.

Dr. rer. nat. Jens O. Krömer

Tel.: +49-341-235 46 88
Fax: +49-341-235 45 46 88
Mail: jens.kroemer@ufz.de



Working Group:

Systems Biotechnology


Research Interests

Since the very early days in my career, my main interest lays in the area of systems biotechnology and here in particular on metabolism. I’m currently mainly focussing on the development of cell factories for the production of fuels, chemicals and therapeutics, but I’m also involved in a range of fundamental projects for instance on the host microbe interaction inside a marine sponge. For me the term systems biotechnology means the application of modelling tools alongside of advanced analytical tools on the design and engineering of cells and the characterization of cell physiology under different conditions. In the group of Systems Biotechnology we apply this approach to heterotrophic systems for valorization of primary phototsynthetic products and on autotrophic systems for valorization of CO2 and sun light.


Education

01/2003 - 06/2006 PhD thesis in the Biochemical Engineering Group of Prof. E. Heinzle and supervision through Prof. C. Wittmann at Saarland University (Saarbrücken, Germany).
10/1996 - 12/2002 Diplom Biologist, Saarland University, Saarbrücken, Germany.
Research thesis: Metabolic characterization and expression analysis of L-Lysine producing strains of Corynebacterium glutamicum
02/1999 - 12/1999 International exchange student (2 semesters) between Saarland University and the University of Technology (UTS) in Sydney, Australia.

Positions

since 2017   Group Leader
at Helmholtz-Centre for Environmental Research, Leipzig, Germany
2012 – 2017   Director of the Centre for Microbial Electrochemical Systems (CEMES) and Senior Research Fellow at the Advanced Water Management Centre (AWMC) at the University of Queensland.
since 2010   Several consulting projects with industry partners on metabolic modelling of production pathways for new biotechnological products in different hosts.
2009   Highly commended finalist „UniQuest trailblazer“ for the production of aromatics in bakers yeast.
2009   Promotion to Research Fellow / Lecturer.
Head of the microbial systems biology team within the group of Prof Lars Nielsen at the Australian Institute for Bioengineering and Nanotechnology (AIBN).
2007 - 2011   Manager of the Queensland node of Metabolomics Australia.
2007 - 2008   Design of laboratory, acquisition and commissioning of analytical instruments (HPLC, GC-MS, LCMS- MS).
Leader of the analytical group.
Member of the executive management group of Metabolomics Australia
2007 - 2009   University of Queensland Postdoctoral Research Fellowship at AIBN.
Scope: Systems biotechnology for rational design of
microbes for the production of biochemicals.
12/2005 - 08/2006   Postdoctoral research Officer Biochemical Engineering, Saarland University (Saarbrücken, Deutschland).
2014   Metabolic Engineering Conference X Poster Award (Student T. Williams) (ME X, 15-19/06/14, Vancouver, Canada)
2010   University of Queensland travel award
2009   Uniquest Trailblazer competition: Highly commended finalist.
Best Performing Team Award: Corporate research centre (CRC) Sugar Industry Innovation Through Biotechnology
2008   Symposium Award
2007   Dr. Eduard Martin Preis
2003   Young Scientist Poster award with Christoph Wittmann.
European Federation for Biotechnology, ECB 11 in Basel.

Index:

2018 (8)
2017 (4)

You could use our publication index for further requests.

2018 (8)

