Shannon Sirk (Bioengineering), who has served as Associate Director since MSI launched in 2020, has transitioned into the role of Director following the departure of founding director Cari Vanderpool (Microbiology).
MSI was launched through the Provost’s Investment for Growth program to coordinate microbiome faculty hiring across five colleges and to develop an online MS degree program. Under the leadership of founding director Cari Vanderpool, the Initiative built momentum quickly — bringing together researchers from multiple colleges, launching networking workshops, strengthening interdisciplinary grant development, and advancing the vision of a data-integrated, systems-level approach to microbiome research. We are grateful to Cari Vanderpool for her visionary leadership in launching the Initiative and building a strong foundation. And we are enthusiastic about what comes next.
Today, MSI supports a campus-wide network of more than 400 members across 13 colleges and over 60 academic units. From its inception, MSI has prioritized community: supporting trainees, creating spaces for collaboration, and positioning Illinois as a leader in cross-disciplinary microbial science. The Initiative has fostered connections among microbiologists, engineers, data scientists, clinicians, agricultural scientists, and computational researchers. Through its newsletter, website, and events, MSI maintains visibility for microbial research and supports professional development across disciplines.
Looking ahead, MSI will continue to strengthen research coordination, support trainees, and expand interdisciplinary visibility. In May 2026, Illinois will host the Midwest Microbiome Symposium, a regional meeting rotating with Purdue and Ohio State, further reinforcing the university’s leadership in microbial systems science.
As Director, Shannon Sirk brings a research program that sits squarely at the interface of bioengineering and microbial systems science. An Associate Professor in Bioengineering, with affiliations spanning Microbiology, the Carl R. Woese Institute for Genomic Biology, the Cancer Center at Illinois, and Carle Illinois College of Medicine, she leads a lab focused on engineering commensal microbes as living therapeutic platforms.
Her group develops molecular toolkits that enable gut-resident bacteria to produce and secrete functional proteins in vivo. In 2024, her team published a Nature Communications study describing a protein secretion toolkit for multiple Bacteroides species, expanding the experimental and translational potential of these key gut microbes. Complementing this work, her lab engineers therapeutic cargo itself, including antibody fragments modified with short FcRn-binding peptides to improve stability and transport. Earlier foundational research includes a 2020 Cell paper identifying a microbial pathway responsible for activating dietary glucosinolates in the human gut.
Sirk's work has been recognized with an NIH NIBIB Trailblazer R21 Award, an American Lung Association COVID-19 Respiratory Virus Research Award, and selection as an inaugural Chan Zuckerberg Biohub Chicago Investigator.
We are excited for this next chapter of MSI under her direction and look forward to the energy, vision, and momentum she brings to advancing microbial systems research at Illinois.
