Paternal microbiome perturbations impact offspring fitness.

Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA

Nature, 2024

doi:10.1038/s41586-024-07336-w.

Gut microbiome integration in drug discovery and development of small molecules.

Jimonet P, Druart C, Blanquet-Diot S, Boucinha L, Kourula S, Le Vacon F, Maubant S, Rabot S, Van de Wiele T, Schuren F, Thomas V, Walther B, Zimmermann M

Drug metabolism and disposition: the biological fate of chemicals, 2024

doi:10.1124/dmd.123.001605.

Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction.

Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC

Cell reports, 2023

doi:10.1016/j.celrep.2023.113517.

Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics.

Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC

Cell reports, 2023

doi:10.1016/j.celrep.2023.113519.

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.

Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L

Nature protocols, 2023

doi:10.1038/s41596-023-00926-4.

Decipher enzymes from human microbiota for drug discovery and development.

Beliaeva MA, Wilmanns M, Zimmermann M

Current opinion in structural biology, 2023

doi:10.1016/j.sbi.2023.102567.

Deciphering enzymes from human microbiota for drug discovery and development – a minireview.

Beliaeva MA, Wilmanns M, Zimmermann M

OSF Preprints, 2023

doi:10.31219/osf.io/243wj.

How the gut microbiota helps keep us vitaminized.

Brauer-Nikonow A, Zimmermann M

Cell host & microbe, 2022

doi:10.1016/j.chom.2022.07.010.

Pharmacological perturbation of thiamine metabolism sensitizes Pseudomonas aeruginosa to multiple antibacterial agents.

Kim HJ, Li Y, Zimmermann M, Lee Y, Lim HW, Leong Tan AS, Choi I, Ko Y, Lee S, Seo JJ, Seo M, Jeon HK, Cechetto J, Hoong Yam JK, Yang L, Sauer U, Jang S, Pethe K

Cell chemical biology, 2022

doi:10.1016/j.chembiol.2022.07.001.

Dynamic tracing of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs.

van Scherpenzeel M, Conte F, Büll C, Ashikov A, Hermans E, Willems A, van Tol W, Kragt E, Noga M, Moret EE, Heise T, Langereis JD, Rossing E, Zimmermann M, Rubio-Gozalbo ME, de Jonge MI, Adema GJ, Zamboni N, Boltje T, Lefeber DJ

Glycobiology, 2022

doi:10.1093/glycob/cwab106.

Metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation.

Hendrix H, Zimmermann-Kogadeeva M, Zimmermann M, Sauer U, De Smet J, Muchez L, Lissens M, Staes I, Voet M, Wagemans J, Ceyssens PJ, Noben JP, Aertsen A, Lavigne R

Cell reports, 2022

doi:10.1016/j.celrep.2022.110372.

Unravelling the collateral damage of antibiotics on gut bacteria.

Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A

Nature, 2021

doi:10.1038/s41586-021-03986-2.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature, 2021

doi:10.1038/s41586-021-03891-8.

Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Konstantinidis D, Pereira F, Geissen EM, Grkovska K, Kafkia E, Jouhten P, Kim Y, Devendran S, Zimmermann M, Patil KR

Molecular systems biology, 2021

doi:10.15252/msb.202010189.

Methodological advances to study contaminant biotransformation: new prospects for understanding and reducing environmental persistence?

Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE

ACS ES&T water, 2021

doi:10.1021/acsestwater.1c00025.

Towards a mechanistic understanding of reciprocal drug-microbiome interactions.

Zimmermann M, Patil KR, Typas A, Maier L

Molecular systems biology, 2021

doi:10.15252/msb.202010116.

The gut microbiome in solid organ transplantation.

Baghai Arassi M, Zeller G, Karcher N, Zimmermann M, Toenshoff B

Pediatric transplantation, 2020

doi:10.1111/petr.13866.

Insights from pharmacokinetic models of host-microbiome drug metabolism.

Zimmermann-Kogadeeva M, Zimmermann M, Goodman AL

2019

doi:10.1080/19490976.2019.1667724.

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

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

Proceedings of the National Academy of Sciences of the United States of America, 2020

doi:10.1073/pnas.1915551117.

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

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

Nature microbiology, 2019

doi:10.1038/s41564-019-0568-5.

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

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL

Nature, 2019

doi:10.1038/s41586-019-1291-3.

Separating host and microbiome contributions to drug pharmacokinetics and toxicity.

Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL

Science (New York, N.Y.), 2019

doi:10.1126/science.aat9931.

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

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

Immunity, 2018

doi:10.1016/j.immuni.2018.08.004.

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

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

Mucosal immunology, 2018

doi:10.1038/s41385-018-0020-9.

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

Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL

Cell host & microbe, 2018

doi:10.1016/j.chom.2018.06.002.

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

Zimmermann M, Kogadeeva M, Gengenbacher M, McEwen G, Mollenkopf HJ, Zamboni N, Kaufmann SHE, Sauer U

mSystems, 2017

doi:10.1128/mSystems.00057-17.

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

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

Cell systems, 2017

doi:10.1016/j.cels.2017.11.002.

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations.

Zampieri M, Zimmermann M, Claassen M, Sauer U

Cell reports, 2017

doi:10.1016/j.celrep.2017.04.002.

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

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

PLoS pathogens, 2017

doi:10.1371/journal.ppat.1006399.

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

Lim B, Zimmermann M, Barry NA, Goodman AL

Cell, 2017

doi:10.1016/j.cell.2017.03.045.

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

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

The ISME journal, 2016

doi:10.1038/ismej.2016.3.

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

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

Nature communications, 2016

doi:10.1038/ncomms12527.

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

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

PLoS genetics, 2016

doi:10.1371/journal.pgen.1006134.

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

Zimmermann M, Kuehne A, Boshoff HI, Barry CE, Zamboni N, Sauer U

Environmental microbiology, 2015

doi:10.1111/1462-2920.13056.

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

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

Cell host & microbe, 2015

doi:10.1016/j.chom.2015.06.001.

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

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

Environmental microbiology, 2015

doi:10.1111/1462-2920.12594.

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

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

PLoS pathogens, 2015

doi:10.1371/journal.ppat.1004623.

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

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

Cell host & microbe, 2014

doi:10.1016/j.chom.2014.09.001.

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

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

The Journal of biological chemistry, 2014

doi:10.1074/jbc.M113.536748.

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

Zimmermann M, Sauer U, Zamboni N

Analytical chemistry, 2014

doi:10.1021/ac500472c.

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

Zimmermann M, Thormann V, Sauer U, Zamboni N

Analytical chemistry, 2013

doi:10.1021/ac401555n.

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

Watanabe S, Zimmermann M, Goodwin MB, Sauer U, Barry CE, Boshoff HI

PLoS pathogens, 2011

doi:10.1371/journal.ppat.1002287.

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.

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

Biochimica et biophysica acta, 2011

doi:10.1016/j.bbamcr.2010.11.004.

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

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

PloS one, 2010

doi:10.1371/journal.pone.0014120.

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

Zimmermann M, Fischbach MA

Chemistry & biology, 2010

doi:10.1016/j.chembiol.2010.08.006.