  • Averesch, N.J.H., Krömer, J.O., (2018):
    Metabolic engineering of the shikimate pathway for production of aromatics and derived compounds – present and future strain construction strategies
    Front. Bioeng. Biotechnol. 6 , art. 32
    full text (url)
  • Averesch, N.J.H., Martínez, V.S., Nielsen, L.K., Krömer, J.O., (2018):
    Toward synthetic biology strategies for adipic acid production: An in silico tool for combined thermodynamics and stoichiometric analysis of metabolic networks
    ACS Synth. Biol. 7 (2), 490 - 509
    full text (url)
  • Kracke, F., Lai, B., Yu, S., Krömer, J.O., (2018):
    Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation – A chance for metabolic engineering
    Metab. Eng. 45 , 109 - 120
    full text (url)
  • Krieg, T., Phan, L.M.P., Wood, J.A., Sydow, A., Vassilev, I., Krömer, J.O., Mangold, K.-M., Holtmann, D., (2018):
    Characterization of a membrane-separated and a membrane-less electrobioreactor for bioelectrochemical syntheses
    Biotechnol. Bioeng. 115 (7), 1705 - 1716
    full text (url)
  • Varela, C., Schmidt, S.A., Borneman, A.R., Pang, C.N.I., Krömer, J.O., Khan, A., Song, X., Hodson, M.P., Solomon, M., Mayr, C.M., Hines, W., Pretorius, I.S., Baker, M.S., Roessner, U., Mercurio, M., Henschke, P.A., Wilkins, M.R., Chambers, P.J., (2018):
    Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains
    Metab. Eng. 49 , 178 - 191
    full text (url)
  • Vassilev, I., Gießelmann, G., Schwechheimer, S.K., Wittmann, C., Virdis, B., Krömer, J.O., (2018):
    Anodic electro-fermentation: Anaerobic production of L-Lysine by recombinant Corynebacterium glutamicum
    Biotechnol. Bioeng. 115 (6), 1499 - 1508
    full text (url)
  • Vassilev, I., Hernandez, P.A., Batlle-Vilanova, P., Freguia, S., Krömer, J.O., Keller, J., Ledezma, P., Virdis, B., (2018):
    Microbial electrosynthesis of isobutyric, butyric, caproic acids, and corresponding alcohols from carbon dioxide
    ACS Sustain. Chem. Eng. 6 (7), 8485 - 8493
    full text (url)
  • Yu, S., Lai, B., Plan, M.R., Hodson, M.P., Lestari, E.A., Song, H., Krömer, J.O., (2018):
    Improved performance of Pseudomonas putida in a bioelectrochemical system through overexpression of periplasmic glucose dehydrogenase
    Biotechnol. Bioeng. 115 (1), 145 - 155
    full text (url)
to index

2017 (4)

  • Averesch, N.J.H., Prima, A., Krömer, J.O., (2017):
    Enhanced production of para-hydroxybenzoic acid by genetically engineered Saccharomyces cerevisiae
    Bioprocess. Biosyst. Eng. 40 (8), 1283 - 1289
    full text (url)
  • Gold, D.A., O'Reilly, S.S., Watson, J., Degnan, B.M., Degnan, S.M., Krömer, J.O., Summons, R.E., (2017):
    Lipidomics of the sea sponge Amphimedon queenslandica and implication for biomarker geochemistry
    Geobiology 15 (6), 836 - 843
    full text (url)
  • Koch, C., Kuchenbuch, A., Kracke, F., Bernhardt, P.V., Krömer, J.O., Harnisch, F., (2017):
    Predicting and experimental evaluating bio-electrochemical synthesis — A case study with Clostridium kluyveri
    Bioelectrochemistry 118 , 114 - 122
    full text (url)
  • Watson, J.R., Krömer, J.O., Degnan, B.M., Degnan, S.M., (2017):
    Seasonal changes in environmental nutrient availability and biomass composition in a coral reef sponge
    Mar. Biol. 164 (6), art. 135
    full text (url)
to index

  • Lai, B, Yu, S., Bernhardt, P.V., Rabaey, K., Virdis, B., Krömer, J.O.* (2016).
    Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system.
    Biotechnol. Biofuels (in press; BBIO-D-15-00478R1)
    This work has just been accepted and demonstrates for the first time that bioelectrochemical systems can be used to replace oxygen in obligate aerobes and enable biochemical production in these organisms under anaerobic conditions. This is expected to have a major impact in the field as it potentially enables completely new biotechnology processes. This is highly relevant for microbial redox processes that underpin most production systems. While being a new journal (2008-2014), it is in the highest quartile of the most important categories in my field and to date has already achieved a respectable H-index.
    *Corresponding author

  • Williams, T.C., Averesch, N., Plan, M., Winter, G., Vickers, C.E., Nielsen, L.K., Krömer, J.O.*(2014). Quorum-Sensing Linked RNAi for Dynamic Pathway Control in Saccharomyces cerevisiae.
    Metab Eng, 29, 124-134 .
    This work has established production of aromatic compounds in bakers yeast using a new method for the control of gene expression. It uses an approach that allows cells to behave like a wildtype during a growth phase, but then turns into a producer for aromatics in an production phase. It addresses two important issues: How to produce aromatics (one of the most important group petrochemicals) from renewable resources and also how to limit biomass production in a biotechnology process. The paper has already collected 9 citations in under 12 months and was also awarded the runner up poster award on the 2014 Metabolic Engineering conference (Vancouver). This is the most important international meeting in the field, organised by the International Metabolic Engineering Society. After Nature Biotechnology, Metabolic Engineering can be considered the 2nd most influential experimental journal in the field of engineering cells for production purposes.
    *Corresponding author

