Puplications 2024

Höhn F, Chaudhry V, Bagci C, Mahmoudi M, Klenk E, Berg L, Stincone P, Hughes CC, Petras D, Brötz-Oesterhelt H, Kemen E, Ziemert N. (2024) Strong pairwise interactions do not drive interactions in a plant leaf associated microbial community, ISME Communications. ycae117. doi: 10.1093/ismeco/ycae117.

Leonidou N, Xia Y, Friedrich L, Schütz MS, Dräger A. (2024) Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. PLoS Pathog. 20(9):e1012528. doi: 10.1371/journal.ppat.1012528.

Garcia-Santamarina S, Kuhn M, Devendran S, Maier L, Driessen M, Mateus A, Mastrorilli E, Brochado AR, Savitski MM, Patil KR, Zimmermann M, Bork P, Typas A. (2024) Emergence of community behaviors in the gut microbiota upon drug treatment. Cell. S0092-8674(24)00966-8. doi: 10.1016/j.cell.2024.08.037.

Pakkir Shah AK, Walter A, Ottosson F, Russo F, Navarro-Diaz M, Boldt J, Kalinski JJ, Kontou EE, Elofson J, Polyzois A, González-Marín C, Farrell S, Aggerbeck MR, Pruksatrakul T, Chan N, Wang Y, Pöchhacker M, Brungs C, Cámara B, Caraballo-Rodríguez AM, Cumsille A, de Oliveira F, Dührkop K, El Abiead Y, Geibel C, Graves LG, Hansen M, Heuckeroth S, Knoblauch S, Kostenko A, Kuijpers MCM, Mildau K, Papadopoulos Lambidis S, Portal Gomes PW, Schramm T, Steuer-Lodd K, Stincone P, Tayyab S, Vitale GA, Wagner BC, Xing S, Yazzie MT, Zuffa S, de Kruijff M, Beemelmanns C, Link H, Mayer C, van der Hooft JJJ, Damiani T, Pluskal T, Dorrestein P, Stanstrup J, Schmid R, Wang M, Aron A, Ernst M, Petras D. (2024) Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nat Protoc. doi: 10.1038/s41596-024-01046-3.

Fehrenbach A, Mitrofanov A, Alkhnbashi OS, Backofen R, Baumdicker F. (2024) SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions. Nucleic Acids Res. gkae772. doi: 10.1093/nar/gkae772.

Timilsina A, Lokesh S, Shahriar A, Numan T, Schramm T, Stincone P, Nyarko LK, Dewey C, Boiteau R, Petras D, Yang Y. (2024) Identifying Quinones in Complex Aqueous Environmental Media (Biochar Extracts) through Tagging with Cysteine and Cysteine-Contained Peptides and High Resolution Mass Spectrometry Analysis. Environ Sci Technol. 58(37):16432-16443. doi: 10.1021/acs.est.4c04049.

Huson DH, Bryant D. (2024) The SplitsTree App: interactive analysis and visualization using phylogenetic trees and networks. Nat Methods. doi: 10.1038/s41592-024-02406-3.

Sekar S, Schwarzbach S, Nega M, Bloes DA, Smeds E, Kretschmer D, Foster TJ, Heilbronner S. (2024) SLUSH peptides of the PSMβ family enable Staphylococcus lugdunensis to use erythrocytes as a sole source of nutrient iron. FASEB J. 38(16):e23881. doi: 10.1096/fj.202400335R.

Ludwig KC, Puls JS, Matos de Opitz CL, Innocenti P, Daniel JM, Bornikoel J, Arts M, Krannich S, Straetener J, Brajtenbach D, Henrichfreise B, Sass P, Mueller A, Martin NI, Brötz-Oesterhelt H, Kubitscheck U, Grein F, Schneider T. (2024) The Dual Mode of Antibacterial Action of the Synthetic Small Molecule DCAP Involves Lipid II Binding. J Am Chem Soc. doi: 10.1021/jacs.4c05138.

