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Staff information

Young-Mo

Young-Mo Kim

Metabolomics
Chemist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352

Biography

Dr. Young-Mo Kim is a senior bioanalytical chemist at Pacific Northwest National Laboratory. Dr. Kim received his Ph.D. from Pohang University of Science and Technology (POSTECH, Pohang, South Korea) in the School of Environmental Science and Engineering studying analysis of metabolites during the bacterial and fungal degradation of xenobiotic substrates using gas/liquid chromatography coupled with various mass spectrometers. After obtaining the degree, he joined in Biological Separation and Mass Spectrometry group at PNNL as a post-doctoral trainee focusing metabolomics analysis with various types of biological and environmental samples. As a senior staff member at Integrative Omics group at PNNL, Dr. Kim has been leading/participating in various research projects using mass spectrometry based metabolomics approaches to solve biological questions from microbial transformation, synthetic biology, biofuel production, microbiome, carbon flow in the environment and a few others. In addition, he has been involved in pulse-chase and isotope based metabolic flux analysis on selected biological systems. He served as a lieutenant officer in Korean Army (2000-2002) after his ROTC training at undergraduate.

Research Interests

  • Metabolomics / Lipidomics
  • Chromatography / Mass Spectrometry
  • Environmental Microbiology
  • Metabolic Flux Analysis
  • Synthetic Biology

Education and Credentials

  • Pacific Northwest National Laboratory, Post-Doctoral, Metabolomics, 2012
  • POSTECH, PhD, Environmental Analytical Chemistry, 2009
  • Sungkyunkwan University, BS, Genetic Engineering, 2000

Affiliations and Professional Service

  • Metabolomics Society
  • American Society for Mass Spectrometry
  • American Society for Microbiology

Awards and Recognitions

  • New Principal Investigator Award (2018)
  • Best Awards, EBSD Paper of the year (2017, 2015)
  • International Collaboration program (UC Riverside, 2004-2005)
  • Korea-Germany Graduate Student Exchange Program (U Hamburg, 2004)

PNNL Publications

2021

  • Kim J., S.T. Coradetti, Y. Kim, Y. Gao, J. Yaegashi, J.D. Zucker, and N. Munoz Munoz, et al. 2021. "Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156767. doi:10.3389/fbioe.2020.612832

2020

  • Bhattacharjee A., A.M. Thompson, K.C. Schwarz, M.C. Burnet, Y. Kim, J. Nunez, and S.J. Fansler, et al. 2020. "Soil microbial EPS resiliency is influenced by carbon source accessibility." Soil Biology and Biochemistry 151. PNNL-SA-153321. doi:10.1016/j.soilbio.2020.108037
  • Chaput G., A. Billings, L. DeDiego, R. Orellana, J.N. Adkins, C.D. Nicora, and Y. Kim, et al. 2020. "Lignin Induced Iron Reduction by Novel sp., Tolumonas lignolytic BRL6-1." PLOS ONE 15, no. 9:e0233823. PNNL-SA-156112. doi:10.1371/journal.pone.0233823
  • Daly P., M. Peng, H.D. Mitchell, Y. Kim, C.K. Ansong, H.M. Brewer, and P. De Gijsel, et al. 2020. "Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation." Environmental Microbiology 22, no. 3:1154-1166. PNNL-SA-150305. doi:10.1111/1462-2920.14907
  • Gao Y., T.L. Fillmore, N. Munoz Munoz, G. Bentley, C.W. Johnson, J. Kim, and J. Meadows, et al. 2020. "High-throughput large-scale targeted proteomics assays for quantifying pathway proteins in Pseudomonas putida KT2440." Frontiers in Bioengineering and Biotechnology 8. PNNL-SA-156111. doi:10.3389/fbioe.2020.603488
  • Ilhan Z.E., J.K. DiBaise, S.E. Dautel, N.G. Isern, Y. Kim, D.W. Hoyt, and A.A. Schepmoes, et al. 2020. "Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery." NPJ Biofilms and Microbiomes 6, no. 1:Article No. 12. PNNL-SA-133750. doi:10.1038/s41522-020-0122-5
  • Mao J., Y. Kim, Y. Zhou, D. Hu, C. Zhong, H. Chang, and C.J. Brislawn, et al. 2020. "Genetic and Metabolic Links Between the Murine Microbiome and Memory." Microbiome 8, no. 1:Article No. 53. PNNL-SA-143770. doi:10.1186/s40168-020-00817-w
  • McClure R.S., J. Lee, T. Chowdhury, E.M. Bottos, R.A. White, Y. Kim, and C.D. Nicora, et al. 2020. "Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations." Scientific Reports 10, no. 1:Article Number 10882. PNNL-SA-153633. doi:10.1038/s41598-020-67878-7
  • Nicora C.D., A. Sims, K.J. Bloodsworth, Y. Kim, R.J. Moore, J.E. Kyle, and E.S. Nakayasu, et al. 2020. "Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection." In MERS Coronavirus: Methods and Protocols, edited by R. Vijay. 173-194. New York, New York:Humana. PNNL-SA-142077. doi:10.1007/978-1-0716-0211-9_14
  • Suskind D., D. Lee, Y. Kim, G. Wahbeh, N. Singh, K. Braly, and M. Nuding, et al. 2020. "The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn’s Disease: A Randomized Diet Controlled Trial." Nutrients 12, no. 12:3749. PNNL-SA-152828. doi:10.3390/nu12123749
  • Taylor S.E., C.I. Pearce, K.A. Sanguinet, D. Hu, W.B. Chrisler, Y. Kim, and Z. Wang, et al. 2020. "Polystyrene Nano- and Microplastic Accumulation at Arabidopsis and Wheat Root Cap Cells, but No Evidence for Uptake into Roots." Environmental Science: Nano 7, no. 7:1942-1953. PNNL-SA-147042. doi:10.1039/d0en00309c
  • Zuniga C., T. Li, M. Guarnieri, J. Jenkins, C. Li, A.K. Bingol, and Y. Kim, et al. 2020. "Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth." Nature Communications 11. PNNL-SA-152360. doi:10.1038/s41467-020-17612-8

