Bugs as Drugs: Engineering Bacterial Biotherapeutics

Seminar Details
Wednesday, May 5, 2021 - 9:00pm to 10:00pm


Shannon J. Sirk, Ph.D.
Assistant Professor, Department of Bioengineering, University of Illinois Urbana-Champaign
Assistant Professor, Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine
Affiliate, Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
Associate Director, Illinois Microbial Systems Initiative



The human body is a complex ecosystem supporting symbiotic relationships with thousands of microbial species. The ubiquity and importance of these commensal communities underscore their potential as an untapped reservoir of biological function, and recent increased interest into commensal microbial species has led to countless insights in this field. Due to these efforts, the opportunity now exists to capitalize on the increasingly sophisticated understanding of the human microbiota and expand research efforts beyond characterization, toward engineering. Commensal microbes are already perfectly suited for safe and effective habitation and colonization of various physiological niches; what remains is to harness their genomic plasticity and promote their capacity to function as robust biochemical factories. The Sirk Lab aims to engineer therapeutic capacity into commensal microorganisms to address unmet needs in human health, with a specific focus on generating strains of human gut bacterial species that can produce disease-fighting biological compounds in the intestinal tract to address key limitations with current therapeutic approaches for important diseases such as recurrent gastrointestinal infections. We are also pursuing studies focused on respiratory disease in both humans and animals of agricultural relevance.  


Prof. Sirk received her AB in Biology from Occidental College in Los Angeles, CA and her Ph.D. in Molecular and Medical Pharmacology from UCLA. Her doctoral studies focused on engineering antibody fragments for targeted tumor imaging using positron emission tomography. Her postdoctoral training began at The Scripps Research Institute in La Jolla, CA, where she continued to work with engineered antibodies while also performing detailed protein engineering studies to generate site-specific nucleases and recombinases for targeted genome modifications, in the era immediately prior to the introduction of CRISPR-based gene editing technology. She then pursued further postdoctoral training at Stanford University where she first began to explore the world of commensal microbes by studying the role that gut bacteria play in the activation of drug-like dietary molecules. At the University of Illinois, her research group aims to leverage the power of protein engineering, therapeutic biomolecules, and the ever-expanding opportunities of commensal microbial species and communities to address critical needs in disease prevention and treatment in humans, animals, insects, and plants.