Li P, Schulte J, Wurpts G, Hornef MW, Wolz C, Yazdi AS, Burian M. (2024) Transcriptional Profiling of Staphylococcus aureus during the Transition from Asymptomatic Nasal Colonization to Skin Colonization/Infection in Patients with Atopic Dermatitis. Int J Mol Sci. 25(17):9165. doi: 10.3390/ijms25179165.

Schmitz LM, Kreitli N, Obermaier L, Weber N, Rychlik M, Angenent LT. (2024) Power-to-vitamins: producing folate (vitamin B₉) from renewable electric power and CO₂ with a microbial protein system. Trends Biotechnol. 2S0167-7799(24)00177-X. doi: 10.1016/j.tibtech.2024.06.014.

Berscheid A, Straetener J, Schilling NA, Ruppelt D, Konnerth MC, Schittek B, Krismer B, Peschel A, Steinem C, Grond S, Brötz-Oesterhelt H. (2024) The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides. mBio. e0057824. doi: 10.1128/mbio.00578-24.

Voitsekhovskaia I, Ho YTC, Klatt C, Müller A, Machell DL, Tan YJ, Triesman M, Bingel M, Schittenhelm RB, Tailhades J, Kulik A, Maier ME, Otting G, Wohlleben W, Schneider T, Cryle M, Stegmann E. (2024) Altering glycopeptide antibiotic biosynthesis through mutasynthesis allows incorporation of fluorinated phenylglycine residues. RSC Chem Biol. 5(10):1017–34. doi: 10.1039/d4cb00140k.

Shahriar A, Lokesh S, Timilsina A, Numan T, Schramm T, Stincone P, Nyarko L, Dewey C, Petras D, Boiteau R, Yang Y. (2024) High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin-Iron Complexes: Novel Pipeline and Complex Structures. Environ Sci Technol. doi: 10.1021/acs.est.4c03608.

Mahmoudi M, Almario J, Lutap K, Nieselt K, Kemen E. (2024) Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues. ISME Commun. 4(1):ycae103. doi: 10.1093/ismeco/ycae103.

Grimm H, Drabesch S, Nicol A, Straub D, Joshi P, Zarfl C, Planer-Friedrich B, Muehe EM, Kappler A. (2024) Arsenic immobilization and greenhouse gas emission depend on quantity and frequency of nitrogen fertilization in paddy soil. Heliyon. 10(16):e35706. doi: 10.1016/j.heliyon.2024.e35706.

Ammanath AV, Matsuo M, Wang H, Kraus F, Bleisch A, Peslalz P, Mohammad M, Deshmukh M, Grießhammer A, Purkayastha M, Vorbach A, Macek B, Brötz-Oesterhelt H, Maier L, Kretschmer D, Peschel A, Jin T, Plietker B, Götz F. (2024) Antimicrobial Evaluation of Two Polycyclic Polyprenylated Acylphloroglucinol Compounds: PPAP23 and PPAP53. Int J Mol Sci. 25(15):8023. doi: 10.3390/ijms25158023.

Zhang Y, Tong M, Lu Y, Zhao F, Zhang P, Wan Z, Li P, Yuan S, Wang Y, Kappler A. (2024) Directional long-distance electron transfer from reduced to oxidized zones in the subsurface. Nat Commun. 15(1):6576. doi: 10.1038/s41467-024-50974-x.

Lewis K, Lee RE, Brötz-Oesterhelt H, Hiller S, Rodnina MV, Schneider T, Weingarth M, Wohlgemuth I. (2024) Sophisticated natural products as antibiotics. Nature. 632(8023):39-49. doi: 10.1038/s41586-024-07530-w.

Spirito CM, Lucas TN, Patz S, Jeon BS, Werner JJ, Trondsen LH, Guzman JJ, Huson DH, Angenent LT. (2024) Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction. mSystems. e0041624. doi: 10.1128/msystems.00416-24.

de Castilhos J, Tillmanns K, Blessing J, Laraño A, Borisov V, Stein-Thoeringer CK. (2024) Microbiome and pancreatic cancer: time to think about chemotherapy. Gut Microbes. 16(1):2374596. doi: 10.1080/19490976.2024.2374596.

