WP 1 Transcriptomics, metagenomics, competitive phenomics and metabolomics

In the overarching Work Package 1 (WP1), the consortium will centralize omics data produced by partners in Jena, Paris, Düsseldorf and Madrid as a hub for data analysis and the identification of commensal-to-pathogen associated genes, molecules, patterns and biomarkers. We will develop novel systems biology approaches for integrative analysis of multi-species data. One focus will be the communication of species in terms of metabolism. State-of-the-art genome scale metabolic models will be developed for C. albicans and the potentially probiotic C. albicans-antagonist yeast Pichia jadinii. Transcriptional data will be integrated into the metabolic models. Information created in this WP1, fed by experimental data of our partners in Jena and Paris, will be used to develop and refine hypotheses to be experimentally tested by partners in Jena, Paris, Düsseldorf and Madrid, e.g. through targeted metabolomics, detailed analysis of key commensal factors or genetic dissection of probiotic yeasts.

References

Karlsson F, Tremaroli V, Nookaew I et al. (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99-103.
PubMed

Shoaie S, Karlsson F, Mardinoglu A et al. (2013) Understanding the interactions between bacteria in the human gut through metabolic modeling. Scientific Reports 3, 2532.
PubMed Open Access PDF

Mardinoglu A, Agren R, Kampf C et al. (2014) Genome-scale metabolic modeling of hepatocytes leads to identification of serine deficiency in non-alcoholic fatty liver disease. Nature Communications 5, 3083.
PubMed

Karlsson FH, Fåk F, Nookaew I et al. (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature Communication 3, 1245.
PubMed Open Access PDF

Mardinoglu A, Agren R, Kampf C et al. (2013) Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol Syst Biol 9, 649.
PubMed Open Access PDF

Related partners

Chalmers University of Technology Göteborg

Chalmers University of Technology Gothenborg

Address

Chalmers University of Technology
Kemivägen 10
41296 Gothenborg, Sweden

Principal Investigator

Jens Nielsen

Jens Nielsen

+46 31 772 3804

www.sysbio.se

Scientists

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Hans Knöll Institute Jena

Hans Knöll Institute Jena

Address

Leibniz Institute for Natural Product Research and Infection Biology
Hans Knöll Institute
Adolf-Reichwein-Str. 23
07745 Jena, Germany

Coordinator and Principal Investigator

Bernhard Hube

Bernhard Hube

+49 3641 532 1401

www.leibniz-hki.de

Scientists

Katja Graf

Katja Graf

+49 3641 532 1218

Antonia Dräger

Antonia Dräger

+49 3641 532 1595

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Institut Pasteur Paris

Institut Pasteur Paris

Address

Institut Pasteur
25, rue du Docteur Roux
75015 Paris, France

Principal Investigator

Christophe d’ Enfert

Christophe d’ Enfert

+33 1 40 61 32 57

www.pasteur.fr

Scientists

Marie-Elisabeth Bougnoux

Marie-Elisabeth Bougnoux
Associate Professor

Natacha Sertour

Natacha Sertour
Technician

Murielle Chauvel

Murielle Chauvel
Technician

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Heinrich Heine University Düsseldorf

Heinrich Heine University Düsseldorf

Address

Heinrich Heine University Düsseldorf
Universitätsstr. 1/26.12
40225 Düsseldorf, Germany

Principal Investigator

Scientists

Christoph Bürth

Christoph Bürth

+49 211 81-15488

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Universidad Complutense de Madrid

Universidad Complutense de Madrid (USM)

Address

Universidad Complutense de Madrid (USM)
Avda. Ramón y Cajal s/n
28040 Madrid, Spain

Principal Investigator

Jesús Pla

Jesús Pla

+34 91 3941617

www.ucm.es

Scientists

Elvira Román

Elvira Román

Daniel Prieto

Daniel Prieto

+34 610 686818

Rebeca Alonso Monge

Rebeca Alonso Monge

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