  • Brennan, T.C.R., Krömer,J.O.*, Nielsen, L.K. (2013)
    Physiological and Transcriptional Responses of Saccharomyces cerevisiae to d-Limonene Show Changes to the Cell Wall but Not to the Plasma Membrane.
    Appl Environ Microbiol 79 (12), 3590-3600.
    This study builds on paper 7. Here we use a systems biology approach to understand the biological mode of monoterpene toxicity. The finding do not only help to address the toxicity issue from a production point of view, but also help to understand the action of antimicrobials in the broader application sense. It is a seminal paper that challenges the wide held belief that solvents will kill cells by impacting the plasma membrane. At least in the case of monoterpenes this is not true. The toolbox used for this study is highly relevant for the current proposal. The journal is the most cited journal in the field of Applied Microbiology and Biotechnology.
    *Corresponding author

  • Brennan, T.C.R., Turner, C.D., Krömer, J.O. *, Nielsen, L.K., (2012).
    Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae.

    Featured article Biotechnol Bioeng 109:2513-2522.
    Production of chemicals in microbial systems is one of the core interests in Systems Biotechnology. But the toxicity of the desired products is in many cases a major problem. In this work we show how an in-situ extraction of toxic monoterpenes can partially address the toxicity problem. The paper provides a technical solution to a biological problem. It has received a very high uptake in my field with 44 citations since 2012. The journal is a top journal in the field.
    *Corresponding author


  • Quek, L.E., Dietmair S., Krömer J.O., and Nielsen L.K., (2010).
    Metabolic flux analysis in mammalian cell culture.
    Metab Eng. 12(2): p. 161-71.
    Analysing the intracellular flux distributions in animal cells is much more complex than analysis of microbes. This wqork provided a state-of-the art method at the date of publication and helped to move the field forward. This is now highly relevant to the current proposal. The paper has a citation count well above the H-index of the journal, meaning that it belongs to the top 69 (top 8.5 %) articles ever published in the journal (1999-2015). Thus my work already contributes two articles to the top 69 (2.89 %).

  • Dietmair, S., Timmins N.E., GrayP.P., Nielsen L.K., and Krömer J.O., (2010).
    Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol.
    Anal Biochem. 404(2): p. 155-64.
    Following the method development in paper number 2, this study provided an essential evaluation and method development for quantitative intracellular metabolite analysis in animal cells. This is highly relevant to the current proposal. Analytical biochemistry is a leading journal in this field and this paper belongs to the top 148 (top 2 %) articles over the live (1960-2015) of the journal. My work already contributes two articles to the top 148 (1.34 %).

  • Quek, L.E., Wittmann C., Nielsen L.K., and Krömer J.O. *, (2009).
    OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis.
    Microb Cell Fact. 8: p. 25.
    This work delivered a comprehensive open source flux analysis package. It has been downloaded 2436 times by academia and industry. The fact that it was provided with a GNU public license meant that it also was used in industry. There are new versions emerging based on the original source code driven by demand in the field rather than individual researchers. The software is easy to use and is even used in our undergraduate teaching of metabolic engineering. It will play an essential part for isotope based flux analysis in the current proposal. The journal is a top journal in my field and this paper belongs to the top 50 most cited articles (2002-2014).

  • Krömer, J.O., Wittmann C., Schröder H., and Heinzle E. (2006).
    Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum.
    Metab Eng. 8(4): p. 353-69.
    This paper describes using in-silico modelling tools for the prediction of optimal biochemical network design for production, leading to an international patent WO2007020295. The study was one of the first of its kind and led to a range of follow-up studies using similar approaches both by myself and by many groups and companies around the world. After Nature Biotechnology, Metabolic Engineering can be considered Biotechnology the 2nd most influential experimental journal in the field of engineering cells for production purposes. The paper has a citation count well above the H-index of the journal, meaning that it belongs to the top 69 (top 8.5 %) articles ever published in the journal (1999-2015).

