Publications 2023

Maier L. Pioneering microbiome engineering. Nat Rev Microbiol 21, 630. (2023) doi: 10.1038/s41579-023-00949-4.

Focken J, Scheurer J, Jäger A, Schürch CM, Kämereit S, Riel S, Schaller M, Weigelin B, Schittek B. Neutrophil extracellular traps enhance S. aureus skin colonization by oxidative stress induction and downregulation of epidermal barrier genes. Cell Rep. 42(10). (2023) doi: 10.1016/j.celrep.2023.113148.

Yang J, Bowring JZ, Krusche J, Lehmann E, Bejder BS, Silva SF, Bojer MS, Grunert T, Peschel A, Ingmer H. Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus. Cell Rep. 42(9). (2023) doi: 10.1016/j.celrep.2023.113154.

Sandforth A, Jumpertz-von Schwartzenberg R, Arreola EV, Hanson RL, Sancar G, Katzenstein S, Lange K, Preißl H, Dreher SI, Weigert C, Wagner R, Kantartzis K, Machann J, Schick F, Lehmann R, Peter A, Katsouli N, Ntziachristas V, Dannecker C, Fritsche L, Birkenfeld AL. Mechanisms of weight loss-induced remission in people with prediabetes: A Post-hoc Analysis of the Randomized Controlled Multicenter Prediabetes Lifestyle Intervention Study (PLIS). Lancet Diabetes Endocrinology (2023) doi:10.1016/S2213-8587(23)00235-8.

Puniya BL, Dräger A. Advancements in computational modelling of biological systems: seventh annual SysMod meeting. Bioinformatics 39(9). (2023) doi: 10.1093/bioinformatics/btad539.

Mannochio-Russo H, Swift SOI, Nakayama KK, Wall CB, Gentry EC, Panitchpakdi M, Caraballo-Rodriguez AM, Aron AT, Petras D, Dorrestein K, Dorrestein TK, Williams TM, Nalley EM, Altman-Kurosaki NT, Martinelli M, Kuwabara JY, Darcy JL, Bolzani VS, Kelly LW, Mora C, Yew JY, Amend Anthony S, McFall-Ngai M, Hynson NA, Dorrestein PC, Nelson CE. Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipidis in marine symbioses. Commun Biol 6, 896. (2023) doi: 10.1038/s42003-023-05230-1.

Schramm T, Lubrano P, Pahl V, Stadelmann A, Verhülsdonk A, Link H. Mapping temperature-sensitive mutations at a genome scale to engineer growth switches in Escherichia coli. Mol. Syst. Biol. (2023) doi:
10.15252/msb.202311596.

Lu L, Rughöft S, Straub D, Joye SB, Kappler A, Kleindienst S. Rhamnolipid Biosurfactants Enhance Microbial Oil Biodegradation in Surface Seawater from the North Sea. ACS EST Water (2023) doi: 10.1021/acsestwater.3c00048.

Otto M, Dickey SW, Wolz C. Editorial: Quorum-sensing in Gram-positive pathogens – mechanisms, role in infection, and potential as a therapeutic target. Front Cell Infect Microbiol. 13:1236705. (2023) doi: 10.3389/fcimb.2023.1236705.

Krupnik L, Joshi P, Kappler A, Flühmann B, Alston AB, Digigow R, Wick P, Neels A. Critical nanomaterial attributes of iron-carbohydrate nanoparticles: Leveraging orthogonal methods to resolve the 3-dimensional structure. Eur J Pharm Sci. 7:106521. (2023) doi: 10.1016/j.ejps.2023.106521.

Schulz S, Sletta H, Fløgstad Degnes K, Krysenko S, Williams A, Olsen SM, Vernstad K, Mitulski A, Wohlleben W. Optimization of FK-506 production in Streptomyces tsukubaensis by modulation of Crp-mediated regulation. Appl Microbiol Biotechnol. 107(9):2871-2886. (2023) doi: 10.1007/s00253-023-12473-9.

Salzer A, Wolz C. Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes. Microlife. 4:uqad009. (2023) doi: 10.1093/femsml/uqad009.

Pais SV, Kim E, Wagner S. Virulence-associated type III secretion systems in Gram-negative bacteria. Microbiology (Reading) 169(6). (2023) doi:10.1099/mic.0.001328.

Lebtig M, Scheurer J, Muenkel M, Becker J, Bastounis E, Peschel A, Kretschmer D. Keratinocytes use FPR2 to detect Staphylococcus aureus and initiate antimicrobial skin defense. Front Immunol. 14:1188555. (2023) doi: 10.3389/fimmu.2023.1188555.