2019

  • Ceja Navarro J., U. Karaoz, M. Bill, Z. Hao, R.A. White, A. Arellano, and L. Ramanculova, et al. 2019. "Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle." Nature Microbiology 4, no. 5:864-875. PNNL-SA-138060. doi:10.1038/s41564-019-0384-y
  • Kim Y., A.M. Snijders, C.J. Brislawn, K.G. Stratton, E.M. Zink, S.J. Fansler, and T.O. Metz, et al. 2019. "Light-stress influences the composition of the murine gut microbiome, memory function, and plasma metabolome." Frontiers in Molecular Biosciences 6. PNNL-SA-144001. doi:10.3389/fmolb.2019.00108
  • Rivas-Ubach A., Y. Liu, A.L. Steiner, J. Sardans, M.M. Tfaily, G.R. Kulkarni, and Y. Kim, et al. 2019. "Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research." Environmental Monitoring and Assessment 191, no. 2:Article No. 78. PNNL-SA-118888. doi:10.1007/s10661-019-7205-x
  • Sharon G., N.J. Cruz, D. Kang, M. Gandal, B. Wang, Y. Kim, and E.M. Zink, et al. 2019. "Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice." Cell 177, no. 6:1600-1618. PNNL-SA-131563. doi:10.1016/j.cell.2019.05.004

2018

  • Cole J.K., B.R. Morton, H.C. Cardamone, H.R. Lake, A. Dohnalkova, Y. Kim, and J.E. Kyle, et al. 2018. "Salinivirga fredricksonii gen. nov. , sp. nov., a heterotrophic halophile isolated from photosynthetic mat of a novel lineage (Salinivirgaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinivirgaceae." International Journal of Systematic and Evolutionary Microbiology 68, no. 5:1591-1598. PNNL-SA-118460. doi:10.1099/ijsem.0.002715
  • Daly P., S.C. Lopez, M. Peng, C.S. Lancefield, S.O. Purvine, Y. Kim, and E.M. Zink, et al. 2018. "Dichomitus squalens partially tailors its molecular responses to the composition of solid wood." Environmental Microbiology 20, no. 11:4141-4156. PNNL-SA-135900. doi:10.1111/1462-2920.14416
  • Khosravi C., E. Battaglia, R.S. Kun, S. Dalhuijsen, J. Visser, M.V. Aguilar-Pontes, and M. Zhou, et al. 2018. "Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans." BMC Genomics 19, no. 1:Article No. 214. PNNL-SA-132841. doi:10.1186/s12864-018-4609-x
  • Moghieb A.M., G. Clair, H.D. Mitchell, J. Kitzmiller, E.M. Zink, Y. Kim, and V.A. Petyuk, et al. 2018. "Time-resolved Proteome Profiling of Normal Lung Development." American Journal of Physiology-Lung Cellular and Molecular Physiology 315, no. 1:L11-L24. PNNL-SA-127218. doi:10.1152/ajplung.00316.2017
  • Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
  • Rosnow J.J., S. Hwang, B.J. Killinger, Y. Kim, R.J. Moore, S.R. Lindemann, and J.A. Maupin-Furlow, et al. 2018. "A cobalamin activity-based probe enables microbial cell growth and finds new cobalamin-protein interactions across domains." Applied and Environmental Microbiology 84, no. 18:e00955-18. PNNL-SA-127734. doi:10.1128/AEM.00955-18
  • Roy Chowdhury T., L.M. Bramer, D.W. Hoyt, Y. Kim, T.O. Metz, L. McCue, and H.L. Diefenderfer, et al. 2018. "Temporal dynamics of CO2 and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils." Ecological Engineering 114. PNNL-SA-123359. doi:10.1016/j.ecoleng.2017.06.041
  • Wu J., A. Sabag-Daigle, M. Borton, L. Kop, B.E. Szkoda, B. Kaiser, and S.R. Lindemann, et al. 2018. "Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut." Infection and Immunity 86, no. 7:e00945-17. PNNL-SA-129012. doi:10.1128/IAI.00945-17
  • Xu L., D. Naylor, Z. Dong, T. Simmons, G. Pierroz, K.K. Hixson, and Y. Kim, et al. 2018. "Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria." Proceedings of the National Academy of Sciences of the United States of America 115, no. 8:E4284-E4293. PNNL-SA-131119. doi:10.1073/pnas.1717308115