  • Krömer, J.O., Sorgenfrei O., Klopprogge K., Heinzle E., and Wittmann C., (2004).
    In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome.
    J Bacteriol. 186(6): p. 1769-84.
    This publication is one of the first of its kind using a systems biology approach in a biotechnology setting. It combined different omics tools and was game changing in the applied field of microbial amino acid production. The approach ever since dominated the field as well as my career. This work also received the young scientist post award of the European Federation for Biotechnology (ECB11, 2003, Basel, Switzerland). In the current proposal a similar systems biology toolbox will be applied. This journal is the number two most cited journal in microbiology and this paper approaches the H-index of the journal, meaning that it is almost belonging to the top 188 articles over the live (1945-2015) of the journal.

  • Wittmann, C., Krömer J.O., Kiefer J., Binz T., and Heinzle E., (2004).
    Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria.
    Anal Biochem. 327(1): p. 135-9.
    An important methodology paper for the quantitative extraction of intracellular metabolites for metabolomics. The paper started a rethinking process among experts and led to a wide range of follow up studies from groups all around the world in many different organisms, that strengthened the conclusions from the paper. The approaches for metabolite extractions are pivotal for the analysis of intracellular metabolic phenotypes that are subject of the current proposal. Despite a relatively low impact factor; Analytical biochemistry is a leading journal in this field and this paper belongs to the top 148 (top 2 %) articles over the live (1960-2015) of the journal

Index

2017          (2)                    2010        (3)   
2016        (10)                    2009        (4)
2015          (4)                    2008        (1)
2014          (7)                    2007        (5)
2013          (3)                    2005        (1)
2012          (3)                    2004        (2)
2011          (5)


2017

  • Daniel Puyol, D., Batstone, D.J., Hülsen, T., Astals, S., Peces M., Krömer, J.O. (2017)
    Resource recovery from wastewater by biological technologies: opportunities, challenges and prospects.
    Frontiers in Microbiology Microbiol. doi: 10.3389/fmicb.2016.02106

  • Lai, B., Plan, M. R., Averesch, N. J., Yu, S., Kracke, F., Lekieffre, N., Bydder, S., Hodson, M. P., Winter, G., Krömer, J.O.* (2017)
    Quantitative analysis of aromatics for synthetic biology using liquid chromatography.
    Biotechnol J. 12.
    *Corresponding author

2016

  • Yu S., Plan M. R., Winter G., Krömer J.O. * (2016)
    Metabolic Engineering of Pseudomonas putida KT2440 for the Production of para-Hydroxy Benzoic Acid. Front Bioeng Biotechnol. 4, 90.
    *Corresponding author

  • Martinez V. S., Krömer J.O. (2016)
    Quantification of Microbial Phenotypes.
    Metabolites. 6.

  • Luna-Flores C. H., Palfreyman R. W., Krömer J.O. , Nielsen L. K., Marcellin E. (2016)
    Improved production of propionic acid using genome shuffling.
    Biotechnol J.

  • Kracke F., Virdis B., Bernhardt P. V., Rabaey K., Krömer J.O.* (2016)
    Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply.
    Biotechnol Biofuels. 9, 249.
    *Corresponding author

  • Hintermayer S., Yu S. Q., Krömer J.O., Weuster-Botz D. (2016)
    Anodic respiration of Pseudomonas putida KT2440 in a stirred-tank bioreactor.
    Biochemical Engineering Journal. 115, 1-13.

  • Averesch N.J.H., Winter G., Krömer J.O. (2016)
    Production of para-aminobenzoic acid from different carbon sources in engineered Saccharomyces cerevisiae.
    Microb Cell Fact. 15, 89
    *Corresponding author

  • Farlow A. Krömer J.O.* (2016)
    Reactions with aminobenzoic acids via diazonium salts open new routes to bio-derived aromatics.
    IJOC Vol.6 No.2, June 2016
    *Corresponding author

  • Lai B., Plan M., Hodson M.P., Krömer J.O.* (2016)
    Simultaneous determination of sugars, carboxylates, alcohols and aldehydes from fermentations by high performance liquid chromatography.
    Fermentation accepted 24/02/2016
    *Corresponding author

  • Lai B., Yu S., Bernhardt P.V., Rabaey K., Virdis B., Krömer J.O.* (2016)
    Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system.
    Biotechnol Biofuels. 9, 39.
    *Corresponding author

  • Virdis B., Millo D., Donose B.C., Lu Y., Batstone D.J., Krömer J.O. (2016)
    Analysis of electron transfer dynamics in mixed community electroactive microbial biofilms.
    Rsc Advances. 6, 3650-3660.

