Works by Benndorf, Dirk

Results: 55

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.

Published in:

Microbiome, 2025, v. 13, n. 1, p. 1, doi. 10.1186/s40168-025-02119-5

By:

Heyer, Robert;
Wolf, Maximilian;
Benndorf, Dirk;
Uzzau, Sergio;
Seifert, Jana;
Grenga, Lucia;
Pabst, Martin;
Schmitt, Heike;
Mesuere, Bart;
Van Den Bossche, Tim;
Haange, Sven-Bastiaan;
Jehmlich, Nico;
Di Luca, Mariagrazia;
Ferrer, Manuel;
Serrano-Villar, Sergio;
Armengaud, Jean;
Bode, Helge B.;
Hellwig, Patrick;
Masselot, Catherine Robbe;
Léonard, Renaud

Publication type:

Article

Metaproteomics Applied to Activated Sludge for Industrial Wastewater Treatment Revealed a Dominant Methylotrophic Metabolism of Hyphomicrobium zavarzinii.

Published in:

Microbial Ecology, 2016, v. 72, n. 1, p. 9, doi. 10.1007/s00248-016-0769-x

By:

Salerno, Carlo;
Benndorf, Dirk;
Kluge, Sabine;
Palese, Luigi;
Reichl, Udo;
Pollice, Alfieri

Publication type:

Article

Adaptation of a microbial community to demand-oriented biological methanation.

Published in:

Biotechnology for Biofuels & Bioproducts, 2022, v. 15, n. 1, p. 1, doi. 10.1186/s13068-022-02207-w

By:

Khesali Aghtaei, Hoda;
Püttker, Sebastian;
Maus, Irena;
Heyer, Robert;
Huang, Liren;
Sczyrba, Alexander;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

Degradation Kinetics of Lignocellulolytic Enzymes in a Biogas Reactor Using Quantitative Mass Spectrometry.

Published in:

Fermentation (Basel), 2023, v. 9, n. 1, p. 67, doi. 10.3390/fermentation9010067

By:

Küchler, Jan;
Willenbücher, Katharina;
Reiß, Elisabeth;
Nuß, Lea;
Conrady, Marius;
Ramm, Patrice;
Schimpf, Ulrike;
Reichl, Udo;
Szewzyk, Ulrich;
Benndorf, Dirk

Publication type:

Article

Generation of "OP7 chimera" defective interfering influenza A particle preparations free of infectious virus that show antiviral efficacy in mice.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-47547-1

By:

Dogra, Tanya;
Pelz, Lars;
Boehme, Julia D.;
Kuechler, Jan;
Kershaw, Olivia;
Marichal-Gallardo, Pavel;
Baelkner, Maike;
Hein, Marc D.;
Gruber, Achim D.;
Benndorf, Dirk;
Genzel, Yvonne;
Bruder, Dunja;
Kupke, Sascha Y.;
Reichl, Udo

Publication type:

Article

Purification and characterization of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3.

Published in:

AMB Express, 2011, v. 1, n. 1, p. 1, doi. 10.1186/2191-0855-1-8

By:

Kolvenbach, Boris;
Lenz, Markus;
Benndorf, Dirk;
Rapp, Erdmann;
Fousek, Jan;
Vlcek, Cestmir;
Schäffer, Andreas;
Gabriel, Frédéric;
Kohler, Hans-Peter;
Corvini, Philippe

Publication type:

Article

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.

Published in:

Nature Protocols, 2020, v. 15, n. 10, p. 3212, doi. 10.1038/s41596-020-0368-7

By:

Schiebenhoefer, Henning;
Schallert, Kay;
Renard, Bernhard Y.;
Trappe, Kathrin;
Schmid, Emanuel;
Benndorf, Dirk;
Riedel, Katharina;
Muth, Thilo;
Fuchs, Stephan

Publication type:

Article

Metaproteomics of complex microbial communities in biogas plants.

Published in:

Microbial Biotechnology, 2015, v. 8, n. 5, p. 749, doi. 10.1111/1751-7915.12276

By:

Heyer, Robert;
Kohrs, Fabian;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

Induction of heat shock proteins in response to primary alcohols in Acinetobacter calcoaceticus.

