Project A1 (PIs Schulenburg, Dierking, Kaleta) aims to enhance our understanding of microbiome-mediated evolution of the metaorganism. Using the nematode C. elegans as a versatile experimental model system, the project will examine the molecular and metabolic processes involved in microbiome-mediated host adaptation and protection against pathogen infection.
A1
Evolution and Ecology
Evolutionary dynamics and molecular basis of C. elegans-microbiome interactions
A1
Researchers
Researchers
A1.1: Evolution of microbiome-mediated effects on host fitness
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Associated Postdoctoral Researcher
Dr. Peter Deines
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A1.2: Molecular basis of microbiome-mediated protection against pathogen infection
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Associated Postdoctoral Researcher
Dr. Barbara Pees
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A1.5: Metabolic modeling of host-microbiome-interactions
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Associated Doctoral Candidate
Rupinder Kaur
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Associated Doctoral Candidate
Florian Krüger
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Associated Doctoral Candidate
Andy Mercado Gamarra
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Associated Doctoral Candidate
Natchapon Srinak
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Associated Postdoctoral Researcher
Dr. Lena Best
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Associated Postdoctoral Researcher
Dr. Georgios Marinos
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Related Publications
Related Publications
2024
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Unanticipated specificity in effector-triggered immunity
Zárate-Potes, A., Schulenburg, H., & Dierking, K. (2024). Trends in Immunology. doi: https://doi.org/10.1016/j.it.2024.10.008
2024
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Wie arbeitet Wissenschaft heute? Vernetzte Zugänge für Universität und Schule
Parchmann, I., Bosch, T. B., Claussen, C., Duscher, T., Enzingmüller, C., Knüver, J., & Schulenburg, H. (2024). MNU-Journal/Verband zur Förderung des MINT-Unterrichts, 2024(1), 29-36.
2024
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Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life
Zimmermann, J., Piecyk, A., Sieber, M., Petersen, C., Johnke, J., Moitinho-Silva, L., Künzel, S., Bluhm, L., Traulsen, A., Kaleta, C., & Schulenburg, H. (2024). Mbio, 15(5), e00012-24. doi: https://doi.org/10.1128/mbio.00012-24
2024
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Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics
Marinos, G., Hamerich, I. K., Debray, R., Obeng, N., Petersen, C., Taubenheim, J., Zimmermann, J., Blackburn, D., Samuel, B. S., Dierking, K., Franke, A., Laudes, M., Waschina, S., Schulenburg, H., & Kaleta, C. (2024). Microbiology Spectrum, 12(2), e01144-23. doi: https://doi.org/10.1128/spectrum.01144-23
2023
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Recurrent phases of strict protein limitation inhibit tumor growth and restore lifespan in a Drosophila intestinal cancer model.
Pfefferkorn RM, Mortzfeld BM, Fink C, von Frieling J, Bossen J, Esser D, Kaleta C, Rosenstiel P, Heine H, Roeder T (2023) Recurrent phases of strict protein limitation inhibit tumor growth and restore lifespan in a Drosophila intestinal cancer model. Aging&Disease in press.
2023
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The nematode Caenorhabditis elegans and diverse potential invertebrate vectors predominantly interact opportunistically
The nematode Caenorhabditis elegans and diverse potential invertebrate vectors predominantly interact opportunistically.
Petersen C, Krahn A, Leippe M. (2023) Front. Ecol. Evol.
doi: 10.3389/fevo.2023.1069056
2023
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Gut-associated functions are favored during microbiome assembly across C. elegans life
Zimmermann J*, Piecyk A*, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H (2023) Gut-associated functions are favored during microbiome assembly across C. elegans life. bioRxiv doi:10.1101/2023.03.25.534195. *Shared first authorship.
2023
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Host and microbiome jointly contribute to environmental adaptation
Petersen C*, Hamerich IK*, Adair KL*, Griem-Krey H, Torres Oliva M, Hoeppner MP, Bohannan BJM*, Schulenburg H* (2023) Host and microbiome jointly contribute to environmental adaptation. ISME Journal doi.org/10.1038/s41396-023-01507-9. *Shared first or senior authorship.
2023
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The intricate triangular interaction between protective microbe, pathogen, and host genetics determines fitness of the metaorganism
Griem-Krey H*, Petersen C*, Hamerich IK, Schulenburg H (2023) The intricate triangular interaction between protective microbe, pathogen, and host genetics determines fitness of the metaorganism. bioRxiv *shared first authors doi:10.1101/2023.03.22.533850.
2023
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The C. elegans proteome response to two protective Pseudomonas symbionts
Barbara Pees*, Lena Peters, Christian Treitz, Inga K. Hamerich, Kohar A. B. Kissoyan, Andreas Tholey, Katja Dierking* (2023) The C. elegans proteome response to two protective Pseudomonas symbionts. bioRxiv doi:10.1101/2023.03.22.533766. *Shared corresponding authors.