2015

  • Kracke F., Vassilev I., Krömer J.O.* (2015)
    Microbial electron transport and energy conservation–the foundation for optimizing bioelectrochemical systems.
    Frontiers in Microbiology 6, 575.
    *Corresponding author

  • Brennan T.C.R., Williams T.C., Schulz B.L., Palfreyman R.W., Krömer J.O.*, Nielsen L.K (2015)
    Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae.
    Appl Environ Microbio 81 (10), 3316-3325
    *Corresponding author

  • Williams T.C., Averesch N., Winter G., Plan M.G., Vickers C.E., Nielsen L.K., Krömer J.O.* (2015).
    Quorum-Sensing Linked RNAi for Dynamic Pathway Control in Saccharomyces cerevisiae.
    Metab Eng, 29, 124-134
    *Corresponding author

  • Harnisch F., Rosa L.F.M., Kracke F., Virdis B., Krömer J.O. (2015)
    Electrifying white biotechnology: Coupling of microbiology & electrochemistry for bioproduction.
    ChemSusChem 8 (5), 758-766 JOURNAL COVER


2014

  • Kracke F., Krömer J.O.*, (2014)
    Identifying target processes for microbial electrosynthesis by elementary mode analysis.
    BMC bioinformatics 15 (1), 6590
    *Corresponding author


  • Turner J., Quek L.-E., Titmarsh D., Krömer J.O., Kao L.-P., Nielsen L.K., Wolvetang E., Cooper-White J. (2014)
    Metabolic flux analysis of human embryonic stem cells.
    PloS one 9 (11), e112757

  • Averesch N., Krömer J.O.*, (2014)
    Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli.
    Metab Eng Comm 1, 19-28
    *Corresponding author

  • Bruschi M., Krömer J.O. *, Steen J.A., Nielsen L.K. (2014)
    Production of the short peptide surfactant DAMP4 from glucose or sucrose in high cell density cultures of Escherichia coli BL21(DE3).
    Micro Cell Fact 13 (1), 99.
    *Corresponding author


  • Arifin Y., Archer C., Lim S., Quek L.-E., Sugiarto H., Marcellin E., Vickers C.E., Krömer J.O. *, Nielsen L.K (2014)
    Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation.
    Appl Microb Biotech, 1-12
    *Corresponding author

  • Winter G., Averesch N., Nunez-Berna, D., Krömer J.O. *, (2014)
    In vivo instability of chorismate causes substrate loss during fermentative production of aromatics.
    Yeast Yeast 31 (9), 333-341
    *Corresponding author

  • Watson J.R., Brennan T.C.R., Degnan B.M., Degnan S.M., Krömer J.O.*, (2014)
    Analysis of the biomass composition of the demosponge Amphimedon queenslandica on Heron Island Reef, Australia.
    Marine drugs 12 (6), 3733-3753
    *Corresponding author


2013

  • Brennan T.C.R., Krömer J.O.*, Nielsen L.K. (2013)
    Physiological and Transcriptional Responses of Saccharomyces cerevisiae to d-Limonene Show Changes to the Cell Wall but Not to the Plasma Membrane.
    Appl Environ Microbiol 79 (12), 3590-3600
    *Corresponding author

  • Winter G. and Krömer J.O. *, (2013).
    Fluxomics - connecting 'omics analysis and phenotypes.
    Environ Microbiol 15(7): 1901-1916.
    *Corresponding author

  • Schmidt S.A., Jacob S.S., Ahn S.B., Rupasinghe T., Krömer J.O., Khan A., Varela C., (2013).
    Two strings to the systems biology bow - co-extracting the metabolome and proteome of wine yeast.
    Metabolomics 9:173-188.


