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).
Supporting the success of the new hires has been a high priority for the MSI Leadership Team since the original cohort arrived in Fall 2020. To increase capacity to support the new faculty, Bioengineering Professor Shannon Sirk joined the MSI Leadership team as Associate Director. As a junior faculty herself, Sirk understands first-hand the points of confusion and bottlenecks during the startup years.
To address these points of confusion and to help the new hires take advantage of the robust microbial systems community that exists at Illinois, Sirk and the MSI team organized “Getting Started at Illinois.” Each webinar in the four-part series was led by a panel of established investigators who shared their experiences and lessons learned regarding research, teaching, and service.
Sirk said, "I’m excited to contribute to the Getting Started at Illinois series, since our goal is to provide targeted support and guidance for new faculty, especially in those first few months when everything is foreign and hectic."
The new cohort’s arrival to campus was further complicated by pandemic-related restrictions on in-person gatherings. The MSI team responded to this challenge by finding ways to virtually introduce the new hires to campus, starting with a new faculty welcome event and a virtual introduction to the cohort in the MSI newsletter. The 2021 Microbial Systems Initiative Virtual Symposium featured the research of many of these new faculty to increase their visibility in the MSI community as well.
These early efforts have paved the way for faculty to find a home at Illinois and contribute to our campus’ highly collaborative research environment. For instance, Microbiology and Statistics Professor Pamela Martinez and Biochemistry Professor Nicholas Wu have worked with seasoned investigators like Professors Rebecca Smith and Christopher Brooke on some of Illinois’ important COVID-19 research. Pathobiology Professor Christopher Gaulke is also collaborating with senior researchers like Professors Sharon Donovan, Jodi Flaws, and Wenyan Mei on research examining the roles of the gut microbiome and herbicide exposure in the development of obesity.
The new faculty are also collaborating with each other. Animal Sciences Professor Brett Loman and KCH Professor Jacob Allen have even published a paper on the role that psychological stress plays in intestinal health.
These faculty are involved on campus in a variety of ways. In addition to the Microbial Systems Initiative, they joined many other interdisciplinary centers and communities across the Illinois campus, including the Personalized Nutrition Initiative, the Cancer Center, and IGB. Pamela Martinez is affiliated with the Center for Latin American & Caribbean Studies.
Our newest faculty member, Alicia Kraay, professor in the Department of Kinesiology and Community Health, makes exceptional use of collaborative campus resources such as the Campus Computing Cluster, while managing national and international partnerships with public health organizations. Department of Statistics Professor Shulei Wang, along with Martinez and Gaulke, were selected to participate in the 2022 NIH Grant Writing Series mentorship program offered by the Interdisciplinary Health Sciences Institute.
This cohort has received over $8M in external research funding from the Roy J. Carver Charitable Trust, the World Health Organization, and the National Institutes of Health. Most recently, Jacob Allen received an R01 award from The National Institute of Diabetes and Digestive and Kidney Diseases to investigate how psychological stress modifies the gut epithelial-microbiome interactions at the mucosal interface and the subsequent impacts on inflammatory bowel disease.
Faculty have also benefitted from institutional grants. For instance, Animal Sciences Professor Adrienne Antonson received an award for her research project on extrinsic regulation of fetal development as part of the Department of Animal Sciences Matchstick Program. The new faculty have also received Personalized Nutrition Initiative Seed Grants, Rodent Gnotobiotic Facility Pilot Project Grants, and the Cancer Center at Illinois Pilot Award.
Combined, these faculty have produced more than 40 publications and have been invited to speak nationally and internationally. They have served on editorial boards for journals such as Brain, Behavior and Immunity-Integrative, The CRISPR Journal, Frontiers in Microbiology, and mBio.
The new faculty are also excelling in the classroom. The Center for Innovation in Teaching and Learning recognized Biochemistry Professor Joseph Sanfilippo for his excellence in teaching in his Fall 2021 Advanced Biochemistry course.
Additionally, many in this cohort have supported the MSI mission through service. Last fall, Jacob Allen kicked off our MicroERA Faculty Q&A series, discussing his passion for science and sharing insights from this career path with University of Illinois graduate and postdoctoral trainees. Microbiology Professor Asma Hatoum-Aslan has also shared her research with the community as an invited speaker for Parkland College’s James B. Kaler Science Lecture Series.
This year, the leadership of Paola Mera and Chris Gaulke will prove indispensable as they co-chair the planning committee for the Microbial Multiverse Symposium on September 14-16, 2023. Supported by the Olga G. Nalbandov Lecture Fund and co-hosted by the Department of Microbiology, the Institute for Genomic Biology, the School of Molecular and Cellular Biology, the College of Veterinary Medicine, and the Personalized Nutrition Initiative, the symposium will highlight the work of our affiliated faculty and bring attention to the innovative microbial research happening here at Illinois.
