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Wook Kim

Assistant Professor
Bayer School of Natural and Environmental Sciences
Biological Sciences

207 Mellon Hall / Lab: 259 Mellon Hall
Phone: 412.396.6319
kimw1@duq.edu

Education:

Postdoctoral Research Associate, University of Oxford, 2010-2016
Postdoctoral Fellow, Harvard University, 2008-2010
Postdoctoral Fellow, Tufts University, 2006-2007
Ph.D., University of Calgary, 2005
M.S., University of Guelph, 2001
B.S., University of Guelph, 1998
Bio

Dr. Wook Kim obtained his B.S. and M.S. in Microbiology from the University of Guelph (Canada), where he acquired training in fundamental concepts of microbiology and microbial pathogenesis. He then pursued broader research topics during his Ph.D. in Microbiology and Infectious Diseases at the University of Calgary (Canada) with Mike Surette: multicellular behaviors, intracellular communication, and antibiotic resistance.

Wook's Ph.D. experience made him realize the importance of exploring the natural environment to gain better understanding of the microbes. He trained as a postdoctoral fellow at Tufts University with Stuart Levy, where he studied novel genes and proteins in a soil microbe that were expressed exclusively in its natural soil environment. He became fascinated with the hidden potential of microbial genomes and the importance of integrating concepts from evolutionary biology and ecology to maximize our understanding of microbes. He began to identify important aspects in the field of microbiology that remained unanswered or overlooked. This also made him realize that his past training was insufficient to address these new interests on his own.

Wook repeatedly observed the emergence of striking phenotypes in bacterial colonies and began to collaborate with Kevin Foster to characterize the phenotypes from an evolutionary angle. This collaboration eventually led to Wook joining the Foster lab at Harvard University and the University of Oxford, where he embedded himself to the study of evolution and systems biology. He invested several years developing various experimental systems that capture the evolution of new multicellular interactions in real-time and natural interactions among ecologically linked microbial species.

Here at Duquesne, Wook continues to utilize his experimental systems to describe the fundamental principles of microbial life. In addition, he strives to translate these principles into our progressive understanding of the microbial world, particularly through the development of new experimental model systems that meaningfully capture various microbiota of the human body.

Research

Mechanisms of microbial interaction and multicellularity

Microbes are often described as simple and selfish creatures that lead a pendulum-like life of feast or famine. Within these boundaries, however, lies a complex world that is shaped by conflict and cooperation among highly interactive cells that closely associate with one another. We hypothesize that many important microbial phenotypes that impact our lives immensely, in both positive and negative ways, have their roots in interactions among the microbes. Therefore, understanding microbes and their societal impacts require us to understand their social adaptation and evolution.

Our research focuses on the mechanisms of microbial interaction at three scales: i) the study of multicellular behaviors that manifest via pre-wired genetic circuits, ii) the study of de novo mutations that forge new interactions, and iii) the study of natural interactions between ecologically and clinically linked strains and species. We employ a multidisciplinary approach that strives to integrate all the way from population biology down to molecular structure and function. We operate at the interface of:

  1. Evolution (phenotypic and genetic bases of multicellular behaviors and adaptations across a wide range of timescales)
  2. Chemistry (intracellular and extracellular compounds that shape and modulate interactions)
  3. Biochemistry (signal transduction systems that govern the production of interactive compounds)
  4. Computational Biology (bioinformatics and mathematical modeling of interactions - currently through collaborations)
  5. Synthetic Biology (genetic and physical engineering of synthetic microbial communities - currently through collaborations)

For those interested in joining our team, they are expected to arrive proficient in at least one of the above disciplines and, more importantly, with motivation and a strong desire to develop and integrate additional expertise toward systems-level understanding of interactions in microbial communities.

Publications

Kim, W., S.B. Levy and K.R. Foster. 2016. Rapid radiation in bacteria leads to a division of labour. Nature Communications. 7:10508.

  • Highlighted by Faculty of 1000 (726132319)

Oliveira, N.M., E. Martinez-Garcia, J. Xavier, W.M. Durham, R. Kolter, W. Kim and K.R. Foster. 2015. Biofilm formation as a response to ecological competition. PLoS Biology. 13:e1002191.

  • Highlighted in Nature (2015, 523:505), Curr Biol (2015, 25:R800), and by Faculty of 1000 (725624201)

Kim, W., F. Racimo, J. Schluter, S.B. Levy and K.R. Foster. 2014. Importance of positioning for microbial evolution. Proceedings of the National Academy of Sciences USA. 111:E1639-47.

  • Highlighted in Nature (2014, 508:435), PNAS (2014, 111:5756), and by Faculty of 1000 (718343887)

Turnbull, A.L., W. Kim and M.G. Surette. 2012. Transcriptional regulation of sdiA by cAMP-receptor protein, LeuO, and environmental signals in Salmonella enterica serovar Typhimurium. Canadian Journal of Microbiology. 58:10-22.

Xavier, J.B., W. Kim and K.R. Foster. 2011. A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa. Molecular Microbiology. 79:166-79.

  • Highlighted in Science (2010, 330:1588), and by Faculty of 1000 (724755282).

Kim, W., M.W. Silby, S.O. Purvine, J.S. Nicoll, K.K. Hixson, M. Monroe, C.D. Nicora, M.S. Lipton, and S.B. Levy. 2009. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1. PLoS ONE. 4:e8455.

Kim, W. and S.B. Levy. 2008. Increased fitness of Pseudomonas fluorescens Pf0-1 leucine auxotrophs in soil. Applied and Environmental Microbiology. 74:3644-51.

White, A.P., D.L. Gibson, W. Kim, W.W. Kay and M.G. Surette. 2006. Multicellular behavior and environmental persistence of Salmonella. Journal of Bacteriology. 188:3219-27.

Kim, W. and M.G. Surette. 2006. Coordinated regulation of two independent cell-cell signaling systems and swarmer differentiation in Salmonella enterica serovar Typhimurium. Journal of Bacteriology. 188:431-40.

Kim, W. and M.G. Surette. 2005. Prevalence of surface swarming behavior in Salmonella. Journal of Bacteriology. 187:6580-3.

Kim, W. and M.G. Surette. 2004. Metabolic differentiation in actively swarming Salmonella. Molecular Microbiology. 54:702-14.

Kim, W. and M.G. Surette. 2003. Swarming populations of Salmonella represent a unique physiological state coupled to multiple mechanisms of antibiotic resistance. Biological Procedures Online. 5:189-96.

Kim, W., T. Killam, V. Sood and M.G. Surette. 2003. Swarm-cell differentiation in Salmonella enterica serovar Typhimurium results in elevated phenotypic resistance to a wide variety of antibiotics. Journal of Bacteriology. 185:3111-7.

Levesque, M., Shasha, D., W. Kim, M.G. Surette and P.N. Benfey. 2003. Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Current Biology. 13:129-33.

  • Highlighted in Nature Reviews Genetics (2003, 4:167), and by Faculty of 1000 (1011745)
Courses

Fall 2016: BIOL 695 - Introduction to Graduate Research I

Spring 2016: BIOL 426/526 - Pathogenic Microbiology

Future: Develop a lab-based undergraduate course in Experimental Evolution to explore the genetic bases of microbial antibiotic resistance and multicellularity in real time.