Cluster of Excellence – Controlling Microbes to Fight Infections

CMFI Publications

2021

  • 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. Unravelling the collateral damage of antibiotics on gut bacteria. Nature, published on 13 October 2021. DOI: 10.1038/s41586-021-03986-2.
  • Payne DD, Renz A, Dunphy LJ, Lewis T, Dräger A, Papin JA. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. NPJ Syst Biol Appl. Oct 8;7(1):37. (2021) doi: 10.1038/s41540-021-00198-2.
  • Kretschmer D, Breitmeyer R, Gekeler C, Lebtig M, Schlatterer K, Nega M, Stahl M, Stapels D, Rooijakkers S, Peschel A. Staphylococcus aureus Depends on Eap Proteins for Preventing Degradation of Its Phenol-Soluble Modulin Toxins by Neutrophil Serine Proteases. Front. Immunol.  12:701093. (2021) doi: 10.3389/fimmu.2021.701093.
  • Conzentino MS, Santos TPC, Selim KA, Wagner B, Alford JT, Deobald N, Paula NM, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Huergo MCC, Reis RA, Huergo LF. Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion using Ni2+ magnetic beads. Anal Biochem. 631:114360. doi: 10.1016/j.ab.2021.114360.
  • Kopparapu PK, Deshmukh M, Hu Z, Mohammad M, Maugeri M, Götz F, Valadi H, Jin T. Lipoproteins Are Responsible for the Pro-Inflammatory Property of Staphylococcus aureus Extracellular Vesicles. Int J Mol Sci. 22(13):7099. (2021) doi: 10.3390/ijms22137099.
  • Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. mSystems. 6(4):e0060121. (2021) doi: 10.1128/mSystems.00601-21.
  • Semanjski M, Gratani FL, Englert T, Nashier P, Beke V, Nalpas N, Germain E, George S, Wolz C, Gerdes K, Macek B. Proteome Dynamics during Antibiotic Persistence and Resuscitation. mSystems 6(4):e00549-21. (2021) doi: 10.1128/mSystems.00549-21.
  • Wang CY, Lempp M, Farke N, Donati S, Glatter T, Link H. Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. Nat Commun 12:4929. (2021). doi: https://doi.org/10.1038/s41467-021-25142-0.
  • Schlatterer K, Beck C, Schoppmeier U, Peschel A, Kretschmer D: Acetate sensing by GPR43 alarms neutrophils and protects from severe sepsis. Communications Biology 4:928. (2021) doi: https://doi.org/10.1038/s42003-021-02427-0.
  • Torres Salazar BO, Heilbronner S, Peschel A, Krismer B. Secondary Metabolites Governing Microbiome Interaction of Staphylococcal Pathogens and Commensals. Microb Physiol Jul 29:1-19. (2021) doi: https://doi.org/10.1159/000517082.
  • Singh N, Kronenberger T, Eipper A, Weichel F, Franz M, Macek B, Wagner S. Conserved salt bridges facilitate assembly of the helical core export apparatus of a Salmonella enterica type III secretion system, J Mol Biol Jul 22:167175. (2021) doi: https://doi.org/10.1016/j.jmb.2021.167175.
  • Fan SH, Matsuo M, Huang L, Tribelli PM, Götz F. The MpsAB Bicarbonate Transporter Is Superior to Carbonic Anhydrase in Biofilm-Forming Bacteria with Limited CO2 Diffusion. Microbiol Spectr. Jul 21:e0030521. (2021) doi: https://doi.org/10.1128/Spectrum.00305-21.
  • Mitousis L, Maier H, Martinovic L, Kulik A, Stockert S, Wohlleben W, Stiefel A, Musiol-Kroll EM. Engineering of Streptoalloteichus tenebrarius 2444 for Sustainable Production of Tobramycin. Molecules. Jul 18;26(14):4343. (2021) doi: https://doi.org/10.3390/molecules26144343.
  • Huang YM, Straub D, Kappler A, Smith N, Blackwell N, Kleindienst S. A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction. Microb Physiol. Jul 2:1-16. (2021) doi: https://doi.org/10.1159/000517083.
  • Rapp J, Wagner B, Brilisauer K, Forchhammer K. In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria. Front Microbiol. 12:692986. (2021) doi: https://doi.org/10.3389/fmicb.2021.692986.
  • Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics Jun 24:btab229. (2021) doi: https://doi.org/10.1093/bioinformatics/btab229.