2023
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Closely related Bacteroides of the murine intestinal microbiota affect each other’s growth positively or negatively
2023
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Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis
Domin H, Zimmermann J, Taubenheim J, Fuentes Reyes G, Saueressig L, Prasse D, Höppner M, Schmitz RA, Hentschel U, Kaleta C, Fraune S (2023) Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis. Microbiome doi:10.1186/s40168-023-01701-z
2022
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Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans
Petersen, C., Dierking, K., Johnke, J., Schulenburg, H. Isolation and Characterization of the Natural Microbiota of the Model Nematode Caenorhabditis elegans. J. Vis. Exp. (186), e64249, doi:10.3791/64249 (2022).
2022
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Exploring Effects of C. elegans Protective Natural Microbiota on Host Physiology.
Kissoyan KAB, Peters L, Giez C, Michels J, Pees B, Hamerich IK, Schulenburg H, Dierking K. (2022) Front Cell Infect Microbiol. 12:775728. doi: 10.3389/fcimb.2022.775728
2021
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Preconditioning with natural microbiota strain Ochrobactrum vermis MYb71 influences Caenorhabditis elegans behavior
Petersen C, Pees B, Martínez Christophersen C, Leippe M (2021) Front Cell Infect Microbiol. 11:775634. doi: 10.3389/fcimb.2021.775634
2021
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In vitro interaction network of a synthetic gut bacterial community.
Weiss AS, Burrichter AG, Durai Raj AC, von Strempel A, Meng C, Kleigrewe K, Münch PC, Rössler L, Huber C, Eisenreich W, Jochum LM, Göing S, Jung K, Lincetto C, Hübner J, Marinos G, Zimmermann J, Kaleta C, Sanchez A, Stecher B (2021) ISME J. doi: 1038/s41396-021-01153-z
2021
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Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis.
Hinrichsen F, Hamm J, Westermann M, Schröder L, Shima K, Mishra N, Walker A, Sommer N, Klischies K, Prasse D, Zimmermann J, Kaiser S, Bordoni D, Fazio A, Marinos G, Laue G, Imm S, Tremaroli V, Basic M, Häsler R, Schmitz RA, Krautwald S, Wolf A, Stecher B, Schmitt-Kopplin P, Kaleta C, Rupp J, Bäckhed F, Rosenstiel P, Sommer F (2021) Cell Metab 33(12):2355-2366.e8. doi: 1016/j.cmet.2021.11.004
2021
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Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria
Giri S, Oña L, Waschina S, Shitut S, Yousif G, Kaleta C, Kost C (2021) Curr Biol. S0960-9822(21)01408-1. doi: 1016/j.cub.2021.10.019.
2021
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Microbes to-go: slugs as source for Caenorhabditis elegans microbiota acquisition.
Pees B, Johnke J, Möhl M, Hamerich IK, Leippe M, Petersen C (2021) Environ. Microbiol. doi:10.1111/1462-2920.15730.
2021
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The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.
Snoek BL, Sterken MG, Nijveen H, Volkers RJM, Riksen J, Rosenstiel PC, Schulenburg H, Kammenga JE. (2021) G3 (Bethesda). 11(10):jkab258. doi: 10.1093/g3journal/jkab258.
2021
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The effects of nested miRNAs and their host genes on immune defense against Bacillus thuringiensis infection in Caenorhabditis elegans.
Zárate-Potes A, Yang W, Andresen B, Nakad B, Haase D, Rosenstiel P, Dierking K*, Schulenburg H* (2021) Dev Comp Immunol. 123:104144 doi: 10.1016/j.dci.2021.104144 *Shared senior authorship.
2021
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Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins.
Pees B, Yang W, Kloock A, Petersen C, Peters L, Fan L, Friedrichsen M, Butze S, Zárate-Potes A, Schulenburg H, Dierking K (2021) PLoS Pathogens. 17(4):e1009454. doi: 10.1371/journal.ppat.1009454
2021
A1
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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Zimmermann J, Kaleta C, Waschina S (2021) Genome Biol. 22(81):1-35. doi: 10.1186/s13059-021-02295-1
2020
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Defining the nutritional input for genome-scale metabolic models: a roadmap
Marinos G, Kaleta C, Waschina S (2020) PLOS ONE 15(8): e0236890. doi: 10.1371/journal.pone.0236890
2020
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Microbiome-mediated plasticity directs host evolution along several distinct time scale
Kolodny O, Schulenburg H (2020) Phil. Trans. R. Soc. B. 375: 20190589. doi: 10.1098/rstb.2019.0589
2020
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Metaorganismusforschung trifft Schule: Wissenschaftskommunikation an der Universität zu Kiel.
Claussen C, Kapitza M, Knapp JM, Bernholt A, Schulenburg H, Kremer KH (2020). Biologie in unserer Zeit (BiuZ), 50(4), 270-277. doi: 10.1002/biuz.202010713
2020
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CeMbio – The Caenorhabditis elegans microbiome resource
2020
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Receptors mediating host-microbiota communication in the metaorganism: the invertebrate perspective.