2012

  • Krömer J.O. *, Nunez-Bernal D., Averesch N., Hampe J., Varela J., Varela C., (2012).
    Production of aromatics in Saccharomyces cerevisiae – a feasibility study.
    J Biotech 163:184-193.
    *Corresponding author

  • Brennan T.C.R., Turner C.D., Krömer J.O. *, Nielsen L.K., (2012).
    Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae.
    Featured article Biotechnol Bioeng 109:2513-2522.
    *Corresponding author

  • Vickers C.E., Klein-Marcuschamer D., Krömer J.O., (2012).
    Examining the feasibility of bulk commodity production in Escherichia coli.
    Biotechnol Lett 34:585–596.


2011

  • Arifin Y., Sabri S., Sugiarto H., Krömer J.O., Vickers C.E., Nielsen L.K., (2011).
    Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxybutyrate (PHB) production from sucrose in fed batch culture.
    J Biotech 156, 275–278.

  • Saunders E.C., Ng W.W., Chambers J.M., Ng M., Naderer T., Krömer J.O., Likic V.A., McConville M.J., (2011).
    Isotopomer Profiling of Leishmania mexicana Promastigotes Reveals Important Roles for Succinate Fermentation and Aspartate Uptake in Tricarboxylic Acid Cycle (TCA) Anaplerosis, Glutamate Synthesis, and Growth.
    J Biol Chem 286, 27706–27717.

  • Varela C., Schmidt S.A., Borneman A.R., Krömer J.O., Khan A., Chambers P.J., (2011).
    Systems biology: a new paradigm for industrial yeast strain development.
    Microbiology Australia, 32(4): 151-155.

  • Krömer J.O. * (2011).
    Quantification of microbial phenotypes using 13C-Fluxomics
    Microbiology Australia, 32(4): 163-165.
    *Corresponding author

  • Krömer J.O. *, Dietmair S., Jacob S.S. and Nielsen L.K. (2011). Quantification of L-Alanyl-L-Glutamine in mammalian cell culture - evaluation of different detectors.
    Anal Biochem. 416(1): p. 129-31
    *Corresponding author


2010

  • Dietmair, S., Timmins N.E., Gray P.P., Nielsen L.K., and Krömer J.O., (2010).
    Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol.
    Anal Biochem. 404(2): p. 155-64.

  • Quek L.E., Dietmair S., Krömer J.O., and Nielsen L.K., (2010).
    Metabolic flux analysis in mammalian cell culture.
    Metab Eng. 12(2): p. 161-71.

  • Vickers C.E., Blank L.M., and Krömer J.O., (2010).
    Grand Challenge Commentary: Chassis cells for industrial biochemical production.
    Nat Chem Biol. 6(12): p. 875-7.


2009

  • Krömer J.O., Quek L.-E., Nielsen L.K., (2009).
    13C-fluxomics: A tool for measuring metabolic phenotypes.
    Austral Biochem, 40(3): 17-20.

  • Marcellin E., Nielsen L.K., Abeydeera P., and Krömer J.O. * (2009).
    Quantitative analysis of intracellular sugar phosphates and sugar nucleotides in encapsulated streptococci using HPAEC-PAD.
    Biotechnol J. 4(1): p. 58-63.
    *Corresponding author

  • Quek, L.E., Wittmann C., Nielsen L.K., and Krömer J.O. * (2009).
    OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis.
    Microb Cell Fact. 8: p. 25.
    *Corresponding author

  • Schneider, K., Krömer J.O., Wittmann C., Alves-Rodriguez I., Meyerhans A., Diez J., and Heinzle E., (2009).
    Metabolite profiling studies in Saccharomyces cerevisiae: an assisting tool to prioritize host targets for antiviral drug screening.
    Microb Cell Fact. 8(1): p. 12.


2008

  • Krömer, J.O., Bolten C.J., Heinzle E., Schröder H., and Wittmann C., (2008).
    Physiological response of Corynebacterium glutamicum to oxidative stress induced by deletion of the transcriptional repressor McbR.
    Microbiology. 154(Pt 12): p. 3917-30.

2007

  • Nicola, C., Kiefer P., Letisse F., Krömer J.O., Massou S., Soucaille P., Wittmann C., Lindley N.D., and Portais J. C., (2007).
    Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase.
    FEBS Lett. 581(20): p. 3771-6.

  • Wittmann C., Weber J., Betiku E., Krömer J.O., Bohm D., and Rinas U., (2007).
    Response of fluxome and metabolome to temperature-induced recombinant protein synthesis in Escherichia coli.
    J Biotechnol. 132(4): p. 375-84.