Zhao Y, Bitzer A, Power JJ, Belikova D, Torres Salazar BO, Adolf LA, Gerlach D, Krismer B, Heilbronner S. (2024) Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability. ISME J. 18(1):wrae123. doi: 10.1093/ismejo/wrae123.

Vitale GA, Geibel C, Minda V, Wang M, Aron AT, Petras D. (2024) Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products. Nat. Prod. Rep. 41:885-904. doi: 10.1039/D3NP00050H.

Puniya BL, Verma M, Damiani C, Bakr S, Dräger A. (2024) Perspectives on computational modeling of biological systems and the significance of the SysMod community. Bioinform Adv. 4(1):vbae090. doi: 10.1093/bioadv/vbae090.

Berasategui A, Salem H, Moller AG, Christopher Y, Vidaurre Montoya Q, Conn C, Read TD, Rodrigues A, Ziemert N, Gerardo N. (2024) Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants. mSystems.:e0057624. doi: 10.1128/msystems.00576-24.

Enav H, Paz I, Ley RE. (2024) Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nat Biotechnol. doi: 10.1038/s41587-024-02276-2.

Peslalz P, Vorbach A, Bleisch A, Liberini E, Kraus F, Izzo F, Brötz-Oesterhelt H, Götz F, Plietker B. (2024) Chemical Predictive Modelling and Natural Product-based Divergent Synthesis - Design of Type B PPAPs with Nanomolar Activities against MRSA. Chemistry. e202401955. doi: 10.1002/chem.202401955.

Kengmo Tchoupa A, Elsherbini AMA, Camus J, Fu X, Hu X, Ghaneme O, Seibert L, Lebtig M, Böcker MA, Horlbeck A, Lambidis SP, Schittek B, Kretschmer D, Lämmerhofer M, Peschel A. (2024) Lipase-mediated detoxification of host-derived antimicrobial fatty acids by Staphylococcus aureus. Commun Biol. 7(1):572. doi: 10.1038/s42003-024-06278-3.

Poxleitner M, Hoffmann SHL, Berezhnoy G, Ionescu TM, Gonzalez-Menendez I, Maier FC, Seyfried D, Ehrlichmann W, Quintanilla-Martinez L, Schmid AM, Reischl G, Trautwein C, Maurer A, Pichler BJ, Herfert K, Beziere N. (2024) Western diet increases brain metabolism and adaptive immune responses in a mouse model of amyloidosis. J Neuroinflammation. 21(1):129. doi: 10.1186/s12974-024-03080-0.

Jumpertz von Schwartzenberg R, Arreola EV, Sandforth A, Hanson RL, Birkenfeld AL. (2024) Role of Weight Loss Induced Prediabetes Remission in the Prevention of Type 2 Diabetes – Time to Improve Diabetes Prevention. Diabetologia. doi: 10.1007/s00125-024-06178-5.

Runge E, Mansor M, Chiu TH, Shuster J, Fischer S, Kappler A, Duda JP. (2024) Hydrothermal sulfidation of biogenic magnetite produces framboid-like pyrite. Communications Earth & Environment 5, 252. doi: 10.1038/s43247-024-01400-z.

Lehmann E, van Dalen R, Gritsch L, Slavetinsky C, Korn N, Rohmer C, Krause D, Peschel A, Weidenmaier C, Wolz C. (2024) The capsular polysaccharide obstructs wall teichoic acid functions in Staphylococcus aureus. J Infect Dis.14:jiae188. doi: 10.1093/infdis/jiae188.

Selim KA, Alva V. (2024) PII-like signaling proteins: a new paradigm in orchestrating cellular homeostasis. Curr Opin Microbiol. 79:102453. doi: 10.1016/j.mib.2024.102453.

Zhou M, Taiwo K, Wang H, Ntihuga JN, Angenent LT, Usack JG. (2024) Anaerobic digestion of process water from hydrothermal treatment processes: a review of inhibitors and detoxification approaches. Bioresour Bioprocess. 11(1):47. doi: 10.1186/s40643-024-00756-6.