Together these faculty have contributed greatly to their fields and individual departments. MSI Director Cari Vanderpool is proud of the microbial systems community’s role in supporting these faculty in their early-career journeys and believes the benefits of supporting these faculty extend beyond their many accomplishments. “Our aim with the strategic hiring plan was to fill gaps in critical expertise and stimulate new interdisciplinary research. What we did not anticipate is how having this new cohort of faculty on campus would reenergize our community and encourage us all to find new ways to create a more inclusive and collaborative environment that benefits all of our members.”
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Recent publications from new faculty
Allen, J. M., Mackos, A. R., Jaggers, R. M., Brewster, P. C., Webb, M., Lin, C. H., Ladaika, C., Davies, R., White, P., Loman, B. R., & Bailey, M. T. (2022). Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes. Gut Microbes, 14 (1), 2035661.
Bari, S. M. N., Chou-Zheng, L., Howell, O., Hossain, M., Hill, C. M., Boyle, T. A., Cater, K., Dandu, V. S., Thomas, A., Aslan, B., & Hatoum-Aslan, A. (2022). A unique mode of nucleic acid immunity performed by a multifunctional bacterial enzyme. Cell Host & Microbe, 30 (4), 570–582.e7.
Carrigee, L. A., Mahmoud, R. M., Sanfilippo, J. E., Frick, J. P., Strnat, J. A., Karty, J. A., Chen, B., Kehoe, D. M., & Schluchter, W. M. (2020). CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I α-subunit in marine Synechococcus. Biochimica et Biophysica Acta- Bioenergetics, 1861 (8), 148215.
Dai, L., Du, Y., Qi, H., Huber, C. D., Chen, D., Zhang, T. H., Wu, N. C., Wang, E., Lloyd-Smith, J. O., & Sun, R. (2021). Quantifying the evolutionary constraints and potential of Hepatitis C virus NS5A protein. mSystems, 6 (2), e01111-20.
Diefenbacher, M., Tan, T. J. C., Bauer, D. L. V., Stadtmueller, B. M., Wu, N. C., & Brooke, C. B. (2022). Interactions between Influenza A virus nucleoprotein and gene segment untranslated regions facilitate selective modulation of viral gene expression. Journal of Virology, 96 (10), e0020522.
Erlandson, A., Gade, P., Menikpurage, I. P., Kim, C. Y., & Mera, P. E. (2022). The UvrA-like protein Ecm16 requires ATPase activity to render resistance against echinomycin. Molecular Microbiology, 117 (6), 1434–1446.
Gaulke, C. A., Schmeltzer, E. R., Dasenko, M., Tyler, B. M., Vega Thurber, R., & Sharpton, T. J. (2021). Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles. mSystems, 6 (5), e0044021.
Haney, A. M., Sanfilippo, J. E., Garczarek, L., Partensky, F., & Kehoe, D. M. (2022). Multiple photolyases protect the marine cyanobacterium Synechococcus from ultraviolet radiation. mBio, 13(4), e0151122.
Hatoum-Aslan A. (2022). A protein-cutting CRISPR complex caught in action. The CRISPR Journal, 5 (5), 631–633.
Hatoum-Aslan A. (2021). Prophages self-destruct to eliminate competitors. Cell Host & Microbe, 29 (11), 1603–1605.
Hatoum-Aslan A. (2021). The phages of staphylococci: critical catalysts in health and disease. Trends in Microbiology, 29 (12), 1117–1129
Hill, E. B., Chen, L., Bailey, M. T., Singh Khalsa, A., Maltz, R., Kelleher, K., Spees, C. K., Zhu, J., & Loman, B. R. (2022). Facilitating a high-quality dietary pattern induces shared microbial responses linking diet quality, blood pressure, and microbial sterol metabolism in caregiver-child dyads. Gut microbes, 14 (1), 2150502.
Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Achenbach, et al. (2022). Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveals limited infectious virus shedding and restricted tissue distribution. Open Forum Infectious Diseases, 9 (7), ofac192.
Khalsa, A. S., Burton, J., Bailey, M. T., Zhu, J., Kelleher, K. J., Maltz, R. M., Loman, B. R., & Spees, C. K. (2022). Collection of biospecimens from parent-child dyads in a community garden-based nutrition intervention: protocol and feasibility. BMC Nutrition, 8 (1), 141.
Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., Deshpande, D., Baykal, P. I., Comarova, Z., Lu, A., Porozov, Y., Vasylyeva, T. I., Wertheim, J. O., Tierney, B. T., Chiu, C. Y., Sun, R., Wu, A., Abedalthagafi, M. S., Pak, V. M., Nagaraj, S. H., … Wu, N. C. … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods, 19 (4), 374–380.
Koenig, P. A., Das, H., Liu, H., Kümmerer, B. M., Gohr, F. N., Jenster, L. M., Schiffelers, L. D. J., Tesfamariam, Y. M., Uchima, M., Wuerth, J. D., Gatterdam, K., Ruetalo, N., Christensen, M. H., Fandrey, C. I., Normann, S., Tödtmann, J. M. P., Pritzl, S., Hanke, L., Boos, J., Yuan, M., … Wu, N. C., Schmidt, F. I. (2021). Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Science (New York, N.Y.), 371 (6530), eabe6230.
Kraay A. N. M., Gallagher M. E., Ge Y., Han P., Baker J. M., Koelle K., Handel A. and Lopman B. A. (2022). The role of booster vaccination and ongoing viral evolution in seasonal circulation of SARS-CoV-2J. R. Soc. Interface.192022047720220477.
Kraay, A. N. M., Steele, M. K., Baker, J. M., Hall, E. W., Deshpande, A., Saidzosa, B. F., Mukaratirwa, A., Boula, A., Mpabalwani, E. M., Kiulia, N. M.,Tsolenyanu, E., Enweronu-Laryea, C., Abebe, A., Beyene, B., Tefera, M., Willilo, R., Batmunkh, N., Pastore, R., Mwenda, J. M., Antoni, S., Cohen, A. L., Pitzer, V. E., Lopman, B. A. (2022). Predicting the long-term impact of rotavirus vaccination in 112 countries from 2006 to 2034: A transmission modeling analysis. Vaccine, 40 (46), 6631-6639.
Lamers, M. M., Mykytyn, A. Z., Breugem, T. I., Wang, Y., Wu, D. C., Riesebosch, S., van den Doel, P. B., Schipper, D., Bestebroer, T., Wu, N. C., & Haagmans, B. L. (2021). Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation. eLife, 10, e66815.
Langen, T. A., Cannon, C. H., Blackburn, D. C., Morgan, E. L., & Mera, P. E. (2021). Discovering and applying the urban rules of life to design sustainable and healthy cities. Integrative and Comparative Biology, 61 (4), 1237–1252.
Li, Y., Sanfilippo, J. E., Kearns, D., & Yang, J. Q. (2022). Corner flows induced by surfactant-producing bacteria Bacillus subtilis and Pseudomonas fluorescens. Microbiology Spectrum, 10 (5), e0323322.
Liu, H., Yuan, M., Huang, D., Bangaru, S., Zhao, F., Lee, C. D., Peng, L., Barman, S., Zhu, X., Nemazee, D., Burton, D. R., van Gils, M. J., Sanders, R. W., Kornau, H. C., Reincke, S. M., Prüss, H., Kreye, J., Wu, N. C., Ward, A. B., & Wilson, I. A. (2021). A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. Cell Host & Microbe, 29 (5), 806–818.e6.
Lv, H., So, R. T. Y., Teo, Q. W., Yuan, M., Liu, H., Lee, C. D., Yip, G. K., Ng, W. W., Wilson, I. A., Peiris, M., Wu, N. C., & Mok, C. K. P. (2022). Neutralizing antibody response to Sarbecovirus is delayed in sequential heterologous immunization. Viruses, 14 (7), 1382.
Lv, H., Tsang, O. T., So, R. T. Y., Wang, Y., Yuan, M., Liu, H., Yip, G. K., Teo, Q. W., Lin, Y., Liang, W., Wang, J., Ng, W. W., Wilson, I. A., Peiris, J. S. M., Wu, N. C., & Mok, C. K. P. (2021). Homologous and heterologous serological response to the N-terminal domain of SARS-CoV-2 in humans and mice. European Journal of Immunology, 51 (9), 2296–2305.
Martinez, P .P., Li, J., Cortes, C. P., Baker, R. E., Mahmud, A. S. (2022). The return of wintertime respiratory virus outbreaks and shifts in the age structure of incidence in the Southern Hemisphere. Open Forum Infectious Diseases, 9 (12), ofac650.
Mena, G. E., Martinez, P. P., Mahmud, A. S., Marquet, P. A., Buckee, C. O., & Santillana, M. (2021). Socioeconomic status determines COVID-19 incidence and related mortality in Santiago, Chile. Science (New York, N.Y.), 372 (6545), eabg5298.
