Microbial Systems Initiative

A New Chapter for the Microbial Systems Initiative

microbialsystems@illinois.edu (MSI) — Mon, 23 Feb 2026 08:00:00 CST

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.

Researcher Spotlight | Santiago Mideros, PhD

microbialsystems@illinois.edu (MSI) — Wed, 30 Oct 2024 14:00:00 CDT

Santiago Mideros is an Assistant Professor in the Department of Crop Sciences at the University of Illinois. His research focuses on developing precision disease management methods for major crop pathogens using genomic tools to identify and characterize pathogen strains. His work aims to improve disease detection and management for key field crops like wheat, maize, and soybeans.

Researcher Spotlight | Rebecca Lee Smith, DVM, PhD

microbialsystems@illinois.edu (MSI) — Fri, 27 Sep 2024 08:00:00 CDT

Becky Smith is an Associate Professor of Epidemiology at the University of Illinois College of Veterinary Medicine, specializing in infectious disease surveillance and control through mathematical modeling. Her research focuses on the transmission of diseases at the human-animal-environment interface, including vector-borne and water-borne pathogens. Becky holds a PhD in Epidemiology from Cornell University and an MS in Biosecurity from Kansas State University, along with a DVM from Cornell. She is actively involved in advancing One Health research and collaborates across several interdisciplinary health sciences institutes, including the Institute for Genomic Biology and the Carle-Illinois College of Medicine.

MSI Year in Review

microbialsystems@illinois.edu (MSI) — Thu, 23 May 2024 08:00:00 CDT

As we close out the 2023-24 academic year, we reflect on the achievements and growth within the Microbial Systems Initiative. This year, our efforts have centered around fostering connections, advancing research, and supporting the professional growth of our community. Here’s a look at how these priorities have shaped our activities over the past year.

Researcher Spotlight | Christopher J. Fields, PhD.

microbialsystems@illinois.edu (MSI) — Fri, 26 Apr 2024 08:00:00 CDT

Christopher J. Fields is the Director of HPCBio, where he develops genomic analysis infrastructure and manages high-throughput data processing workflows. His work includes implementing pipelines like MAKER and Interproscan and tailoring solutions for specific research needs. He collaborates with the IGB Computer Network Resource Group on scalability and efficiency. Chris earned his PhD in Molecular Microbiology from the University of North Texas, where he also completed his undergraduate studies in Biology. A seasoned BioPerl core developer, Chris contributes to several open-source bioinformatics projects and serves as the Secretary of the Board for the Open Bioinformatics Foundation, promoting advancements in the field.

Researcher Spotlight | Maria Elisa Caetano-Silva, PhD.

microbialsystems@illinois.edu (MSI) — Wed, 27 Mar 2024 15:30:00 CDT

Maria Elisa Caetano-Silva is currently a postdoctoral associate in Integrative Microbiota & Physiology under Jacob Allen in the Department of Health and Kinesiology. Her work explores the intersection of psychological stress, epithelial ROS signaling, and their impact on mucosal dysfunction and colitis predisposition. She earned her PhD in Food and Nutrition from the University of Campinas, including a stint at the University of Valencia, Spain, and holds a Bachelor's degree in Food Science from the University of São Paulo and the University of Trás-os-Montes and Alto Douro, Portugal. With over a decade of experience in research spanning food science, neuroimmunology, and integrative microbiota, Caetano-Silva is deeply passionate about advancing science in these interdisciplinary fields.

Researcher Spotlight | Alvaro G. Hernandez, Ph.D.

microbialsystems@illinois.edu (MSI) — Thu, 22 Feb 2024 08:30:00 CST

Alvaro Hernandez serves as the Director of DNA Services at Roy J. Carver Biotechnology Center, leading the next-generation sequencing division for both academic and corporate partners. After joining the Roy J. Carver Biotechnology Center in 2001 as a postdoctoral student, he became Assistant Director in 2005 and Director in 2008. Hernandez is an expert in next-generation sequencing, focusing on DNA and RNA sample preparation for NGS. The DNA Services lab provides advanced equipment and expertise to faculty, private, and academic collaborators.

Researcher Spotlight | Sierra S. Raglin, Ph.D.

microbialsystems@illinois.edu (MSI) — Thu, 16 Nov 2023 15:30:00 CST

Sierra Raglin is a postdoctoral research fellow in Angela Kent's Microbial Ecology Research Lab. She received her B.S. in Animal Science at Rutgers and completed her Ph.D. in Natural Resources and Environmental Sciences from The University of Illinois in 2023. Her fellowship is within the Infection Genomics for One Health research theme at the Carl R. Woese Institute for Genomic Biology (IGB). Her current research focuses on how humans manipulate soil microbiomes in agricultural systems, including through crop breeding and management practices.

