Publications of Dirk Benndorf

Journal Article (58)

2021
Journal Article
Walke, D., Schallert, K., Ramesh, P., Benndorf, D., Lange, E., Reichl, U., & Heyer, R. (2021)MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic PathwaysInternational Journal of Molecular Sciences, 22 (20), 10992doi: 10.3390/ijms222010992.
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2020
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Heyer, R., Klang, J., Hellwig, P., Schallert, K., Kress, P., Huelsemann, B., Theuerl, S., Reichl, U., & Benndorf, D. (2020)Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plantsBioresource Technology, 314, 123679doi: 10.1016/j.biortech.2020.123679.
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Maus, I., Tubbesing, T., Wibberg, D., Heyer, R., Hassa, J., Tomazetto, G., Huang, L., Bunk, B., Spröer, C., Benndorf, D., Zverlov, V., Pühler, A., Klocke, M., Sczyrba, A., & Schlüter, A. (2020)The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics AnalysesMicroorganisms, 8 (12), 2024doi: 10.3390/microorganisms8122024.
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Schiebenhoefer, H., Schallert, K., Renard, B. Y., Trappe, K., Schmid, E., Benndorf, D., Riedel, K., Muth, T., & Fuchs, S. (2020)A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and ProphaneNature Protocols, 15, 3212–3239doi: 10.1038/s41596-020-0368-7.
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Schütze, A., Benndorf, D., Püttker, S., Kohrs, F., & Bettenbrock, K. (2020)The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12Frontiers in Microbiology, 11, 233doi: 10.3389/fmicb.2020.00233.
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Scoma, A., Khor, W. C., Coma, M., Heyer, R., Props, R., Schoelynk, J., Bouts, T., Benndorf, D., Li, D., Zhang, H., & Rabaey, K. (2020)Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to LactateFrontiers in Microbiology, 11, 530doi: 10.3389/fmicb.2020.00530.
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Van Den Bossche, T., Verschaffelt, P., Schallert, K., Barsnes, H., Dawyndt, P., Benndorf, D., Renard, B. Y., Mesuere, B., Martens, L., & Muth, T. (2020)Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data AnalysisJournal of Proteome Research, 19 (8), 3562–3566doi: 10.1021/acs.jproteome.0c00136 .
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2019
Journal Article
Heyer, R., Schallert, K., Büdel, A., Zoun, R., Dorl, S., Behne, A., Kohrs, F., Püttker, S., Siewert, C., Muth, T., Saake, G., Reichl, U., & Benndorf, D. (2019)A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzerFrontiers in Microbiology, 10, 1883doi: 10.3389/fmicb.2019.01883.
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Heyer, R., Schallert, K., Siewert, C., Kohrs, F., Greve, J., Maus, I., Klang, J., Klocke, M., Heiermann, M., Hoffmann, M., Püttker, S., Calusinska, M., Zoun, R., Saake, G., Benndorf, D., & Reichl, U. (2019)Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plantsMicrobiome, (7), 69doi: 10.1186/s40168-019-0673-y.
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Koch, S., Kohrs, F., Lahmann, P., Bissinger, T., Wendschuh, S., Benndorf, D., Reichl, U., & Klamt, S. (2019)RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestionPLoS Computational Biology, 15 (2), e1006759doi: 10.1371/journal.pcbi.1006759.
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Lehmann, T., Schallert, K., Vilchez-Vargas, R., Benndorf, D., Püttker, S., Sydor, S., Schulz, C. U., Bechmann, L. P., Canbay, A. E., Heidrich, B., Reichl, U., Link, A., & Heyer, R. (2019)Metaproteomics of fecal samples of Crohn's disease and Ulcerative ColitisJournal of Proteomics, 201, 93–103doi: 10.1016/j.jprot.2019.04.009.
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Scoma, A., Heyer, R., Rifai, R., Dandyk, C., Marshall, I., Kerckhof, F.-M., Marietou, A., Boshker, H. T. S., Meysman, F. J. R., Malmos, K. G., Vosegaard, T., Vermeir, P., Banat, I. M., Benndorf, D., & Boon, N. (2019)Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communitiesThe ISME Journal, 13 (4), 1004–1018doi: 10.1038/s41396-018-0324-5.
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Thorn, C. E., Bergesch , C., Joyce, A., Sambrano, G., McDonnell, K., Brennan, F., Heyer, R., Benndorf, D., & Abram, F. (2019)A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure culturesMolecular Ecology Resources, 19 (2), 439–455doi: 10.1111/1755-0998.12979.
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Weinrich, S., Koch, S., Bonk, F., Popp, D., Benndorf, D., Klamt, S., & Centler, F. (2019)Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic ActivityFrontiers in Microbiology, 10, 1095doi: 10.3389/fmicb.2019.01095.
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2018
Journal Article
Muth, T., Kohrs, F., Heyer, R., Benndorf, D., Rapp, E., Reichl, U., Martens, L., & Renard, B. Y. (2018)MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the GoAnalytical Chemistry, 90, 685–689doi: 10.1021/acs.analchem.7b03544.
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Vodovnik, M., Vrabec, K., Hellwig, P., Benndorf, D., Sezun, M., Gregori, A., Gottumukkala, L. D., Anderson, R. C., & Reichl, U. (2018)Valorisation of deinking sludge as a substrate for lignocellulolytic enzymes production by Pleurotus ostreatusJournal of Cleaner Production, 197 (Part 1), 253–263doi: 10.1016/j.jclepro.2018.06.163.
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Wenzel, L., Heyer, R., Schallert, K., Löser, L., Wünschiers, R., Reichl, U., & Benndorf, D. (2018)SDS-PAGE fractionation to increase metaproteomic insight into the taxonomic and functional composition of microbial communities for biogas plant samplesEngineering in Life Sciences, 18 (7), 498–509doi: 10.1002/elsc.201800062.
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2017
Journal Article
Heyer, R., Schallert, K., Zoun, R., Becher, B., Saake, G., & Benndorf, D. (2017)Challenges and perspectives of metaproteomic data analysisJournal of Biotechnology, 261, 24–36doi: 10.1016/j.jbiotec.2017.06.1201.
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Kohrs, F., Heyer, R., Bissinger, T., Kottler, R., Schallert, K., Püttker, S., Behne, A., Rapp, E., Benndorf, D., & Reichl, U. (2017)Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community compositionAnaerobe, 46, 56–68doi: 10.1016/j.anaerobe.2017.02.005.
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Ricken, B., Kolvenbach, B. A., Bergesch, C., Benndorf, D., Kroll, K., Strnad, H., Vlcek, C., Adaixo, R., Hammes, F., Shahgaldian, P., Schäffer, A., Kohler, H.-P. E., & Corvini , P. F.-X. (2017)FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp. strain BR1 subsisting on sulfonamide antibioticsScientific Reports, 7, 15783doi: 10.1038/s41598-017-16132-8.
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