2017

  • Bernstein H.C., R.S. McClure, V. Thiel, N.C. Sadler, Y. Kim, W.B. Chrisler, and E.A. Hill, et al. 2017. "Indirect interspecies regulation; transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership." mSystems 2, no. 2:Article No. e00181-16. PNNL-SA-113682. doi:10.1128/mSystems.00181-16
  • Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
  • Dautel S.E., J.E. Kyle, G. Clair, R.L. Sontag, K.K. Weitz, A.K. Shukla, and S.N. Nguyen, et al. 2017. "Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung." Scientific Reports 7. PNNL-SA-121148. doi:10.1038/srep40555
  • Eisfeld A.J., P. Halfmann, J.P. Wendler, J.E. Kyle, K.E. Burnum-Johnson, Z. Peralta, and T. Maemura, et al. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22, no. 6:817-829. PNNL-SA-120881. doi:10.1016/j.chom.2017.10.011
  • Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
  • Kyle J.E., C.P. Casey, K.G. Stratton, E.M. Zink, Y. Kim, X. Zheng, and M.E. Monroe, et al. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31, no. 5:447-456. PNNL-SA-121197. doi:10.1002/rcm.7808
  • Romine M.F., D.A. Rodionov, Y. Maezato, L.N. Anderson, P. Nandhikonda, I.A. Rodionova, and A. Carre, et al. 2017. "Elucidation of new roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism." Proceedings of the National Academy of Sciences of the United States of America 114, no. 7:E1205-E1214. PNNL-SA-119181. doi:10.1073/pnas.1612360114
  • Snijders A.M., S.A. Langley, Y. Kim, C.J. Brislawn, C. Noecker, E.M. Zink, and S.J. Fansler, et al. 2017. "Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome." Nature Microbiology 2, no. 2:Article No. 16221. PNNL-SA-118063. doi:10.1038/nmicrobiol.2016.221
  • White R.A., A. Rivas-Ubach, M.I. Borkum, M. Koberl, A. Bilbao Pena, S.M. Colby, and D.W. Hoyt, et al. 2017. "The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies." Rhizosphere 3, no. 2:212-221. PNNL-SA-124859. doi:10.1016/j.rhisph.2017.05.003

2016

  • Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
  • Pomraning K.R., Y. Kim, C.D. Nicora, R.K. Chu, E.L. Bredeweg, S.O. Purvine, and D. Hu, et al. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17, no. 138:1-18. PNNL-SA-112784. doi:10.1186/s12864-016-2471-2
  • Rivas Ubach A., J.A. Hodar, J. Sardans, J.E. Kyle, Y. Kim, M. Oravec, and O. Urban, et al. 2016. "Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?." Ecology and Evolution 6, no. 13:4372-4386. PNNL-SA-116150. doi:10.1002/ece3.2206
  • Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
  • Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002

