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Metabolomics Technology Group

Technical advances in DNA sequencing and manipulation have lead to an explosion in the sequenced universe. However, defining the functions of these remains slow and tedious. Our lab is using mass spectrometry based metabolite profiling to provide direct biochemical datasets to improve our understanding of microbial metabolism. Of particular interest is understanding the distributed and dynamic metabolite networks of environmental microbes and how they transform their environment. These processes underlie all biomes and yet are poorly understood. We are using exometabolomics to directly measure the exogenous metabolic transformations of microbes to gain insights into the coupling of microbial metabolism in microbial communities to create distributed and robust metabolic networks.  This understanding will be critical in understanding how to predict and manage microbial communities for long-term sustainability.

See Metabolomics Technology for more information on and how to include this capability in your research.

Research Team

lr_2_Trent_portrait_pix Ben_Bowen lr_Katherine_Louie
Trent Northen,
Metabolomics Program Lead 		 Ben Bowen, Computational Metabolomics Lead Katherine Louie, Metabolomics Platform Lead
[email protected]  [email protected] [email protected]

 

Headshot of Thomas Harwood Headshot of Meghana Faltane Headshot of MiMi Lynde.
Thomas Harwood, Computational Metabolomics Meghana Faltane, Metabolomics MiMi Lynde, Metabolomics

Selected Publications

  1. Bowen, B., Fischer, C., Baran, R., Banfield, J., & Northen, T. (2011). Improved genome annotation through untargeted detection of pathway-specific metabolites. BMC Genomics, 12(Suppl 1), S6. BioMed Central Ltd. doi:10.1186/1471-2164-12-S1-S6  PMCID: PMC32223729  DOI: 10.1186/1471-2164-12-S1-S6
  2. B Baran, Richard, Bowen, Benjamin, Northen, Trent R. Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Molecular BioSystems 2011,7, 3200-3206 DOI: 10.1039/c1mb05196b
  3. Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR.   Metabolic Footprinting of Mutant Libraries To Map Metabolite Utilization to Genotype. ACS Chemical Biology.  2013, 8 (1), 189-199.  DOI: 10.1021/cb300477w
  4. Louie KB, Bowen BP, McAlhany S,  Huang Y, Mao JH, Hellerstein M and Northen TR  Kinetic mass spectrometry imaging for in situ kinetic histochemistry, Nature Scientific Reports, 2013 Apr 15;3:1656  PMCID: PMC3625901  DOI: 10.1038/srep01656
  5. Rajeev L, Nunes da Rocha U, Klitgord N, Luning EG, Fortney J, Axen SP, Shih PM, Bouskill NJ, Bowen BP, Kerfield C, Ferran Garcia-Pichel F, Brodie EL,  Northen TR*, Mukhopadhyay, A* Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust, ISME Journal, 2013  7, 2178–2191; doi:10.1038/ismej.2013.83
  6. Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF Stable-isotope probing reveals hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific, ACS Chemical Biology 2013, 8 (8), 1755–1763 DOI: 10.1021/cb400210q
  7. Baran R, Ivanova N, Jose N, Garcia-Pichel F, Kyrpides N, Gugger M, Northen T. Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. Marine Drugs 2013, 11(10), 3617-3631; doi:10.3390/md11103617
  8. Katherine B. Louie, Benjamin P. Bowen, Xiaoliang Cheng, James
    Berleman, Romy Chakraborty, Adam Deutschbauer, Adam Arkin and Trent R.
    Northen. Replica-extraction-transfer’ for nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria and microbial communities, Analytical Chemistry  2013, 85(22) 10856-62. DOI: 10.1021/ac402240q
  9. Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, OpenMSI: High-performance web-based visualization, analysis and management of mass spectrometry imaging data, Analytical Chemistry, 2013 85(21):10354-61. doi: 10.1021/ac402540a.
  10. Cheng X, Hiras J, Deng K, Simmons BA,Adams PD, Singer SW and Northen TR. HT NIMS screening of environmental microbial isolate growth conditions for maximal enzyme activity. Frontiers in Microbiology, 2013, 4, 365. DOI: doi: 10.3389/fmicb.2013.00365
  11. Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid Kinetic Characterization of Glycosyl hydrolases (GHs) based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chemical Biology 2014, (in press, cover) DOI: 10.1021/cb5000289
  12. Heins R, Cheng X, Nath S, Deng K, Bowen B; Chivian D, Datta S, Friedland G, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin C, Singh S, Shi W, Hamilton M, Bendall M, Sczyrba A, Thompson J, Feldman T, Guenther J, Gladden J, Cheng JF, Adams P, Rubin E, Simmons BA, Sale K, Northen, T, Deutsch S. Phylogenomic Guided Identification of Industrially Relevant GH1 β-Glucosidases Through Coupled DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chemical Biology 2014, (in press)