  • Schmid R, Petras D, Nothias LF et al. Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment. Nat Commun 12: 3832. (2021) doi: https://doi.org/10.1038/s41467-021-23953-9.
  • Brötz-Oesterhelt H, Vorbach A. Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential. Front Mol Biosci 8: 690902. (2021) doi: https://doi.org/10.3389/fmolb.2021.690902.
  • Hottmann I, Borisova M, Schäffer C, Mayer C. Peptidoglycan Salvage Enables the Periodontal Pathogen Tannerella forsythia to Survive within the Oral Microbial Community. Microb Physiol (2021) doi: https://doi.org/10.1159/000516751.
  • Du X, Larsen J, Li M, Walter A, Slavetinsky C, Both A, Sanchez Carballo P M, Stegger M, Lehmann E, Liu Y, Liu J, Slavetinsky J, Duda K A, Krismer B, Heilbronner S, Weidenmaier C, Mayer C, Rohde H, Winstel V, Peschel A. Staphylococcus epidermidis clones express Staphylococcus aureus-type wall teichoic acid to shift from commensal to pathogen behavior. Nature Microbiology 6:757–768. (2021) doi: https://doi.org/10.1038/s41564-021-00913-z.
  • Rozbeh R, Forchhammer K. Split NanoLuc technology allows quantitation of interactions between PII protein and its receptors with unprecedented sensitivity and reveals transient interactions. Sci Rep 11:12535. (2021) doi:
  • https://doi.org/10.1038/s41598-021-91856-2.
  • Renz A, Widerspick L, Dräger A. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target. Genes 12:796. (2021) doi: https://doi.org/10.3390/genes12060796.
  • How Can We Effectively Combat Antibiotic Resistant Bacterial Pathogens?, interview with Andreas Peschel. Latest Thinking Video Publication. (2021) doi: https://doi.org/10.21036/LTPUB10921.
  • Bier K, Schittek B. Beneficial effects of coagulase-negative Staphylococci on Staphylococcus aureus skin colonization. Exp Dermatol. May 6:1-11. (2021) doi: https://doi.org/10.1111/exd.14381.
  • Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz-Oesterhelt H, Gross H. Nocathioamides, uncovered by a Tunable Metabologenomic Approach, define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl. May 14. (2021) doi: https://doi.org/10.1002/anie.202102571.
  • Neumann N, Doello S, Forchhammer K. Recovery of Unicellular Cyanobacteria from Nitrogen Chlorosis: A Model for Resuscitation of Dormant Bacteria. Microb Physiol. Apr 20:1-10. (2021) doi: 10.1159/000515742. Online ahead of print.
  • Fišarová L, Botka T, Du X, Mašlaňová I, Bárdy P, Pantůček R, Benešík M, Roudnický P, Winstel V, Larsen J, Rosenstein R, Peschel A, Doškař J. Staphylococcus epidermidis Phages Transduce Antimicrobial Resistance Plasmids and Mobilize Chromosomal Islands. mSphere. 6: e00223-21. (2021) doi: https://doi.org/10.1128/mSphere.00223-21.
  • Reich M, Spomer L, Klindt C, Fuchs K, Stindt J, Deutschmann K, Höhne J, Liaskou E, Hov JR, Karlsen TH, Beuers U, Verheij J, Ferreira-Gonzalez S, Hirschfield G, Forbes SJ, Schramm C, Esposito I, Nierhoff D, Fickert P, Fuchs CD, Trauner M, García-Beccaria M, Gabernet G, Nahnsen S, Mallm JP, Vogel M, Schoonjans K, Lautwein T, Köhrer K, Häussinger D, Luedde T, Heikenwalder M, Keitel V. Downregulation of TGR5 (GPBAR1) in biliary epithelial cells contributes to the pathogenesis of sclerosing cholangitis. J Hepatol. Apr 16:1–42. (2021) doi: 10.1016/j.jhep.2021.03.029. Online ahead of print.
  • Walter A, Friz S, Mayer C. Chitin, Chitin Oligosaccharide, and Chitin Disaccharide Metabolism of Escherichia coli Revisited: Reassignment of the Roles of ChiA, ChbR, ChbF, and ChbG. Microb Physiol. Apr 1:1–17. ( 2021) doi: 10.1159/000515178. Online ahead of print.
  • Rapp J, Rath P, Kilian J, Brilisauer K, Grond S, Forchhammer K. A bioactive molecule made by unusual salvage of radical SAM enzyme by-product 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. J Biol Chem. Mar 31:100621. (2021) doi: 10.1016/j.jbc.2021.100621. Online ahead of print.
  • Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol. 17:e10116. (2021) doi: 10.15252/msb.202010116.
  • Huergo LF, Selim KA, Conzentino MS, Gerhardt ECM, Santos ARS, Wagner B, Alford JT, Deobald N, Pedrosa FO, de Souza EM, Nogueira MB, Raboni SM, Souto D, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Fornazari B, Morales HMP, Borges VA, Nelde A, Walz JS, Becker M, Schneiderhan-Marra N, Rothbauer U, Reis RA, Forchhammer K. Magnetic Bead-Based Immunoassay Allows Rapid, Inexpensive, and Quantitative Detection of Human SARS-CoV-2 Antibodies. ACS Sens. Mar 26;6(3):703-708. (2021) doi: 10.1021/acssensors.0c02544.
  • Hörömpöli D, Ciglia C, Glüsenkamp KH, Haustedt LO, Falkenstein-Paul H, Bendas G, Berscheid A, Brötz-Oesterhelt H. The Antibiotic Negamycin Crosses the Bacterial Cytoplasmic Membrane by Multiple Routes. Antimicrob Agents Chemother. 65:e00986-20. (2021) doi: 10.1128/AAC.00986-20.
  • Müller M, Calvert M, Hottmann I, Kluj RM, Teufel T, Balbuchta K, Engelbrecht A, Selim KA, Xu Q, Borisova M, Titz A, Mayer C. The exo-β-N-acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases. J Biol Chem. Mar 5:100519. (2021) doi: 10.1016/j.jbc.2021.100519. Online ahead of print.
  • Silber N, Mayer C, Matos de Opitz CL, Sass P. Progression of the late-stage divisome is unaffected by the depletion of the cytoplasmic FtsZ pool. Commun Biol. 4(1):270. (2021) doi: 10.1038/s42003-021-01789-9.
  • Renz A, Widerspick L, Dräger A. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. Metabolites. 11(4):232. (2021) doi: 10.3390/metabo11040232.
  • Mohammad M, Na M, Hu Z, Nguyen MT, Kopparapu PK, Jarneborn A, Karlsson A, Ali A, Pullerits R, Götz F, Jin T. Staphylococcus aureus lipoproteins promote abscess formation in mice, shielding bacteria from immune killing. Commun Biol. 4(1):432. (2021) doi: 10.1038/s42003-021-01947-z.
  • Ortiz A, Vega NM, Ratzke C, Gore J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. ISME J. Feb 15. (2021) doi: 10.1038/s41396-021-00910-4. Online ahead of print.
  • Selim KA, Maldener I. Cellular and Molecular Strategies in Cyanobacterial Survival-"In Memory of Prof. Dr. Wolfgang Lockau". Life (Basel). Feb 9;11(2):132. (2021) doi: https://doi.org/10.3390/life11020132.
  • Doello S, Burkhardt M, Forchhammer K. The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium. Curr Biol. 31:1-10. (2021) doi: 10.1016/j.cub.2021.01.065. Online ahead of print.
  • Michaelis L, Treß M, Löw HC, Klees J, Klameth C, Lange A, Grießhammer A, Schäfer A, Menz S, Steimle A, Schulze-Osthoff K, Frick JS. Gut Commensal-Induced IκBζ Expression in Dendritic Cells Influences the Th17 Response.  Front Immunol. Jan 19;11:612336. (2021) doi: 10.3389/fimmu.2020.612336.
  • Saur J S, Wirtz S N, Schilling N A, Krismer B, Peschel A, Grond S. Distinct Lugdunins from a New Efficient Synthesis and BroadExploitation of Its MRSA-Antimicrobial Structure. J Med Chem (2021) doi: 10.1021/acs.jmedchem.0c02170.
  • Wex K W, Saur J S, Handel F, Ortlieb N, Mokeev V, Kulik A, Niedermeyer T H J, Mast Y, Grond S, Berscheid A, Brötz-Oesterhelt H. Bioreporters for direct mode of action-informed screening of antibiotic producer strains. CellChemBio (2021) doi: 10.1016/j.chembiol.2021.02.022.
  • Koeninger L, Osbelt L, Berscheid A, Wendler J, Berger J, Hipp K, Lesker TR, Pils MC, Malek NP, Jensen BAH, Brötz-Oesterhelt H, Strowig T, Wehkamp J. Curbing gastrointestinal infections by defensin fragment modifications without harming commensal microbiota. Commun Biol. 4(1):47. (2021) doi: 10.1038/s42003-020-01582-0.
  • Esquivel-Elizondo S, Bağcı C, Temovska M, Jeon BS, Bessarab I, Williams RBH, Huson DH, Angenent LT. The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria. Front Microbiol. Jan 14;11:594524. (2021) doi: 10.3389/fmicb.2020.594524.