Published in:

Electrophoresis, 1999, v. 20, n. 4/5, p. 781, doi. 10.1002/(SICI)1522-2683(19990101)20:4/5<781::AID-ELPS781>3.0.CO;2-A

By:

Benndorf, Dirk;
Loffhagen, Norbert;
Babel, Wolfgang

Publication type:

Article

Quantification of intracellular influenza A virus protein dynamics in different host cells after seed virus adaptation.

Published in:

Applied Microbiology & Biotechnology, 2025, v. 109, n. 1, p. 1, doi. 10.1007/s00253-025-13423-3

By:

Küchler, Jan;
Opitz, Patricia;
Jordan, Ingo;
Genzel, Yvonne;
Benndorf, Dirk;
Reichl, Udo

Publication type:

Article

Advances in the clinical use of metaproteomics.

Published in:

2023

By:

Wolf, Maximilian;
Schallert, Kay;
Knipper, Luca;
Sickmann, Albert;
Sczyrba, Alexander;
Benndorf, Dirk;
Heyer, Robert

Publication type:

Report

Chemicals and heat generate different protein patterns in Acinetobacter calcoaceticus.

Published in:

Journal of Basic Microbiology, 1997, v. 37, n. 3, p. 167, doi. 10.1002/jobm.3620370304

By:

Benndorf, Dirk;
Loffhagen, Norbert;
Babel, Wolfgang

Publication type:

Article

Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins.

Published in:

Applied Microbiology & Biotechnology, 2021, v. 105, n. 5, p. 1861, doi. 10.1007/s00253-021-11150-z

By:

Pech, Sabine;
Rehberg, Markus;
Janke, Robert;
Benndorf, Dirk;
Genzel, Yvonne;
Muth, Thilo;
Sickmann, Albert;
Rapp, Erdmann;
Reichl, Udo

Publication type:

Article

OP7, a novel influenza A virus defective interfering particle: production, purification, and animal experiments demonstrating antiviral potential.

Published in:

Applied Microbiology & Biotechnology, 2021, v. 105, n. 1, p. 129, doi. 10.1007/s00253-020-11029-5

By:

Hein, Marc D.;
Kollmus, Heike;
Marichal-Gallardo, Pavel;
Püttker, Sebastian;
Benndorf, Dirk;
Genzel, Yvonne;
Schughart, Klaus;
Kupke, Sascha Y.;
Reichl, Udo

Publication type:

Article

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome.

Published in:

Applied Microbiology & Biotechnology, 2015, v. 99, n. 18, p. 7791, doi. 10.1007/s00253-015-6627-9

By:

Theuerl, Susanne;
Kohrs, Fabian;
Benndorf, Dirk;
Maus, Irena;
Wibberg, Daniel;
Schlüter, Andreas;
Kausmann, Robert;
Heiermann, Monika;
Rapp, Erdmann;
Reichl, Udo;
Pühler, Alfred;
Klocke, Michael

Publication type:

Article

Proteome analysis of virus-host cell interaction: rabies virus replication in Vero cells in two different media.

Published in:

Applied Microbiology & Biotechnology, 2013, v. 97, n. 12, p. 5493, doi. 10.1007/s00253-013-4939-1

By:

Kluge, Sabine;
Rourou, Samia;
Vester, Diana;
Majoul, Samy;
Benndorf, Dirk;
Genzel, Yvonne;
Rapp, Erdmann;
Kallel, Héla;
Reichl, Udo

Publication type:

Article

Functional metaproteome analysis of protein extracts from contaminated soil and groundwater.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2007, v. 1, n. 3, p. 224, doi. 10.1038/ismej.2007.39

By:

Benndorf, Dirk;
Balcke, Gerd U.;
Harms, Hauke;
Von Bergen, Martin

Publication type:

Article

SDS‐PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samples.

Published in:

Engineering in Life Sciences, 2018, v. 18, n. 7, p. 498, doi. 10.1002/elsc.201800062

By:

Wenzel, Lisa;
Heyer, Robert;
Schallert, Kay;
Löser, Lucy;
Wünschiers, Röbbe;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

Proteomics in environmental and technical microbiology.

Published in:

Engineering in Life Sciences, 2014, v. 14, n. 1, p. 27, doi. 10.1002/elsc.201200205

By:

Benndorf, Dirk;
Reichl, Udo

Publication type:

Article

Detection, isolation and characterization of phage-host complexes using BONCAT and click chemistry.