Researcher Spotlight | Guillermo L. Monroy, Ph.D.

microbialsystems@illinois.edu (MSI) — Mon, 23 Oct 2023 08:00:00 CDT

Guillermo Monroy is a postdoctoral research associate in Stephen Boppart's Biophotonics Imaging Laboratory at the Beckman Institute for Advanced Science and Technology. He received his B.S., M.S., and Ph.D from the University of Illinois. He completed a postdoctoral ORISE Fellowship with the Division of Biomedical Physics in the Office of Science and Engineering Laboratories (OSEL), at the FDA before returning to Illinois in 2020. Monroy's research on diagnostic imaging for otitis media focuses on developing new therapeutic techniques that avoid antibiotics and preserve patients’ microbial diversity.

Empowering Collaboration and Innovation: Highlights from the 2023 Microbial Multiverse Symposium

microbialsystems@illinois.edu (MSI) — Fri, 29 Sep 2023 12:00:00 CDT

The 2023 Microbial Multiverse Symposium, hosted by the Microbial Systems Initiative (MSI) September 14-16, manifested a vital component of MSI’s priorities to promote collaboration, advance research, and support faculty and trainees. The event served as a unique opportunity for microbial systems researchers across campus to convene and connect.

Microbial Multiverse Symposium lines up national speakers, strengthens bonds across disciplines

microbialsystems@illinois.edu (MSI) — Thu, 24 Aug 2023 12:00:00 CDT

The 2023 Microbial Multiverse Symposium on September 14-16, 2023 will highlight MSI’s work by showcasing the breadth of microbial systems research on campus and how this work is driven through collaboration. This event brings together microbial systems researchers from across the nation and calls attention to the work of Illinois investigators and trainees.

Reflecting on a year of MSI Community

microbialsystems@illinois.edu (MSI) — Thu, 18 May 2023 12:00:00 CDT

In 2019, nearly 100 people came together to explore what it would mean to build community and collaboration among microbiome and microbial sciences researchers at Illinois. Four years later, the community includes nearly 400 members engaging and collaborating in exciting ways. While the Microbial Systems Initiative (MSI) team fosters collaboration and networking, participation from Illinois researchers and trainees created this community. As the academic year wraps up, we reflect on the programming and events that brought us together.

Researcher Spotlight | Wenyan Mei, PhD

microbialsystems@illinois.edu (MSI) — Mon, 17 Apr 2023 10:00:00 CDT

Wenyan Mei is a professor in the Department of Comparative Biosciences in the College of Veterinary Medicine. She earned her Ph.D from Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences and completed a postdoc at the University of Pennsylvania School of Medicine. Her lab investigates the reciprocal interactions between the host and gut microbiota and their impact on host health. Current work includes the development of knockout mouse models and germ-free zebrafish lines to study the impact of potentially disease-promoting microbes.

Researcher Spotlight | Matthew Stasiewicz, PhD

microbialsystems@illinois.edu (MSI) — Wed, 22 Mar 2023 10:00:00 CDT

Dr. Matthew Stasiewicz is an associate professor of Applied Food Safety in the Department of Food Science and Human Nutrition at the College of Agricultural, Consumer and Environmental Sciences.He earned his Ph.D. and M.S. in Food Science at Cornell University, a B.S. in Biosystems and Agriculture Engineering, and a B.A. in Philosophy from Michigan State University. His work focuses on applying engineering and data analytic approaches to modern microbiology problems to advance food safety microbiology with the mission of leveraging food safety innovation to achieve food security.

MicroERA Symposium highlights trainee accomplishments; offers opportunities to develop crucial skills

microbialsystems@illinois.edu (MSI) — Thu, 16 Feb 2023 08:00:00 CST

The Microbial Early-career Researchers Association will host the 3rd Annual MicroERA Research Symposium on Monday, April 10, 2023 at the Campus Instructional Facility. Trainees can submit an abstract by March 1 to give a poster presentation or lightning talk.

Researcher Spotlight | Sumiti Vinayak Alam, PhD

microbialsystems@illinois.edu (MSI) — Wed, 15 Feb 2023 10:00:00 CST

Dr. Sumiti Vinayak Alam is an associate professor of parasitology in the Department of Pathobiology at the College of Veterinary Medicine. She received her PhD from All India Institute of Medical Sciences (AIIMS) and completed postdoctoral training at the Center for Tropical and Emerging Global Diseases at University of Georgia. Her reseach in the Vinayak Lab is focused on the protozoan parasite Cryptosporidium parvum, a leading cause of diarrheal disease and mortality in young children and ruminant livestock. The lab uses a combination of molecular genetics, cellular biology, and animal infection models to study parasite biology and identify new targets for the development of effective therapies against cryptosporidiosis. Their three main research focus areas are unraveling signaling mechanisms that regulate the proliferation and development of Cryptosporidium, identifying and genetically validating new anti-cryptosporidial drug targets, and developing new genetic tools to study parasite gene function.

New faculty contribute to MSI Community’s growth and success

microbialsystems@illinois.edu (MSI) — Mon, 23 Jan 2023 12:00:00 CST

Since 2020, the Microbial Systems Initiative (MSI) has welcomed 11 new faculty into our research community across six departments, including Animal Sciences, Biochemistry, Kinesiology and Community Health (KCH), Pathobiology, Microbiology, and Statistics. Seven of these faculty were hired through the strategic hiring plan facilitated by MSI and funded through the Investment for Growth Program. To learn more about how cluster hires facilitate long-term institutional success, check out this recent story from the Carl R. Woese Institute for Genomic Biology (IGB).