  • Krömer J.O., Heinzle E., Schröder H. and Wittmann C., (2006).
    Accumulation of homolanthionine and activation of a novel pathway for isoleucine biosynthesis in Corynebacterium glutamicum McbR deletion strains.
    J Bacteriol. 188(2): p. 609-18.

  • Krömer J.O., Heinzle E. and Wittmann C., (2006).
    Quantification of S-adenosyl methionine in microbial cell extracts.
    Biotechnol Lett. 28(2): p. 69-71

  • Krömer J.O., Wittmann C., Schröder H., and Heinzle E., (2006).
    Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum.
    Metab Eng. 8(4): p. 353-69.


2005

  • Krömer, J.O., Fritz M., Heinzle E., and Wittmann C., (2005).
    In vivo quantification of intracellular amino acids and intermediates of the methionine pathway in Corynebacterium glutamicum.
    Anal Biochem. 340(1): p. 171-3.


2004

  • Krömer J.O., Sorgenfrei O., Klopprogge K., Heinzle E. and Wittmann C., (2004).
    In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome.
    J Bacteriol. 186(6): p. 1769-84.

  • Wittmann, C., Krömer J.O., Kiefer P., Binz T., and Heinzle E., (2004).
    Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria.
    Anal Biochem. 327(1): p. 135-9

Books

2014

  • Krömer, J.O.*, Blank, L., Nielsen , L.K. (2014) Metabolic Flux Analysis - Methods in Molecular Biology, Volume 1191 Humana Press
    * Corresponding author

  • Watson, J., Degnan, B., Degnan, S., Krömer, J.O. Determining the biomass composition of a sponge holobiont for flux analysis in Krömer, J.O$, Blank, L., Nielsen , L.K. (2014)Metabolic Flux Analysis - Methods in Molecular Biology, Volume 1191 , Humana Press


Patents

  • WO2007051725: New L-methionine-overproducing microorganism, where the formation and/or accumulation of homolanthionine in the methionine pathway is reduced and/or prevented, useful for producing L-methionine

  • WO2007020295: Determining organism with increased efficiency for methionine synthesis comprises parameterizing metabolic flux of an initial methionine synthesizing organism based on pre-known metabolic pathways related to methionine synthesis

  • WO2007135188: Preparing L-methionine in a microorganism by cultivating the microorganism, where the amount of serine available for the metabolism of the microorganism is increased; and isolating L-methionine.

Research Thesis

  • Systembiotechnologische Studien an Corynebacterium glutamicum zur Charakterisierung der Methioninsynthese. doctor rerum naturalium (summa cum laude 30.06.2006 – Saarland University, Germany).
    hyperlink: PhD thesis

  • Metabolische Charakterisierung und Expressionsanalyse L-Lysin produzierender Staemme von Corynebacterium glutamicum. Diplom Biologe (30.10.2002 – Saarland University, Germany)

Conference Paper

2012

  • Dietmair, S., Timmins, N.E., Chrysanthopoulos, P., Gray, P.P., Krömer, J.O., Nielsen, L.K., (2012).
    Metabolomic Analysis of CHO Cultures with Different Growth Characteristics–Development of a Metabolite Extraction Protocol for Suspension Adapted Mammalian Cells. Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009.


2010

  • Arifin, Y., Sugiarto, H., Sabri, S., Krömer, J.O., Vickers, C.E., Nielsen, L.K. (2010)
    Metabolic engineering of sucrose utilizing Escherichia coli for polyhydroxybutyrate production. 14th International Biotechnology Symposium and Exhibition (IBS-2008)
    Rimini, ITALY Date: SEP 14-18, 2010. DOI: 10.1016/j.jbiotec.2010.08.189


2009

  • Schneider, K., Krömer, J.O., Wittmann, C., I. Alves-Rodriguez, A. Meyerhans, J. Diez, and E. Heinzle (2009).
    Metabolite profiling studies in Saccharomyces cerevisiae: an assisting tool to prioritize host targets for antiviral drug screening. New Biotechnology Volume: 25 Pages: S4 Published: SEP 2009


Conference Presentations

2015

  • invited: Metabolic Engineering of Saccharomyces cerevisiae for the production of aromatics. YEAST: PRODUCTS AND DISCOVERY 2015 (Adelaide, 12/ 2015)