Michaelis L, Berg L, Maier L. Confounder or confederate? The interactions between drugs and the gut microbiome in psychiatric and neurological diseases. Biol Psychiatry. 16:S0006-3223(23)01358-6. (2023) doi: 10.1016/j.biopsych.2023.06.004.

Schwedt I, Collignon M, Mittelstädt C, Giudici F, Rapp J, Meißner J, Link H, Hertel R, Commichau FM. Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism. Environ Microbiol Rep. (2023) doi: 10.1111/1758-2229.13184.

Zhao G, Tan M, Wu B, Zheng X, Xiong R, Chen B, Kappler A, Chu C. Redox Oscillations Activate Thermodynamically Stable Iron Minerals for Enhanced Reactive Oxygen Species Production. Environ Sci Technol. 13;57:8628-8637. doi: 10.1021/acs.est.3c02302.

Lauterbur ME, Cavassim MIA, Gladstein AL, Gower G, Pope NS, Tsambos G, Adrion J, Belsare S, Biddanda A, Caudill V, Cury J, Echevarria I, Haller BC, Hasan AR, Huang X, Iasi LNM, Noskova E, Obsteter J, Pavinato VAC, Pearson A, Peede D, Perez MF, Rodrigues MF, Smith CCR, Spence JP, Teterina A, Tittes S, Unneberg P, Vazquez JM, Waples RK, Wohns AW, Wong Y, Baumdicker F, Cartwright RA, Gorjanc G, Gutenkunst RN, Kelleher J, Kern AD, Ragsdale AP, Ralph PL, Schrider DR, Gronau I. Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. elife 12:RP84874. (2023) doi: 10.7554/eLife.84874.

Fink C, Martinez-Cano G, Shuster J, Panzera A, Rennhack KE, Rohbohm N, Angenent LT, Molitor B. The Targeted Deletion of Genes Responsible for Expression of the Mth60 Fimbriae Leads to Loss of Cell-Cell Connections in Methanothermobacter thermautotrophicus ΔH. Appl Environ Microbiol. 13:e0057523. (2023) doi: 10.1128/aem.00575-23.

Leonidou N, Fritze E, Renz A, Dräger A. SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms. Bioinformatics btad437. (2023) doi: 10.1093/bioinformatics/btad437.

Fiskal A, Shuster J, Fischer S, Joshi P, Raghunatha Reddy L, Wulf SE, Kappler A, Fischer H, Herrig I, Meier J. Microbially influenced corrosion and rust tubercle formation on sheet piles in freshwater systems. Environ Microbiol. (2023) doi: 10.1111/1462-2920.16393.

Goldfinger V, Spohn M, Rodler JP, Sigle M, Kulik A, Cryle M, Rapp J, Link H, Wohlleben W, Stegmann E. Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production. Metab Eng. 25:S1096-7176(23)00079-4. (2023) doi: 10.1016/j.ymben.2023.05.005.

Hauke M, Metz F, Rapp J, Faass L, Bats SH, Radziej S, Link H, Eisenreich W, Josenhans C.Helicobacter pylori Modulates Heptose Metabolite Biosynthesis and Heptose-Dependent Innate Immune Host Cell Activation by Multiple Mechanisms. Microbiol Spectr. e0313222. (2023) doi: 10.1128/spectrum.03132-22.

Walzl A, Marbach H, Belikova D, Vogl C, Ehling-Schulz M, Heilbronner S, Grunert T. Prevalence of the SigB-Deficient Phenotype among Clinical Staphylococcus aureus Isolates Linked to Bovine Mastitis. Antibiotics (Basel). 12(4):699. (2023) doi: 10.3390/antibiotics12040699.

Bastounis E, Buttery S. Publishing protocols as a new PI. STAR Protoc. 4(2):102173. (2023) doi: 10.1016/j.xpro.2023.102173.

Maia A, Cardona Gloria Y, Fuchs K, Chang TH, Engels P, Zhou M, Hinnenthal T, Rusch E, Gouttefangeas C, Weber ANR. Chitin oligomers promote lymphoid innate and adaptive immune cell activation. J Leukoc Biol. (2023) doi: 10.1093/jleuko/qiad044.

Mantovani O, Haffner M, Selim KA, Hagemann M, Forchhammer K. Roles of second messengers in the regulation of cyanobacterial physiology: the carbon-concentrating mechanism and beyond. Microlife 23(4). (2023) doi: 10.1093/femsml/uqad00.