Published in:

Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1434301

By:

Hellwig, Patrick;
Dittrich, Anna;
Heyer, Robert;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

Microbiome modeling: a beginner's guide.

Published in:

Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2024.1368377

By:

Lange, Emanuel;
Kranert, Lena;
Krüger, Jacob;
Benndorf, Dirk;
Heyer, Robert

Publication type:

Article

Improved biological methanation using tubular foam-bed reactor.

Published in:

Biotechnology for Biofuels & Bioproducts, 2024, v. 17, n. 1, p. 1, doi. 10.1186/s13068-024-02509-1

By:

Khesali Aghtaei, Hoda;
Heyer, Robert;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes and pure cultures.

Published in:

Molecular Ecology Resources, 2019, v. 19, n. 2, p. 439, doi. 10.1111/1755-0998.12979

By:

Thorn, Camilla E.;
Bergesch, Christian;
Joyce, Aoife;
Sambrano, Gustavo;
McDonnell, Kevin;
Abram, Florence;
Brennan, Fiona;
Heyer, Robert;
Benndorf, Dirk

Publication type:

Article

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006759

By:

Koch, Sabine;
Kohrs, Fabian;
Lahmann, Patrick;
Bissinger, Thomas;
Wendschuh, Stefan;
Benndorf, Dirk;
Reichl, Udo;
Klamt, Steffen

Publication type:

Article

Discovering Biomarkers for Non-Alcoholic Steatohepatitis Patients with and without Hepatocellular Carcinoma Using Fecal Metaproteomics.

Published in:

International Journal of Molecular Sciences, 2022, v. 23, n. 16, p. 8841, doi. 10.3390/ijms23168841

By:

Sydor, Svenja;
Dandyk, Christian;
Schwerdt, Johannes;
Manka, Paul;
Benndorf, Dirk;
Lehmann, Theresa;
Schallert, Kay;
Wolf, Maximilian;
Reichl, Udo;
Canbay, Ali;
Bechmann, Lars P.;
Heyer, Robert

Publication type:

Article

MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 20, p. 10992, doi. 10.3390/ijms222010992

By:

Walke, Daniel;
Schallert, Kay;
Ramesh, Prasanna;
Benndorf, Dirk;
Lange, Emanuel;
Reichl, Udo;
Heyer, Robert

Publication type:

Article

Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study.

Published in:

Proteomics, 2015, v. 15, n. 20, p. 3596, doi. 10.1002/pmic.201400559

By:

Püttker, Sebastian;
Kohrs, Fabian;
Benndorf, Dirk;
Heyer, Robert;
Rapp, Erdmann;
Reichl, Udo

Publication type:

Article

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities.

Published in:

Proteomics, 2015, v. 15, n. 20, p. 3585, doi. 10.1002/pmic.201400557

By:

Kohrs, Fabian;
Wolter, Sophie;
Benndorf, Dirk;
Heyer, Robert;
Hoffmann, Marcus;
Rapp, Erdmann;
Bremges, Andreas;
Sczyrba, Alexander;
Schlüter, Andreas;
Reichl, Udo

Publication type:

Article

Proteomic tracking and analysis of a bacterial mixed culture.

Published in:

Proteomics, 2012, v. 12, n. 12, p. 1893, doi. 10.1002/pmic.201100362

By:

Kluge, Sabine;
Hoffmann, Marcus;
Benndorf, Dirk;
Rapp, Erdmann;
Reichl, Udo

Publication type:

Article

Metaproteome analysis of sewage sludge from membrane bioreactors.

Published in:

Proteomics, 2011, v. 11, n. 13, p. 2738, doi. 10.1002/pmic.201000590

By:

Kuhn, Ramona;
Benndorf, Dirk;
Rapp, Erdmann;
Reichl, Udo;
Palese, Luigi Leonardo;
Pollice, Alfieri

Publication type:

Article

Vitellogenin cleavage products as indicators for toxic stress in zebra fish embryos: A proteomic approach.

Published in:

Proteomics, 2007, v. 7, n. 24, p. 4541, doi. 10.1002/pmic.200700381

By:

Gündel, Ulrike;
Benndorf, Dirk;
von Bergen, Martin;
Altenburger, Rolf;
Küster, Eberhard

Publication type:

Article

Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites.