Gemeinhardt K, Park H, Won JI, Lee JH, Hwang ET, Angenent LT, Jeon BS. (2024) Draft genome sequence of Magnusiomyces sp. LA-1 isolated from a C6-C8 acid-producing bioreactor. Microbiol Resour Announc. e0093523. doi: 10.1128/mra.00935-23.

Smith CF, Modahl CM, Ceja-Galindo D, Larson KY, Maroney SP, Bahrabadi L, Brandehoff NP, Perry BW, McCabe MC, Petras D, Lomonte B, Calvete JJ, Castoe TA, Mackessy SP, Hansen KC, Saviola AJ. (2024) ASSESSING TARGET SPECIFICITY OF THE SMALL MOLECULE INHIBITOR MARIMASTAT TO SNAKE VENOM TOXINS: A NOVEL APPLICATION OF THERMAL PROTEOME PROFILING. Mol Cell Proteomics. 100779. doi: 10.1016/j.mcpro.2024.100779.

Leonidou N, Ostyn L, Coenye T, Crabbé A, Dräger A. (2024) Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities. Microbiol Spectr. e0400623. doi: 10.1128/spectrum.04006-23.

Maier L, Stein-Thoeringer C, Ley RE, Brötz-Oesterhelt H, Link H, Ziemert N, Wagner S, Peschel A. Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective. Lancet Microbe S2666-5247(24)00049-1. doi: 10.1016/S2666-5247(24)00049-1.

Ruppelt D, Trollmann MFW, Dema T, Wirtz SN, Flegel H, Mönnikes S, Grond S, Böckmann RA, Steinem C. (2024) The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes. Nat Commun 15, 3521. doi: 10.1038/s41467-024-47803-6.

Weber ANR, Tortola MM, Kuemmerle-Deschner JB. (2024) Cracking the NLRP3 code: Pioneering precision medicine for inflammation. J Exp Med. 221(5):e20240221. doi: 10.1084/jem.20240221.

Mantovani O, Haffner M, Walke P, Elshereef AA, Wagner B, Petras D, Forchhammer K, Selim KA, Hagemann M. (2024) The redox-sensitive R-loop of the carbon control protein SbtB contributes to the regulation of the cyanobacterial CCM. Sci Rep. 14:7885. doi: 10.1038/s41598-024-58354-7.

Bossert L, Höll D. (2024) Narrating the Uncanny Triad: Imagining Microbe, Animal, and Human Entanglements within the Planetary Health Humanities, in: Heike Härting and Heather Meek (eds.), Planetary Health Humanities and Pandemics, New York: Routledge, 233–253. doi: 10.4324/9781003367581.

Beck C, Krusche J, Notaro A, Walter A, Kränkel L, Vollert A, Stemmler R, Wittmann J, Schaller M, Slavetinsky C, Mayer C, De Castro C, Peschel A. (2024) Wall teichoic acid substitution with glucose governs phage susceptibility of Staphylococcus epidermidis. mBio. e0199023. doi: 10.1128/mbio.01990-23.

Castro-Falcón G, Straetener J, Bornikoel J, Reimer D, Purdy TN, Berscheid A, Schempp FM, Liu DY, Linington RG, Brötz-Oesterhelt H, Hughes CC. (2024) Antibacterial Marinopyrroles and Pseudilins Act as Protonophores. ACS Chem Biol. 19(3):743-752. doi: 10.1021/acschembio.3c00773.

Michaelis L, Berg L, Maier L. (2024) Confounder or Confederate? The Interactions Between Drugs and the Gut Microbiome in Psychiatric and Neurological Diseases. Biol. Psychiatry 95(4):361–369. doi: 10.1016/j.biopsych.2023.06.004.

Akbuğa-Schön T, Suzuki TA, Jakob D, Vu DL, Waters JL, Ley RE. (2024) The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice. mBio. 15(2):e0283623. doi: 10.1128/mbio.02836-23.

Beck C, Krusche J, Elsherbini AMA, Du X, Peschel A. (2024) Phage susceptibility determinants of the opportunistic pathogen Staphylococcus epidermidis. Curr Opin Microbiol. 78:102434. doi: 10.1016/j.mib.2024.102434.

