providing drugs at a reduced cost (by using the bacteria as on-site drug production machines that produce and deliver the drug inside the gastrointestinal tract). Because our focus is on biological therapeutics rather than traditional drugs, our approach has the potential to decrease antibiotic use, which would positively impact human health in a number of ways, as well as decrease negative side effects associated with treatments like chemotherapy.
Do you have a personal story to share or path that led to your interest in this area of study?
I think we all have personal stories of losing loved ones to disease, watching people we care about suffer, or indeed suffering ourselves through the physical and financial trauma of sickness. My path to this area of study began with a fascination at the inner workings of cells and has developed into a unique set of tools, skills, training, and perspective that allow me to formulate solutions to interesting and important problems that affect many people – some that I know and love, and some that I’ll never meet.