2020

  • Belikova D, Jochim A, Power J, Holden MTG, Heilbronner S. "Gene accordions" cause genotypic and phenotypic heterogeneity in clonal populations of Staphylococcus aureus. Nat Commun. Jul 14;11(1):3526. (2020) doi: 10.1038/s41467-020-17277-3.
  • Ehmann D, Koeninger L, Wendler J, Malek NP, Stange EF, Wehkamp J, Jensen BAH. Fragmentation of Human Neutrophil α-Defensin 4 to Combat Multidrug Resistant Bacteria. Front. Microbiol. (2020) https://doi.org/10.3389/fmicb.2020.01147.
  • van Dalen R, Peschel A, van Sorge NM. Wall Teichoic Acid in Staphylococcus aureus Host Interaction. Trends Microbiol. (2020) doi:10.1016/j.tim.2020.05.017.
  • Jochim A, Adolf L, Belikova D, Schilling NA, Setyawati I, Chin D, Meyers S, Verhamme P, Heinrichs DE, Slotboom DJ, Heilbronner S. An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis. Elife 9 (2020) doi: https://doi.org/10.7554/eLife.57322.
  • Luqman A, Muttaqin MZ, Yulaipi S, Ebner P, Matsuo M, Zabel S, Tribelli PM, Nieselt K, Hidayati D, Götz F. Trace amines produced by skin bacteria accelerate wound healing in mice. Commun Biol 3:277 (2020) doi: https://doi.org/10.1038/s42003-020-1000-7.
  • Klask CM, Kliem-Kuster N, Molitor B, Angenent L. Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO2 and H2, but Results in Stochastic Inhibition Events. Front. Microbiol. (2020) doi: https://doi.org/10.3389/fmicb.2020.00724.
  • Walter A, Unsleber S, Rismondo J, Jorge AM, Peschel A, Gründling A, Mayer C. Phosphoglycerol-type wall and lipoteichoic acids are enantiomeric polymers differentiated by the stereospecific glycerophosphodiesterase GlpQ. J Biol Chem. 295(12):4024-4034 (2020) doi: https://doi.org/10.1074/jbc.RA120.012566.
  • Wagner S, Diepold A. A Unified Nomenclature for Injectisome-Type Type III Secretion Systems. Curr Top Microbiol Immunol. 10.1007/82 (2020) doi: https://doi.org/10.1007/82_2020_210.
  • Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, et al. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol 38:272–276 (2020) doi: https://doi.org/10.1038/s41587-020-0446-y.
  • Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38:276–278 (2020) doi: https://doi.org/10.1038/s41587-020-0439-x.
  • Bafna JA, Sans-Serramitjana E, Acosta-Gutiérrez S, Bodrenko I, Hörömpöli D, Berscheid A, Brötz-Oesterhelt H, Winterhalter M, Ceccarelli M. Kanamycin Uptake into E. Coli Is Facilitated by OmpF and OmpC Porin Channels Located in the Outer Membrane. ACS Infect Dis. (2020) doi: https://doi.org/10.1021/acsinfecdis.0c00102.
  • Xia PF, Casini I, Schulz S, Klask CM, Angenent LT, Molitor B. Reprogramming acetogenic bacteria with CRISPR-targeted base editing via deamination. ACS Synth. Biol. (2020) doi: https://doi.org/10.1021/acssynbio.0c00226.
  • Malik IT, Pereira R, Vielberg MT, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz‐Oesterhelt H. Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. ChemBioChem 21 (2020) doi: https://doi.org/10.1002/cbic.201900787.
  • Renz A, Widerspick L, Dräger A. FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2. Zenodo (2020) doi: http://doi.org/10.5281/zenodo.3752641.

