Biosciences and Biotechnology Division
Microbial Systems Biology Group
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The Microbial Systems Biology Group probes basic biology and designs engineered microbial systems with applications in environmental biotechnology, biomanufacturing, and human health.
Using systems biology approaches, we uncover foundational mechanisms driving system level behavior and seek a predictive understanding of complex microbes and microbial communities. We harness this fundamental science to design systems at the protein, microbe, and community levels to confer biotechnological functions. We strive to develop basic knowledge and practical solutions to benefit national security.
Our research and capabilities
Our major research areas include:
- Systems-level studies of microbial community interactions for sustainable bioenergy
- Development of biocontainment strategies for environmental biotechnology
- Biomanufacturing of DOE-relevant products such as chemicals and biocement materials
Our capabilities include:
- Multi-omic analyses (genomics, RNA-seq, proteomics, metabolite profiling) and bioinformatics
- Advanced genetic engineering of model and non-model microbes
- Enzyme engineering
- Stable isotope probing
- Advanced imaging, including cryoNanoSIMS and superresolution fluorescence microscopy
- Microbiome and microbial consortia manipulation
Image shows a transmission electron micrograph of encapsulin nanocompartments. We study the mechanisms of encapsulin nanocompartment biosynthesis and regulation and engineer encapsulin systems to achieve new biosynthetic functions.

In the news
Not all bacteria are created equal
Electronic “programming” of cell populations
Select publications
Dynamic Phaeodactylum tricornutum exometabolites shape surrounding bacterial communities
New Phytologist, 2023
V. Brisson, C. Swink, J. Kimbrel, X. Mayali, T. Samo, S. M. Kosina, M. Thelen, T. R. Northen, R. K. Stuart
Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis
Biotechnology and Bioengineering, 2023
E. VanArsdale, A. Navid, M. J. Chu, T. M. Halvorsen, G. F. Payne, Y. Jiao, W. E. Bentley, M. C. Yung
Prolonging genetic circuit stability through adaptive evolution of overlapping genes
Nucleic Acids Research, 2023
J. L. Chlebek, S. P. Leonard, C. Kang-Yun, M. C. Yung, D. P. Ricci, Y. Jiao, D. M. Park
Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum
Nature Communications, 2023
X. Mayali, T. J. Samo, J. A. Kimbrel, M. M. Morris, K. Rolison, C. Swink, C. Ramon, Y.-M. Kim, N. Munoz-Munoz, C. Nicora, S. Purvine, M. Lipton, R. K. Stuart, P. K. Weber
Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina
mSphere, 2022
M. M. Morris, J. A. Kimbrel, H. Geng, M. B. Tran-Gyamfi, E. T. Yu, K. L. Sale, T. W. Lane, X. Mayali
Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity
FEMS Microbiology Ecology, 2022
M. Windler, R. Stuart, J. S. Deutzmann, X. Mayali, A. Navid, P. D’haeseleer, O. E Marcu, M. Lipton, C. Nicora, A. M. Spormann
Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape
ACS Synth Biol, 2022
T, M. Halvorsen, D, P. Ricci, D, M. Park, Y. Jiao, M. C. Yung
Microbial Carbonation of Monocalcium Silicate
ACS Omega, 2022
M. S. Guzman, J. Iyer, P. Kim, D. Kopp, Z. Dong, P. Foroughi, M. C. Yung, R. E. Riman, Y. Jiao
Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar
Phytobiomes Journal, 2022
V. L. Brisson, J. Richardy, S. M. Kosina, T. R. Northen, J. P. Vogel, A. C. M. Gaudin
Plant-associated fungi support bacterial resilience following water limitation
The ISME Journal, 2022
R. Hestrin, M. Kan, M. Lafler, J. Wollard, J. A. Kimbrel, P. Ray, S. J. Blazewicz, R. Stuart, K. Craven, M. Firestone, E. E. Nuccio, J. Pett-Ridge
Comparative Genomics Reveals Insights into Induction of Violacein Biosynthesis and Adaptive Evolution in Janthinobacterium
Microbiology Spectrum, 2021
X. Wu, A. E. Kazakov, S. Gushgari-Doyle, X. Yu, V. Trotter, R. K. Stuart, R. Chakraborty
Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities
Algal Research, 2021
C. S. Ward, K. Rolison, M. Li, S. Rozen, C. L. Fisher, T. W. Lane, M. P. Thelen, R. K. Stuart
Prokaryotic Genome Annotation
Methods in Molecular Biology, 2021
J. A. Kimbrel, B. M. Jeffrey, and C. S. Ward
Metabolomic Analysis Reveals Contributions of Citric and Citramalic Acids to Rare Earth Bioleaching by a Paecilomyces Fungus
Front. Microbiolo., 2020
V. L. Brisson, W.-Q. Zhuang, L. Alvarez-Cohen
Encapsulin carrier proteins for enhanced expression of antimicrobial peptides
Biotechnology and Bioengineering, 2019
T.-H. Lee, T. S. Carpenter, P. D’haeseleer, D. F. Savage, M. C. Yung
Selective collection of iron-rich dust particles by natural Trichodesmium colonies
The ISME Journal, 2019
N. Kessler, R. Armoza-Zvuloni, S. Wang, S. Basu, P. K Weber, R. K Stuart, Y. Shaked