Our research focus is metabolomics and systems medicine by application of advanced analytical techniques within preclinical and clinical research. For that we have specialized in chromatography, mass spectrometry and NMR spectroscopy and the use of metabolomics and lipidomics for systems biology and personalized medicine. Our expertise covers the complete workflow from sample preparation to analytical data acquisition, including QC measures, until statistical evaluation. The methodology of the lab ranges from ex-vivo tissue, feces/stool and cell culture investigations under application of two-phase extraction SOPs for polar and lipid metabolites until quantitative analysis of murine and human biofluids such as serum, urine and CSF. Using established SOPs and assays we are involved in a wide range of research projects in the realms of cancer, neurology, immunology, metabolic disorders and cardiovascular diseases.
Metabolomics & Systems Medicine
Head of Core Facility Metabolomics, Research Group Leader WSIC/M3
Publications: ORCID Profile
Publications: Web of Science
Biosketch
Christoph Trautwein finished his first degree at the University Stuttgart in 2006 as environmental engineer (Dipl.-Ing.) where he specialized in analytical chemistry and environmental microbiology. Awarded with a scholarship from the German Environmental Agency (DBU) he started his PhD in 2007 at the University of Freiburg in collaboration with the University Hospital Freiburg. Herein he investigated the microbial degradation and distribution of drugs in the aquatic environment using chromatography coupled with ion trap and triple quadrupole mass spectrometry. Fascinated by the potential use of advanced analytical chemistry within clinical resaerch, he started a second career in Molecular Medicine at the same time. Christoph Trautweil obtained his doctor title in 2012 (Dr. rer. nat.) and graduated in 2014 as Dipl. mol. med. at the University of Freiburg. In order to expand his analytical knowledge towards NMR spectroscopy, he was working from 2015-2016 at the Karlsruhe Institute for Technology (KIT) as postdoc for NMR based metabolomics. In 2017, he joined the WSIC at the University Hospital Tübingen and since then build up the research field of preclinical and clinical metabolomics including a magnitude of internal and external collaborations. Since 2019 he is heading his own research group supported by the WSIC foundation and proper 3rd party funding. Currently he is in process of finalizing his habilitation and assembling the new metabolomics core facility at the M3 center equipped with latest ion mobility mass spectrometry and MALDI-2 technology.
Interview
Metabolomics & Systems Medicine – Interview with Dr. Christoph Trautwein
Join Dr. Christoph Trautwein and his research group as they dive into how advanced analytical techniques – like mass spectrometry, chromatography and NMR spectroscopy – are revolutionizing our understanding of metabolism in health and disease. From sample prep to statistical analysis, discover how their expertise in metabolomics and lipidomics is driving personalized medicine and contributing to cutting-edge projects in cancer, neurology, immunology, metabolic disorders and cardiovascular disease. Learn how their work with human and murine samples is shaping the future of systems biology – one molecule at a time.
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Team
Core Facility Metabolomics, Akademische Mitarbeiter
Publications: LinkedIn profile
ex-vivo tissue
feces/stool and cell culture investigations
two-phase
extraction SOPs for polar and lipid metabolites
analysis
of murine and human biofluids
Selected publications
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2026
Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems
Mohammadzadeh R, Mahnert A, Zurabishvili T, Wink L, Kumpitsch C, Habisch H, Sprengel J, Filek K, Mertelj P, Pernitsch D, Hingerl K, Durdevic M, Gorkiewicz G, Diener C, Loy A, Kolb D, Trautwein C, Madl T, Moissl-Eichinger C. Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems.
Nat Commun. 2026 Feb 20. doi: 10.1038/s41467-026-69711-7. Epub ahead of print. PMID: 41720792. https://doi.org/10.1038/s41467-026-69711-7 -
2026
CAR-adapted PIK3CD base editing enhances T cell anti-tumor potency
Bucher P, Brückner N, Kortendieck J, Grimm M, Schleicher JT, Bartels K, Hardy S, Rausch M, Wurzer H, Thiemann M, May C, Mitstorfer M, Letzgus D, Quach J, Schneider C, Ispan DA, Gonzalez-Menendez I, Jain N, Ho YJ, Chen J, Sánchez-Rivera FJ, Sun J, Quintanilla-Martinez L, Trautwein C, Weigelin B, Claassen M, Sadelain M, Feucht J, Leibold J. CAR-adapted PIK3CD base editing enhances T cell anti-tumor potency.
Nat Cancer. 2026 Feb;7(2):368-383. doi: 10.1038/s43018-025-01099-7. Epub 2026 Jan 6. PMID: 41495526; PMCID: PMC12948676. https://doi.org/10.1038/s43018-025-01099-7 -
2025
Cryogenic mouse tissue homogenization as an alternative to fresh-frozen biopsy use for genomics, transcriptomics, proteomics and metabolomics
Zizmare L, Hofmann U, Jarboui MA, Klose F, Fraschka S, Matthes J, Krüger M, Schaeffeler E, Schwab M, Ueffing M, Pichler BJ, Boldt K, Casadei N, Trautwein C. Cryogenic mouse tissue homogenization as an alternative to fresh-frozen biopsy use for genomics, transcriptomics, proteomics and metabolomics.