2019

  • Macek B, Forchhammer K, Hardouin J, Weber-Ban E, Grangeasse C, Mijakovic I. Protein post-translational modifications in bacteria. Nat Rev Microbiol. 17(11):651-664. (2019) doi: 10.1038/s41579-019-0243-0.
  • Schilling NA, Berscheid A, Schumacher J, Saur JS, Konnerth MC, Wirtz SN, Beltrán Beleña JM, Zipperer A, Krismer B, Peschel A, Kalbacher H, Brötz-Oesterhelt H, Steinem C, Grond SC. Synthetic lugdunin analogues reveal essential structural motifs for antimicrobial action and proton translocation capability. Angew Chem Int Ed Engl. (2019) May 6 doi: https://doi.org/10.1002/anie.201901589.
  • George SE, Hrubesch J, Breuing I, Vetter N, Korn N, Hennemann K, Bleul L, Willmann M, Ebner P, Götz F, Wolz C. Oxidative stress drives the selection of quorum sensing mutants in the Staphylococcus aureus population. Proceedings of the National Academy of Sciences 116(38) (2019) doi: https://doi.org/10.1073/pnas.1902752116.

Preprints

  • Burger KE, Pfaffelhuber P, Baumdicker F. Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown. bioRxiv Preprint (2021) doi: https://doi.org/10.1101/2021.09.02.457550.
  • Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman CE, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong HY, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. bioRxiv Preprint (2021) doi: https://doi.org/10.1101/2021.08.31.457499.
  • Reher R, Aron AT, Fajtova P, Liu C, Shalom IYB, Bittremieux W, Wang M, Matos-Hernandez ML, Alexander KL, Caro-Diaz EJ, Naman CB, Dorrestein PC, O’Donoghue AJ, Gerwick WH, Petras D. Native Metabolomics Identifies the Rivulariapeptolide Family of Protease Inhibitors. bioRxiv Preprint (2021) doi: https://doi.org/10.1101/2021.09.03.458897.
  • Klask CM, Jäger B, Angenent LT, Molitor B. Genetic evidence reveals the indispensable role of the rseC gene for autotrophy and the importance of a functional electron balance for nitrate reduction in Clostridium ljungdahlii. bioRxiv Preprint (2021) doi: https://doi.org/10.1101/2021.08.03.455012.
  • Maier L, Goemans CV, Pruteanu M, Wirbel J, Kuhn M, Cacace E, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zeller G, Bork P, Typas A. Dissecting the collateral damage of antibiotics on gut microbes. bioRxiv Preprint (2020) doi: https://doi.org/10.1101/2020.01.09.893560.
  • Bittner Z, Liu X, Shankar S, Tapia-Abellán A, Kalbacher H, Andreeva L, Mangan M, Düwell P, Lovotti M, Bosch K, Dickhöfer S, Marcu A, Stevanović S, Herster F, Löffler MW, Wolz OO, Schilling N, Kümmerle-Deschner J, Wagner S, Delor A, Grimbacher B, Wu H, Latz E, Weber ANR. BTK operates a phospho-tyrosine switch to regulate NLRP3 inflammasome activity. bioRxiv 864702 Preprint (2020) doi: https://doi.org/10.1101/864702.