Published in:

Proteomics, 2006, v. 6, n. 11, p. 3319, doi. 10.1002/pmic.200500781

By:

Dirk Benndorf;
Markus Thiersch;
Norbert Loffhagen;
Christfried Kunath;
Hauke Harms

Publication type:

Article

Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics.

Published in:

Proteomics, 2004, v. 4, n. 9, p. 2640, doi. 10.1002/pmic.200300793

By:

Pedro M. Santos;
Dirk Benndorf;
Isabel Sá-Correia

Publication type:

Article

Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440.

Published in:

Proteomics, 2003, v. 3, n. 8, p. 1544, doi. 10.1002/pmic.200300477

By:

Martin Krayl;
Dirk Benndorf;
Norbert Loffhagen;
Wolfgang Babel

Publication type:

Article

A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer.

Published in:

Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.01883

By:

Heyer, Robert;
Schallert, Kay;
Büdel, Anja;
Zoun, Roman;
Dorl, Sebastian;
Behne, Alexander;
Kohrs, Fabian;
Püttker, Sebastian;
Siewert, Corina;
Muth, Thilo;
Saake, Gunter;
Reichl, Udo;
Benndorf, Dirk

Publication type:

Article

Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity.

Published in:

Frontiers in Microbiology, 2019, p. N.PAG, doi. 10.3389/fmicb.2019.01095

By:

Weinrich, Sören;
Koch, Sabine;
Bonk, Fabian;
Popp, Denny;
Benndorf, Dirk;
Klamt, Steffen;
Centler, Florian

Publication type:

Article

smORFer: a modular algorithm to detect small ORFs in prokaryotes.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 15, p. e89, doi. 10.1093/nar/gkab477

By:

Bartholomäus, Alexander;
Kolte, Baban;
Mustafayeva, Ayten;
Goebel, Ingrid;
Fuchs, Stephan;
Benndorf, Dirk;
Engelmann, Susanne;
Ignatova, Zoya

Publication type:

Article

Integrated Cycles for Urban Biomass as a Strategy to Promote a CO 2 -Neutral Society—A Feasibility Study.

Published in:

Sustainability (2071-1050), 2021, v. 13, n. 17, p. 9505, doi. 10.3390/su13179505

By:

Meinusch, Nicole;
Kramer, Susanne;
Körner, Oliver;
Wiese, Jürgen;
Seick, Ingolf;
Beblek, Anita;
Berges, Regine;
Illenberger, Bernhard;
Illenberger, Marco;
Uebbing, Jennifer;
Wolf, Maximilian;
Saake, Gunter;
Benndorf, Dirk;
Reichl, Udo;
Heyer, Robert

Publication type:

Article

Advanced tool for characterization of microbial cultures by combining cytomics and proteomics.

Published in:

Applied Microbiology & Biotechnology, 2010, v. 88, n. 2, p. 575, doi. 10.1007/s00253-010-2753-6

By:

Jehmlich, Nico;
Hübschmann, Thomas;
Gesell Salazar, Manuela;
Völker, Uwe;
Benndorf, Dirk;
Müller, Susann;
Bergen, Martin;
Schmidt, Frank

Publication type:

Article

Laundry Isolate Delftia sp. UBM14 Capable of Biodegrading Industrially Relevant Aminophosphonates.

Published in:

Microorganisms, 2024, v. 12, n. 8, p. 1664, doi. 10.3390/microorganisms12081664

By:

Riedel, Ramona;
Meißner, Karsten;
Kaschubowski, Arne;
Benndorf, Dirk;
Martienssen, Marion;
Braun, Burga

Publication type:

Article

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics.

Published in:

Microorganisms, 2023, v. 11, n. 10, p. 2412, doi. 10.3390/microorganisms11102412

By:

Hassa, Julia;
Tubbesing, Tom Jonas;
Maus, Irena;
Heyer, Robert;
Benndorf, Dirk;
Effenberger, Mathias;
Henke, Christian;
Osterholz, Benedikt;
Beckstette, Michael;
Pühler, Alfred;
Sczyrba, Alexander;
Schlüter, Andreas

Publication type:

Article

Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study.