  • Selected from abstracts: Quorum-Sensing Linked RNA interference for Dynamic Metabolic Pathway Control in Saccharomyces cerevisiae for the production of aromatics. EMBO | EMBL Symposium: Enabling Technologies for Eukaryotic Synthetic Biology (06/2015)

2014

  • Selected from abstracts: Unravelling sucrose metabolism of E. coli using Systems Biology and 13C fluxomics. B3 Systems Biology and Bioinformatics Symposium
    2014 Symposium, Brisbane, 11/2014


2013

  • invited: Overcoming the toxicity hurdle for renewable jet fuels. Bioenergy Australian, Hunter Valley, 11/2013.

  • invited: Propionibacterium revisited - Shifting fermentative metabolism using mediated electron transport on cathodes. 4th Microbial Fuel Cell Conference, Cairns, 09/2013

  • Selected from abstracts: (presented by PhD-student Kracke): Understanding benefits and limitations of Microbial Electrosynthesis: An elementary mode analysis of microbial production during electrically enhanced fermentation. 4th Microbial Fuel Cell Conference, Cairns, 09/201


2011

  • invited: Characterization of Escherichia coli W during growth on sucrose or glucose using systems biology. Australian Bioprocessing Network, Annual Conference, Adelaide, 10/2011

  • Selected from abstracts: OpenFlux: efficient modelling software for 13C-based metabolic flux analysis. Metabolomics 2011, Cairns, Australia, 06/2011

  • invited: 13C-fluxomics and metabolomics - important additions to the systems biology toolbox. 16th Proteomics Symposium of the Australian Proteomics Society, Lorne, 02/2011


2010

  •  invited: Systems Biotechnology for Industrial Microbiology. AusBiotech 2010, Melbourne 10/2010

  • Selected from abstracts: In-depth analysis of the respiro-fermentative metabolism in bakers yeast using 13C-fluxomics and metabolomics 2nd Australasian Symposium on Metabolomics in Melbourne, Australia 10/2010.

  • Selected from abstracts: Quantitative Metabolomics and 13C Fluxomics reveal redistribution of fluxes in Saccharomyces cerevisiae growing at different rates on glucose and glutamate. 11th International Symposium on the Genetics of Industrial Microorganisms, Melbourne 06/2010


2009

  • invited (Keynote): Metabolomics and Fluxomics - Invaluable tools for the modern metabolic engineer. 1st Australasian Symposium on Metabolomics in Auckland, New Zealand 07/2009


Invited Presentations (Workshop and Seminars)

2015

  • Joint workshop Tianjin University - University of Queensland on Synthetic Biology. Tjianjin, China, 10/2015

  • Joint Symposium Technical University Munich - University of Queensland on Water, Environment and Sustainability. Munich, Germany, 06/2015


2014

  • Industrial Biotechnology at the Centre for Microbial Electrosynthesis. DECHEMA, Frankfurt, Germany 02/2014

  • Industrial Biotechnology at the Centre for Microbial Electrosynthesis. University of Ghent, Ghent, Belgium, 02/2014

  • Industrial Biotechnology at the Centre for Microbial Electrosynthesis. Bioprocess Engineering Seminar, TU Munich, Germany, 02/2014


2012

  • Systems Biotechnology - how in-depth analysis and modelling helps to improve microbial production systems. School of Molecular Bioscience - Seminar Series University of Sydney, Sydney, NSW 04/2012.


2010

  • Metabolomics and Fluxomics - Invaluable tools for Systems Biology. University of Luxembourg Seminar series, Luxembourg, 01/2010

  • Development of Metabolomics and Fluxomics as tools for Systems Biotechnology. Weekly seminar, Department of biological and chemical engineering, Technical University Dortmund, Dortmund, Germany 01/2010


2009

  • Metabolomics and Fluxomics - Invaluable tools for Systems Biology. Seminar Microbiology Saarland University, Saarbruecken, Germany 12/2009

  • Microbial Metabolomics and Fluxomics -Tools for understanding and engineering cells. CSIRO systems biology workshop, Brisbane, QLD, Australia 06/2009

  • Fluxomics. Bioplatforms Australia Systems Biology Consortium kick-off meeting. Australian Wine Research Institute, Adelaide, SA Australia 05/2009.