Sci Rep. 2025 Jun 23;15(1):20254. https://doi.org/10.1038/s41598-025-06438-3 -
2025
Identification and impact of microbiota-derived metabolites in ascites of ovarian and gastrointestinal cancer
Deng S, Kim W, Cheng K, Yang Q, Singh Y, Bae G, Bézière N, Mager L, Kommoss S, Sprengel J, Trautwein C. Identification and impact of microbiota-derived metabolites in ascites of ovarian and gastrointestinal cancer.
Cancer Metab. 2025 May 13;13(1):21. doi: 10.1186/s40170-025-00391-5. PMID: 40361187; PMCID: PMC12076955. https://doi.org/10.1186/s40170-025-00391-5 -
2024
Retinal metabolism displays evidence for uncoupling of glycolysis and oxidative phosphorylation via Cori-, Cahill-, and mini-Krebs-cycle
Chen Y, Zizmare L, Calbiague V, Wang L, Yu S, Herberg FW, Schmachtenberg O, Paquet-Durand F, Trautwein C. Retinal metabolism displays evidence for uncoupling of glycolysis and oxidative phosphorylation via Cori-, Cahill-, and mini-Krebs-cycle.
Elife. 2024 May 13;12:RP91141. doi: 10.7554/eLife.91141. PMID: 38739438; PMCID: PMC11090511. https://doi.org/10.7554/elife.91141 -
2024
Quantitative Metabolomics and Lipoprotein Analysis of PDAC Patients Suggests Serum Marker Categories for Pancreatic Function, Pancreatectomy, Cancer Metabolism, and Systemic Disturbances
Bae G, Berezhnoy G, Flores A, Cannet C, Schäfer H, Dahlke MH, Michl P, Löffler MW, Königsrainer A, Trautwein C. Quantitative Metabolomics and Lipoprotein Analysis of PDAC Patients Suggests Serum Marker Categories for Pancreatic Function, Pancreatectomy, Cancer Metabolism, and Systemic Disturbances.
J Proteome Res. 2024 Apr 5;23(4):1249-1262. doi: 10.1021/acs.jproteome.3c00611. Epub 2024 Feb 26. PMID: 38407039; PMCID: PMC11003419. https://doi.org/10.1021/acs.jproteome.3c00611 -
2024
mage-guided metabolomics and transcriptomics reveal tumour heterogeneity in luminal A and B human breast cancer beyond glucose tracer uptake
Yang Q, Deng S, Preibsch H, Schade TC, Koch A, Berezhnoy G, Zizmare L, Fischer A, Gückel B, Staebler A, Hartkopf AD, Pichler BJ, la Fougère C, Hahn M, Bonzheim I, Nikolaou K, Trautwein C. Image-guided metabolomics and transcriptomics reveal tumour heterogeneity in luminal A and B human breast cancer beyond glucose tracer uptake.
Clin Transl Med. 2024 Feb;14(2):e1550. doi: 10.1002/ctm2.1550. PMID: 38332687; PMCID: PMC10853679. https://doi.org/10.1002/ctm2.1550 -
2024
A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1
Gallage S, Ali A, Barragan Avila JE, Seymen N, Ramadori P, Joerke V, Zizmare L, Aicher D, Gopalsamy IK, Fong W, Kosla J, Focaccia E, Li X, Yousuf S, Sijmonsma T, Rahbari M, Kommoss KS, Billeter A, Prokosch S, Rothermel U, Mueller F, Hetzer J, Heide D, Schinkel B, Machauer T, Pichler B, Malek NP, Longerich T, Roth S, Rose AJ, Schwenck J, Trautwein C, Karimi MM, Heikenwalder M. A 5:2 intermittent fasting regimen ameliorates NASH and fibrosis and blunts HCC development via hepatic PPARα and PCK1.
Cell Metab. 2024 Jun 4;36(6):1371-1393.e7. doi: 10.1016/j.cmet.2024.04.015. Epub 2024 May 7. PMID: 38718791. https://doi.org/10.1016/j.cmet.2024.04.015 -
2024
Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients
Sala S, Nitschke P, Masuda R, Gray N, Lawler NG, Wood JM, Buckler JN, Berezhnoy G, Bolaños J, Boughton BA, Lonati C, Rössler T, Singh Y, Wilson ID, Lodge S, Morillon AC, Loo RL, Hall D, Whiley L, Evans GB, Grove TL, Almo SC, Harris LD, Holmes E, Merle U, Trautwein C, Nicholson JK, Wist J. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients.
J Proteome Res. 2024 Mar 1;23(3):956-970. doi: 10.1021/acs.jproteome.3c00654. Epub 2024 Feb 4. PMID: 38310443; PMCID: PMC10913068. https://doi.org/10.1021/acs.jproteome.3c00654 -
2023
Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD+ pathway and SIRT1 activation
Lonati C, Berezhnoy G, Lawler N, Masuda R, Kulkarni A, Sala S, Nitschke P, Zizmare L, Bucci D, Cannet C, Schäfer H, Singh Y, Gray N, Lodge S, Nicholson J, Merle U, Wist J, Trautwein C. Urinary phenotyping of SARS-CoV-2 infection connects clinical diagnostics with metabolomics and uncovers impaired NAD+pathway and SIRT1 activation.
Clin Chem Lab Med. 2023 Nov 14;62(4):770-788. doi: 10.1515/cclm-2023-1017. PMID: 37955280. https://doi.org/10.1515/cclm-2023-1017