Published in:

Microorganisms, 2022, v. 10, n. 5, p. 978, doi. 10.3390/microorganisms10050978

By:

Scoma, Alberto;
Khor, Way Cern;
Coma, Marta;
Heyer, Robert;
Props, Ruben;
Bouts, Tim;
Benndorf, Dirk;
Li, Desheng;
Zhang, Hemin;
Rabaey, Korneel

Publication type:

Article

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants.

Published in:

Microorganisms, 2021, v. 9, n. 7, p. 1457, doi. 10.3390/microorganisms9071457

By:

Hassa, Julia;
Klang, Johanna;
Benndorf, Dirk;
Pohl, Marcel;
Hülsemann, Benedikt;
Mächtig, Torsten;
Effenberger, Mathias;
Pühler, Alfred;
Schlüter, Andreas;
Theuerl, Susanne

Publication type:

Article

The Role of Petrimonas mucosa ING2-E5A T in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses.

Published in:

Microorganisms, 2020, v. 8, n. 12, p. 2024, doi. 10.3390/microorganisms8122024

By:

Maus, Irena;
Tubbesing, Tom;
Wibberg, Daniel;
Heyer, Robert;
Hassa, Julia;
Tomazetto, Geizecler;
Huang, Liren;
Bunk, Boyke;
Spröer, Cathrin;
Benndorf, Dirk;
Zverlov, Vladimir;
Pühler, Alfred;
Klocke, Michael;
Sczyrba, Alexander;
Schlüter, Andreas

Publication type:

Article

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.

Published in:

2021

By:

Van Den Bossche, Tim;
Arntzen, Magnus Ø.;
Becher, Dörte;
Benndorf, Dirk;
Eijsink, Vincent G. H.;
Henry, Céline;
Jagtap, Pratik D.;
Jehmlich, Nico;
Juste, Catherine;
Kunath, Benoit J.;
Mesuere, Bart;
Muth, Thilo;
Pope, Phillip B.;
Seifert, Jana;
Tanca, Alessandro;
Uzzau, Sergio;
Wilmes, Paul;
Hettich, Robert L.;
Armengaud, Jean

Publication type:

Letter

Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments.

Published in:

Biodegradation, 2009, v. 20, n. 6, p. 737, doi. 10.1007/s10532-009-9261-3

By:

Benndorf, Dirk;
Vogt, Carsten;
Jehmlich, Nico;
Schmidt, Yvonne;
Thomas, Henrik;
Woffendin, Gary;
Shevchenko, Andrej;
Richnow, Hans-Hermann;
von Bergen, Martin

Publication type:

Article

Kinetics of chlorobenzene biodegradation under reduced oxygen levels.

Published in:

Biodegradation, 2008, v. 19, n. 4, p. 507, doi. 10.1007/s10532-007-9156-0

By:

Balcke, Gerd Ulrich;
Wegener, Silke;
Kiesel, Bärbel;
Benndorf, Dirk;
Schlömann, Michael;
Vogt, Carsten

Publication type:

Article

Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate.

Published in:

Frontiers in Microbiology, 2020, p. 1, doi. 10.3389/fmicb.2020.00530

By:

Scoma, Alberto;
Khor, Way Cern;
Coma, Marta;
Heyer, Robert;
Props, Ruben;
Schoelynck, Jonas;
Bouts, Tim;
Benndorf, Dirk;
Li, Desheng;
Zhang, Hemin;
Rabaey, Korneel

Publication type:

Article

The Impact of ackA, pta , and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12.

Published in:

Frontiers in Microbiology, 2020, p. 1, doi. 10.3389/fmicb.2020.00233

By:

Schütze, Andrea;
Benndorf, Dirk;
Püttker, Sebastian;
Kohrs, Fabian;
Bettenbrock, Katja

Publication type:

Article

An Investigation of Alternatives to Transform Protein Sequence Databases to a Columnar Index Schema.

Published in:

Algorithms, 2021, v. 14, n. 2, p. 59, doi. 10.3390/a14020059

By:

Zoun, Roman;
Schallert, Kay;
Broneske, David;
Trifonova, Ivayla;
Chen, Xiao;
Heyer, Robert;
Benndorf, Dirk;
Saake, Gunter;
Rizzi, Antonello

Publication type:

Article