Yilmaz TM, Mungan MD, Berasategui A, Ziemert N.  FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. Nucleic Acids Res. gkad386. (2023) doi: 10.1093/nar/gkad386.

Baumdicker F, Kupczok A. Tackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes. Genome Biol Evol. 15(5). (2023) doi: 10.1093/gbe/evad067.

Brauny MM, Maier L. Gut bacteria thwart the blood sugar-lowering effect of acarbose. Nat Metab (2023) doi: 10.1038/s42255-023-00798-8.

Adolf LA, Müller-Jochim A, Kricks L, Puls JS, Lopez D, Grein F, Heilbronner S.  Functional membrane microdomains and the hydroxamate siderophore transporter ATPase FhuC govern Isd-dependent heme acquisition in Staphylococcus aureus. eLife 12:e85304. (2023) doi: 10.7554/eLife.85304.

Selim KA, Zimmer E. SbtB — der fehlende Sensor für anorganischen Kohlenstoff in Cyanobakterien. Biospektrum 29:140–143. (2023) doi: 10.1007/s12268-023-1902-2.

Olalekan A, Bader BA, Iwalokun A, Wolf S,  Lalremruata A, Dike A, Mannie-Udoh M, Lo Presti L, Liese J, Guther J, D’alvise A, Peter S. High incidence of carbapenemase-producing Pseudomonas aeruginosa clinical isolates from Lagos, Nigeria. JAC-Antimicrobial Resistance 5(2). (2023) doi: 10.1093/jacamr/dlad038.

Eggers O, Renschler FA, Michalek LA, Wackler N, Walter E, Smollich F, Klein K, Sonnabend MS, Egle V, Angelov A, Engesser C, Borisova M, Mayer C, Schütz M, Bohn E. YgfB increases β-lactam resistance in Pseudomonas aeruginosa by counteracting AlpA-mediated ampDh3 expression. Commun Biol 6, 254. (2023) doi: 10.1038/s42003-023-04609-4.

Stein-Thoeringer  C, Saini NY, Zamir E, et al. A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy. Nat Med. (2023) doi: 10.1038/s41591-023-02234-6.

Pendergraft MA, Belda-Ferre P, Petras D, Morris CK, Mitts BA, Aron AT, Bryant M, Schwartz T, Ackermann G, Humphrey G, Kaandorp E, Dorrestein PC, Knight R, Prather KA. Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol. Environ Sci Technol. Mar 2. (2023) doi: 10.1021/acs.est.2c02312. Epub ahead of print. PMID: 36862087.

Gautam A, Zeng W, Huson DH. MeganServer: facilitating interactive access to metagenomic data on server. Bioinformatics 39(3). (2023) doi: 10.1093/bioinformatics/btad105.

Segrè D, Mitri S, Shou W, Süel GM, Mizrahi I, Kelly L, Rebolleda-Gómez M, Ratzke C, Ogbunugafor CB, Schwartzman JA, Kryazhimskiy S, Leventhal GE, Kost C, Bell T. What do you most want to understand about how collective features emerge in microbial communities? Cell Syst. 14(2): 91–97. (2023) doi: 10.1016/j.cels.2023.01.001.

Selim KA, Haffner M, Mantovani O, Hartmann MD. Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. Proc. Natl. Acad. Sci. 120(8): e2205882120. (2023) doi: 10.1073/pnas.2205882120.

Dahal S, Renz A, Dräger A, Yang L. Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation. Commun. Biol. 6, 165. (2023) doi: 10.1038/s42003-023-04540-8.

Glöckler M, Dräger A, Mostolizadeh R. Hierarchical modelling of microbial communities. Bioinformatics 39(1). (2023) doi: 10.1093/bioinformatics/btad040.

Farke N, Schramm T, Verhülsdonk A, Rapp J, Link H. Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. Anal. Biochem.  664: 115036. (2023) doi: 10.1016/j.ab.2023.115036.

Constantinou I, Bastounis EE. Cell-stretching devices: advances and challenges in biomedical research and live-cell imaging. Trends Biotechnol. S0167–7799(22)00332-8. (2023) doi: 10.1016/j.tibtech.2022.12.009.

Clasen SJ, Bell MEW, Borbón A, Lee D, Henseler ZM, De La Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y, Ley RE. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci. Immunol. 8(79). (2023) doi: 10.1126/sciimmunol.abq7001.