Schütterle DM, Hegner R, Temovska M, Ortiz-Ardila AE, Angenent LT. (2024) Exclusive D-lactate-isomer production during a reactor-microbiome
conversion of lactose-rich waste by controlling pH and temperature. Water Research 250:121045. doi: 10.1016/j.watres.2023.121045.

Vitale GA, Geibel C, Minda V, Wang M, Aron AT, Petras D. (2024) Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products. Nat Prod Rep. doi: 10.1039/d3np00050h.

Solar Venero EC, Galeano MB, Luqman A, Ricardi MM, Serral F, Fernandez Do Porto D, Robaldi SA, Ashari BAZ, Munif TH, Egoburo DE, Nemirovsky S, Escalante J, Nishimura B, Ramirez MS, Götz F, Tribelli PM. (2024) Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo. BMC Biol 22(27) doi: 10.1186/s12915-024-01830-3.

Knoll J, Amend B, Harland N, Isser S, Bézière N, Kraushaar U, Stenzl A, Aicher WK. (2024) Cell Therapy by Mesenchymal Stromal Cells Versus Myoblasts in a Pig Model of Urinary Incontinence. Tissue Eng Part A. 30(1-2):14-30. doi: 10.1089/ten.TEA.2023.0103.

Stein-Thoeringer CK, Renz BW, De Castilhos J, von Ehrlich-Treuenstätt V, Wirth U, Tschaidse T, Hofmann FO, Koch DT, Beirith I, Ormanns S, Guba MO, Angele MK, Andrassy J, Niess H, D'Haese JG, Werner J, Ilmer M. (2024) Microbiome Dysbiosis with Enterococcus Presence in the Upper Gastrointestinal Tract is A Risk Factor for Mortality in Patients Undergoing Surgery for Pancreatic Cancer. Ann Surg. doi: 10.1097/SLA.0000000000006210.

Lo Presti L, Link H. (2024) Mobile CRISPRi moves through the complexity of bacterial genetics. Cell Rep Methods. 4(1). doi: 10.1016/j.crmeth.2024.100697.

Sehnal L, Lo Presti L, Ziemert N. (2024) Discovering cryptic natural products by substrate manipulation. Nat Chem. doi: 10.1038/s41557-023-01433-5.

Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Macek B, Stafforst T. (2024) Profiling the Interactome of Oligonucleotide Drugs by Proximity Biotinylation. Nat Chem Biol. doi: 10.1038/s41589-023-01530-z.

Illigmann A, Vielberg MT, Lakemeyer M, Wolf F, Dema T, Stange P, Kuttenlochner W, Liebhart E, Kulik A, Staudt ND, Malik I, Grond S, Sieber SA, Kaysser L, Groll M, Brötz-Oesterhelt H. (2024) Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A. Angew Chem Int Ed Engl. 63(3):e202314028. doi: 10.1002/anie.202314028.

Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. (2024) Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol.9(1):200-213. doi: 10.1038/s41564-023-01544-2.

Brenzinger S, Airoldi M, Ogunleye AJ, Jugovic K, Amstalden MK, Brochado AR. (2024) The Vibrio cholerae CBASS phage defence system modulates resistance and killing by antifolate antibiotics. Nat Microbiol. 9(1):251–262. doi: 10.1038/s41564-023-01556-y.

Zilkenat S, Kim E, Dietsche T, Monjarás Feria JV, Torres-Vargas CE, Mebrhatu MT, Wagner S. (2024) Blue Native PAGE Analysis of Bacterial Secretion Complexes. Methods Mol Biol. 2715:331-362. doi: 10.1007/978-1-0716-3445-5_22.

Bianchi M, Winterhalter M, Harbig TA, Hörömpöli D, Ghai I, Nieselt K, Brötz-Oesterhelt H, Mayer C, Borisova-Mayer M. (2024) Fosfomycin Uptake in Escherichia coli Is Mediated by the Outer-Membrane Porins OmpF, OmpC, and LamB. ACS Infect. Dis. 10(1): 127–137. doi: 10.1021/acsinfecdis.3c00367.