Researcher Spotlight | Holly Tuten, PhD

microbialsystems@illinois.edu (MSI) — Mon, 21 Nov 2022 10:00:00 CST

Dr. Holly Tuten is an associate scientist and vector ecologist at the Prairie Research Institute. She received her PhD from Clemson University and completed postdoctoral training at the University of Kentucky on Wolbachia-modified mosquitoes and at the Institute of Parasitology at the University of Zurich on invasive vectors. She has also worked as a risk analyst for invasive species introductions at USDA. At the Illinois Natural History Survey, she leads the statewide tick & tick-borne pathogen surveillance program in collaboration and supported by the Illinois Department of Public Health and CDC. This program updates our knowledge of the distribution and abundance of ticks of human health importance throughout the state, and tests ticks collected by ourselves and partners at public health districts, forest preserve districts, and other stakeholders for a suite of tick-borne pathogens. Data are shared and presented on maps on the IDPH website with ongoing updates, to provide the public and health care providers with the most up-to-date information regarding potential tick-borne disease exposure people may experience throughout the state. Other research interests include regulatory issues regarding genetically-modified vectors, development of taxonomic resources for vectors, developing control measures for vector-borne diseases, and developing training and outreach materials related to tick-borne disease prevention.

Why networking is still important to your research and three easy ways to reach out

ressing@illinois.edu (Sara Ressing) — Wed, 19 Oct 2022 15:45:00 CDT

Networking is a critical competency in today’s rapidly changing environment. Research shows that strong and diverse networks help researchers generate more innovative ideas. Networking enables shared learning, new research opportunities and research projects, joint applications for funding, technology transfer, and more citations of published works. MSI facilitates a variety of networking opportunities as part of our mission to strengthen microbial sciences research and education at Illinois. Read more about how networking can benefit your research.

Researcher Spotlight | Kristin R. Farley, PhD

microbialsystems@illinois.edu (MSI) — Wed, 21 Sep 2022 08:00:00 CDT

Dr. Kristin Farley is a postdoctoral fellow in the Vanderpool Lab in the Department of Microbiology and serves as one of two postdoctoral advisors for the Microbial Early-Career Researchers Association (MicroERA).

Introducing the Inaugural MicroERA Executive Board

ressing@illinois.edu (Sara Ressing) — Tue, 23 Aug 2022 14:45:00 CDT

MicroERA aids in carrying MSI’s educational mission through the sponsorship of networking and professional development opportunities for trainees and post docs. MicroERA has continued to grow and develop since its inception. In 2021, MicroERA began the process of organizing as a registered student organization. Meet the inaugural executive board.

Researcher Spotlight | Yumi Iwadate, PhD

microbialsystems@illinois.edu (MSI) — Wed, 27 Jul 2022 08:00:00 CDT

Dr. Yumi Iwadate is a postdoctoral fellow in the Slauch Lab in the Department of Microbiology and serves as one of two postdoctoral advisors for the Microbial Early-Career Researchers Association (MicroERA).

Should you join an MSI writing group this fall? Two faculty weigh in

meberg@illinois.edu (Maggie Berg) — Tue, 26 Jul 2022 14:45:00 CDT

After a successful pilot year, the Microbial Systems Initiative is organizing another round of MSI writing groups for the 2022-2023 academic year. If you have never been a part of a writing group before, you might be wondering what it is and why you might join one. Adrienne Antonson, assistant professor of Animal Sciences, and Chris Gaulke, assistant professor of Pathobiology, shared their thoughts on how the MSI writing groups were a boon to their productivity and career development. Learn more about writing groups and how the MSI writing groups have helped these faculty members reach important research goals.

MSI Administrator Spotlight | Sara Ressing, M.S., M.S.Ed.

microbialsystems@illinois.edu (MSI) — Tue, 21 Jun 2022 08:00:00 CDT

Sara Ressing is the visiting assistant director of the Microbial Systems Initiative. She began this role in September 2021 to implement the mission and educational plans of MSI and lead the development and delivery of the forthcoming Microbial Systems Analytics MS program within the School of Molecular and Cellular Biology.

Researcher Spotlight | Thomas Kehl-fie, PhD

microbialsystems@illinois.edu (MSI) — Thu, 26 May 2022 08:00:00 CDT

Dr. Thomas Kehl-Fie is an assistant professor in the Department of Microbiology. Dr. Kehl-fie's research is focused on exploring bacterial and antibiotic resistant infections and gaining a more complete understanding of what is important for pathogens to cause infections and disease. The Kehl-Fie lab is also focused on leveraging interdisciplinary microbiological approaches, biochemical studies and advanced elemental analysis in order to understand how nutrient starvation impacts bacterial pathogens during infection and identify new opportunities for therapuetic intervention. In his researcher spotlight, Dr. Kehl-Fie discusses how his research aims to make positive impact on human health and its ties to the collaborative environment of the Illinois community.