Menikpurage I. P., Puentes-Rodriguez, S. G., Elaksher, R. A., Mera, P. E. (2022) ParA and its functions that go beyond chromosome segregation in Caulobacter crescentus. [preprint] BioRxiv.
Menikpurage, I. P., Woo, K., & Mera, P. E. (2021). Transcriptional activity of the bacterial replication initiator DnaA. Frontiers in Microbiology, 12, 662317.
Mera P. E. (2020). mSphere of influence: Communication is complicated- just ask a bacterial cell. mSphere, 5 (4), e00580-20.
Montague, Z., Lv, H., Otwinowski, J., DeWitt, W. S., Isacchini, G., Yip, G. K., Ng, W. W., Tsang, O. T., Yuan, M., Liu, H., Wilson, I. A., Peiris, J. S. M., Wu, N. C., Nourmohammad, A., & Mok, C. K. P. (2021). Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19. Cell Reports, 35 (8), 109173.
Otero, A. M., & Antonson, A. M. (2022). At the crux of maternal immune activation: Viruses, microglia, microbes, and IL-17A. Immunological Reviews, 311 (1), 205–223.
Rodrigues, R. R., Gurung, M., Li, Z., García-Jaramillo, M., Greer, R., Gaulke, C., Bauchinger, F., You, H., Pederson, J. W., Vasquez-Perez, S., White, K. D., Frink, B., Philmus, B., Jump, D. B., Trinchieri, G., Berry, D., Sharpton, T. J., Dzutsev, A., Morgun, A., & Shulzhenko, N. (2021). Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes. Nature Communications, 12 (1), 101.
Smith, R. L., Gibson, L. L., Martinez, P. P., Ke, R., Mirza, A., Conte, M., Gallagher, N., Conte, A., Wang, L., Fredrickson, R., Edmonson, D. C., Baughman, M. E., Chiu, K. K., Choi, H., Jensen, T. W., Scardina, K. R., Bradley, S., Gloss, S. L., Reinhart, C., Yedetore, J., … Brooke, C. B. (2021). Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. The Journal of Infectious Diseases, 224 (6), 976–982.
Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., Brooke, C. B., Wilson, I. A., & Wu, N. C. (2021). Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain. Nature Communications, 12 (1), 3815.
VanderHoek, Z. K., Browning, A. M., Washburn, Q., Kent, M. L., Sharpton, T. J., & Gaulke, C. A. (2022). Draft genome sequence of Plesiomonas shigelloides strain zfcc0051 (Phylum Proteobacteria). Microbiology Resource Announcements, 11 (7), e0007422.
Yang, J. Q., Sanfilippo, J. E., Gitai, Z., Bassler B. L., & Stone, H. A. (2021). Surfactant-producing bacteria self-generate flows along corners in unsaturated porous media. PNAS, 118 (38), e2111060118.
Yuan, F., Sharma, J., Nanjappa, S. G., Gaulke, C. A., & Fang, Y. (2022). Effect of killed PRRSV vaccine on gut microbiota diversity in pigs. Viruses, 14 (5), 1081.
Yuan, M., Huang, D., Lee, C. D., Wu, N. C., Jackson, A. M., Zhu, X., Liu, H., Peng, L., van Gils, M. J., Sanders, R. W., Burton, D. R., Reincke, S. M., Prüss, H., Kreye, J., Nemazee, D., Ward, A. B., & Wilson, I. A. (2021). Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Science (New York, N.Y.), 373 (6556), 818–823.
Wang, S. (2022). Robust differential abundance test in compositional data, Biometrika, asac029.
Wang, S. (2022). Self-supervised metric learning in multi-view data: A downstream task perspective. Journal of the American Statistical Association.
Wang, S., Yuan, M. (2021). Revisiting colocalization via optimal transport. Nature Computational Science, 1, 177–178.
Wang, Y., Yuan, M., Lv, H., Peng, J., Wilson, I. A., & Wu, N. C. (2022). A large-scale systematic survey reveals recurring molecular features of public antibody responses to SARS-CoV-2. Immunity, 55 (6), 1105–1117.e4.
Wang, Y., Lei, R., Nourmohammad, A., & Wu, N. C. (2021). Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing. eLife, 10, e72516.
Watson, K. M., Gardner, I. H., Anand, S., Siemens, K. N., Sharpton, T. J., Kasschau, K. D., Dewey, E. N., Martindale, R., Gaulke, C. A., & Tsikitis, V. L. (2021). Colonic microbial abundances predict adenoma formers. Annals of Surgery, 10.1097/SLA.0000000000005261. Advance online publication.