2015

  • Kim Y., S. Nowack, M. Olsen, E. Becraft, J.M. Wood, V. Thiel, and I. Klapper, et al. 2015. "Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms." Frontiers in Microbiology 6. PNNL-SA-107334. doi:10.3389/fmicb.2015.00209
  • Lovelace E.S., J. Wagoner, J. MacDonald, T. Bammler, J. Bruckner, J. Brownell, and R. Beyer, et al. 2015. "Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling." Journal of Natural Products 78, no. 8:1990-2000. PNNL-SA-109357. doi:10.1021/acs.jnatprod.5b00288
  • Pomraning K.R., S. Wei, S.A. Karagiosis, Y. Kim, A. Dohnalkova, B.W. Arey, and E.L. Bredeweg, et al. 2015. "Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis." PLoS One 10, no. 4:e0123188. PNNL-SA-105704. doi:10.1371/journal.pone.0123188

2014

  • Anderson J.C., Y. Wan, Y. Kim, L. Pasa-Tolic, T.O. Metz, and S.C. Peck. 2014. "Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae." Proceedings of the National Academy of Sciences of the United States of America 111, no. 18:6846-6851. PNNL-SA-97264. doi:10.1073/pnas.1403248111
  • Boaro A.A., Y. Kim, A. Konopka, S.J. Callister, and B.K. Ahring. 2014. "Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture." FEMS Microbiology Ecology 90, no. 3:802-15. PNNL-SA-105700. doi:10.1111/1574-6941.12435
  • Boaro A.A., Y. Kim, A.E. Konopka, S.J. Callister, and B.K. Ahring. 2014. "Integrated ‘omics Analysis for Studying the Microbial Community Response to a pH Perturbation of a Cellulose-Degrading Bioreactor Culture." FEMS Microbiology Ecology 90, no. 3:802-815. PNNL-SA-106822. doi:10.1111/1574-6941.12435
  • Cole J.K., J.R. Hutchison, R.S. Renslow, Y. Kim, W.B. Chrisler, H.E. Engelmann, and A. Dohnalkova, et al. 2014. "Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions." Frontiers in Microbiology 5. PNNL-SA-99657. doi:10.3389/fmicb.2014.00109
  • Huang E.L., F.O. Aylward, Y. Kim, B.M. Webb-Robertson, C.D. Nicora, Z. Hu, and T.O. Metz, et al. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6, no. 4:389-95. PNNL-SA-96938. doi:10.1111/1758-2229.12163
  • Webb-Robertson B.M., Y. Kim, E.M. Zink, K.A. Hallaian, Q. Zhang, R. Madupu, and K.M. Waters, et al. 2014. "A Statistical Analysis of the Effects of Urease Pre-Treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry." Metabolomics 10, no. 5:897-908. PNWD-SA-10204. doi:10.1007/s11306-014-0642-1

2013

  • Ansong C., A.C. Rutledge, H.D. Mitchell, S. Chauhan, M.B. Jones, Y. Kim, and K. Mcateer, et al. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9, no. 1:44-54. PNNL-SA-89164. doi:10.1039/C2MB25287B
  • Kaiser B., J. Li, J.A. Sanford, Y. Kim, S.R. Kronewitter, M.B. Jones, and C. Peterson, et al. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8, no. 6:Article No. e67155. PNNL-SA-85342. doi:10.1371/journal.pone.0067155
  • Kim Y., B. Schmidt, A.S. Kidwai, M.B. Jones, B.L. Deatherage, H.M. Brewer, and H.D. Mitchell, et al. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9, no. 6:1522-1534. PNNL-SA-89810. doi:10.1039/C3MB25598K

2012

  • Ansong C.K., B.L. Deatherage, D.R. Hyduke, B. Schmidt, J.E. McDermott, M.B. Jones, and S. Chauhan, et al. 2012. "Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated ‘Omics and Modeling." In Systems Biology. Current Topics in Microbiology and Immunology, edited by M Katze. 21-41. PNNL-SA-135981. doi:10.1007/82_2012_247
  • Bordbar A., M.L. Mo, E.S. Nakayasu, A.C. Rutledge, Y. Kim, T.O. Metz, and M.B. Jones, et al. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8. PNNL-SA-87903. doi:10.1038/msb.2012.21
  • Hu Z., Y. Kim, M.B. Sowa, R.J. Robinson, X. Gao, T.O. Metz, and W.F. Morgan, et al. 2012. "Metabolomic Response of Human Skin Tissue to Low Dose Ionizing Radiation." Molecular Biosystems 8, no. 7:1979-1986. PNNL-SA-84921. doi:10.1039/C2MB25061F

2011

  • Kim Y., T.O. Metz, Z. Hu, S.D. Wiedner, J. Kim, R.D. Smith, and W.F. Morgan, et al. 2011. "Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics." Rapid Communications in Mass Spectrometry 25. PNNL-SA-78517. doi:10.1002/rcm.5134

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