EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

ORCID iD: iD icon0000-0002-5797-3589


  • PhD 2015, ETH Zurich.
    Postdoctoral researcher at Yale University.
    Group leader at EMBL since August 2019.


Total: 30 publication(s)


Zimmermann M, Patil KR, Typas A, Maier L. (2021)

Towards a mechanistic understanding of reciprocal drug-microbiome interactions.

Mol Syst Biol 17(3) doi: 10.15252/msb.202010116
Europe PMC | doi


Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B. (2020)

The gut microbiome in solid organ transplantation.

Pediatr Transplant 24(7) doi: 10.1111/petr.13866
Europe PMC | doi

Zimmermann-Kogadeeva M, Zimmermann M, Goodman AL. (2020)

Insights from pharmacokinetic models of host-microbiome drug metabolism.

Gut Microbes 11(3):587-596. doi: 10.1080/19490976.2019.1667724
Europe PMC | doi

Øyås O, Borrell S, Trauner A, Zimmermann M, Feldmann J, Liphardt T, Gagneux S, Stelling J, Sauer U, Zampieri M. (2020)

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis.

Proc. Natl. Acad. Sci. U.S.A. 117(15):8494-8502. doi: 10.1073/pnas.1915551117
Europe PMC | doi


Wotzka SY, Kreuzer M, Maier L, Arnoldini M, Nguyen BD, Brachmann AO, Berthold DL, Zund M, Hausmann A, Bakkeren E, Hoces D, Gul E, Beutler M, Dolowschiak T, Zimmermann M, Fuhrer T, Moor K, Sauer U, Typas A, Piel J, Diard M, Macpherson AJ, Stecher B, Sunagawa S, Slack E, Hardt WD. (2019)

Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice.

Nat Microbiol 4(12):2164-2174. doi: 10.1038/s41564-019-0568-5
Europe PMC | doi

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. (2019)

Mapping human microbiome drug metabolism by gut bacteria and their genes.

Nature 570(7762) doi: 10.1038/s41586-019-1291-3
Europe PMC | doi

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. (2019)

Separating host and microbiome contributions to drug pharmacokinetics and toxicity.

Science 363(6427) doi: 10.1126/science.aat9931
Europe PMC | doi


Uchimura Y, Fuhrer T, Li H, Lawson MA, Zimmermann M, Yilmaz B, Zindel J, Ronchi F, Sorribas M, Hapfelmeier S, Ganal-Vonarburg SC, Gomez de Agüero M, McCoy KD, Sauer U, Macpherson AJ. (2018)

Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response.

Immunity 49(3):545-559.e5. doi: 10.1016/j.immuni.2018.08.004
Europe PMC | doi

Schmaler M, Colone A, Spagnuolo J, Zimmermann M, Lepore M, Kalinichenko A, Bhatia S, Cottier F, Rutishauser T, Pavelka N, Egli A, Azzali E, Pieroni M, Costantino G, Hruz P, Mori L, Sauer U, De Libero G. (2018)

Modulation of bacterial metabolism by the microenvironment controls MAIT cell stimulation.

Mucosal Immunol 11(4):1060-1070. doi: 10.1038/s41385-018-0020-9
Europe PMC | doi

Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL. (2018)

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.

Cell Host Microbe 24(1):120-132.e6. doi: 10.1016/j.chom.2018.06.002
Europe PMC | doi


Zimmermann M, Kogadeeva M, Gengenbacher M, McEwen G, Mollenkopf HJ, Zamboni N, Kaufmann SHE, Sauer U. (2017)

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection.

mSystems 2(4) doi: 10.1128/mSystems.00057-17
Europe PMC | doi

Blattmann P, Henriques D, Zimmermann M, Frommelt F, Sauer U, Saez-Rodriguez J, Aebersold R. (2017)

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.

Cell Syst 5(6) doi: 10.1016/j.cels.2017.11.002
Europe PMC | doi

Zampieri M, Zimmermann M, Claassen M, Sauer U. (2017)

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations.

Cell Rep 19(6):1214-1228. doi: 10.1016/j.celrep.2017.04.002
Europe PMC | doi

Rieck B, Degiacomi G, Zimmermann M, Cascioferro A, Boldrin F, Lazar-Adler NR, Bottrill AR, le Chevalier F, Frigui W, Bellinzoni M, Lisa MN, Alzari PM, Nguyen L, Brosch R, Sauer U, O'Hare HM, Manganelli R. (2017)

PknG senses amino acid availability to control metabolism and virulence of Mycobacterium tuberculosis.

PLoS Pathog 13(5) doi: 10.1371/journal.ppat.1006399
Europe PMC | doi

Lim B, Zimmermann M, Barry NA, Goodman AL. (2017)

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut.

Cell 169(3):547-558.e15. doi: 10.1016/j.cell.2017.03.045
Europe PMC | doi


De Smet J, Zimmermann M, Kogadeeva M, Ceyssens PJ, Vermaelen W, Blasdel B, Bin Jang H, Sauer U, Lavigne R. (2016)

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection.

ISME J 10(8):1823-35. doi: 10.1038/ismej.2016.3
Europe PMC | doi

Murima P, Zimmermann M, Chopra T, Pojer F, Fonti G, Dal Peraro M, Alonso S, Sauer U, Pethe K, McKinney JD. (2016)

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria.

Nat Commun 7 doi: 10.1038/ncomms12527
Europe PMC | doi

Chevallereau A, Blasdel BG, De Smet J, Monot M, Zimmermann M, Kogadeeva M, Sauer U, Jorth P, Whiteley M, Debarbieux L, Lavigne R. (2016)

Next-Generation "-omics" Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa.

PLoS Genet 12(7) doi: 10.1371/journal.pgen.1006134
Europe PMC | doi


Zimmermann M, Kuehne A, Boshoff HI, Barry CE, Zamboni N, Sauer U. (2015)

Dynamic exometabolome analysis reveals active metabolic pathways in non-replicating mycobacteria.

Environ Microbiol 17(11):4802-15. doi: 10.1111/1462-2920.13056
Europe PMC | doi

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R. (2015)

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.

Cell Host Microbe 18(1):96-108. doi: 10.1016/j.chom.2015.06.001
Europe PMC | doi

Cambré A, Zimmermann M, Sauer U, Vivijs B, Cenens W, Michiels CW, Aertsen A, Loessner MJ, Noben JP, Ayala JA, Lavigne R, Briers Y. (2015)

Metabolite profiling and peptidoglycan analysis of transient cell wall-deficient bacteria in a new Escherichia coli model system.

Environ Microbiol 17(5):1586-99. doi: 10.1111/1462-2920.12594
Europe PMC | doi

Ehebauer MT, Zimmermann M, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Lanéelle MA, Daffé M, Sachse C, Dziembowski A, Sauer U, Wilmanns M. (2015)

Characterization of the Mycobacterial Acyl-CoA Carboxylase Holo Complexes Reveals Their Functional Expansion into Amino Acid Catabolism.

PLoS Pathog. 11(2) doi: 10.1371/journal.ppat.1004623
Europe PMC | doi


Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. (2014)

Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.

Cell Host Microbe 16(4):495-503. doi: 10.1016/j.chom.2014.09.001
Europe PMC | doi

Machová I, Snašel J, Zimmermann M, Laubitz D, Plocinski P, Oehlmann W, Singh M, Dostál J, Sauer U, Pichová I. (2014)

Mycobacterium tuberculosis phosphoenolpyruvate carboxykinase is regulated by redox mechanisms and interaction with thioredoxin.

J Biol Chem 289(19):13066-78. doi: 10.1074/jbc.M113.536748
Europe PMC | doi

Zimmermann M, Sauer U, Zamboni N. (2014)

Quantification and mass isotopomer profiling of α-keto acids in central carbon metabolism.

Anal Chem 86(6):3232-7. doi: 10.1021/ac500472c
Europe PMC | doi


Zimmermann M, Thormann V, Sauer U, Zamboni N. (2013)

Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry.

Anal Chem 85(17):8284-90. doi: 10.1021/ac401555n
Europe PMC | doi


Watanabe S, Zimmermann M, Goodwin MB, Sauer U, Barry CE, Boshoff HI. (2011)

Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis.

PLoS Pathog 7(10) doi: 10.1371/journal.ppat.1002287
Europe PMC | doi

Dagher R, Peng S, Gioria S, Fève M, Zeniou M, Zimmermann M, Pigault C, Haiech J, Kilhoffer MC. (2011)

A general strategy to characterize calmodulin-calcium complexes involved in CaM-target recognition: DAPK and EGFR calmodulin binding domains interact with different calmodulin-calcium complexes.

Biochim Biophys Acta 1813(5):1059-67. doi: 10.1016/j.bbamcr.2010.11.004
Europe PMC | doi


Zimmermann M, Atmanene C, Xu Q, Fouillen L, Van Dorsselaer A, Bonnet D, Marsol C, Hibert M, Sanglier-Cianferani S, Pigault C, McNamara LK, Watterson DM, Haiech J, Kilhoffer MC. (2010)

Homodimerization of the death-associated protein kinase catalytic domain: development of a new small molecule fluorescent reporter.

PLoS One 5(11) doi: 10.1371/journal.pone.0014120
Europe PMC | doi

Zimmermann M, Fischbach MA. (2010)

A family of pyrazinone natural products from a conserved nonribosomal peptide synthetase in Staphylococcus aureus.

Chem Biol 17(9):925-30. doi: 10.1016/j.chembiol.2010.08.006
Europe PMC | doi