Dierking K, Pita L (2020) Front. Immunol. 11:1251. doi: 10.3389/fimmu.2020.01251
2020
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The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans
Zimmermann J*, Obeng N*, Yang W, Pees B, Petersen C, Waschina S, Kissoyan KAB, Aidley J, Hoeppner MP, Bunk B, Spröer C, Leippe M, Dierking K, Kaleta C*, Schulenburg H* (2019) ISME J. 14: 26–38. * Shared first or senior authorship doi: 10.1038/s41396-019-0504-y
2019
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Prdx4 limits caspase-1 activation and restricts inflammasome-mediated signaling by extracellular vesicles
Lipinski S, Pfeuffer S, Arnold P, Treitz C, Aden K, Ebsen H, Falk-Paulsen M, Gisch N, Fazio A, Kuiper J, Luzius A, Billmann-Born S, Schreiber S, Nuñez G, Beer HD, Strowig T, Lamkanfi M, Tholey A, Rosenstiel P (2019) EMBO J. 38(20) doi: 10.15252/embj.2018101266.
2019
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Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling J, Hentschel U, Heinsen F-A, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF (2019) Microbiome, doi: 10.1186/s40168-019-0743-1
2019
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The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiome across development and adult life
Yang W#, Petersen C#, Pees B#, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C*, Schulenburg H*. Front Microbiol. 10:1793. # Equal contribution as first authors, * Equal contribution as senior authors doi: 10.3389/fmicb.2019.01793.
2019
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aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data
Yang W, Rosenstiel P, Schulenburg H (2019) BMC Genomics, 20:364, 1-17. doi: 10.1186/s12864-019-5686-1
2019
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A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life-history traits
Snoek BL, Volkers RJM, Nijveen H, Petersen C, Dirksen P, Sterken MG, Nakad R, Riksen J, Rosenstiel P, Stastna JJ, Braeckman BP, Harvey SC, Schulenburg H*, Kammenga JE* (2019) BMC Biol. 17:24. * Shared senior authorship doi: 10.1186/s12915-019-0642-8
2019
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Natural C. elegans microbiota protects against infection via production of a cyclic lipopeptide of the viscosin group
Kohar Kissoyan, Moritz Drechsler, Eva-Lena Stange, Johannes Zimmermann, Christoph Kaleta, Helge Bode und Katja Dierking (2019) Current Biology. DOI: 10.1016/j.cub.2019.01.050
2018
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The Saposin-Like Protein AplD Displays Pore-Forming Activity and Participates in Defense Against Bacterial Infection During a Multicellular Stage of Dictyostelium discoideum.
Dhakshinamoorthy R, Bitzhenner M, Cosson P, Soldati T, Leippe M (2018); Front. Cell. Infect. Microbiol., 8:73. doi: 10.3389/fcimb.2018.00073
2018
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The Caenorhabditis elegans proteome response to naturally associated microbiome members of the genus Ochrobactrum
Cassidy L, Petersen C, Treitz C, Dierking K, Schulenburg H, Leippe M, Tholey A (2018); Proteomics, doi: 10.1002/pmic.201700426
2018
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Miniaturized dispersive liquid-liquid microextraction and MALDI MS using ionic liquid matrices for the detection of bacterial communication molecules and virulence factors.
Leipert J, Bobis I, Schubert S, Fickenscher H, Leippe M, Tholey A (2018); Anal Bioanal Chem. , pp 1–12. doi: 10.1007/s00216-018-0937-6
2018
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?
Bang C, Dagan T, Deines P, Dubilier N, Duschl W J, Fraune S, Hentschel U, Hirt H, Hülter N, Lachnit T, Picazo D, Galan P L, Pogoreutz C, Rädecker N, Saad M M, Schmitz R A, Schulenburg H, Voolstra C R, Weiland-Bräuer N, Ziegler M, Bosch T C G (2018); Zoology, doi: 10.1016/j.zool.2018.02.004
2017
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We Are Not Alone: The iMOP Initiative and Its Roles in a Biology- and Disease-Driven Human Proteome Project.
Tholey A, Taylor N L, Heazlewood J L, Bendixen E (2017); J Proteome Res., 16(12):4273-4280. doi: 10.1021/acs.jproteome.7b00408
2017
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Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches.
Krohn-Molt I, Alawi M, Förstner K U, Wiegandt A, Burkhardt L, Indenbirken D, Thieß M, Grundhoff A, Kehr J, Tholey A, Streit W R (2017); Front Microbiol., doi: 10.3389/fmicb.2017.01941
2017
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Identification and Quantification of N-Acyl Homoserine Lactones Involved in Bacterial Communication by Small-Scale Synthesis of Internal Standards and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry.
Leipert J, Treitz C, Leippe M, Tholey A (2017); J Am Soc Mass Spectrom., 28(12):2538-2547. doi: 10.1007/s13361-017-1777-x
2017
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The Natural Biotic Environment of Caenorhabditis elegans.
Schulenburg H, Félix M A (2017); Genetics., 206(1):55-86. doi: 10.1534/genetics.116.195511
2017
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Caenorhabditis elegans as a model for microbiome research.
Zhang F, Berg M, Dierking K, Félix M A, Shapira M, Samuel B, Schulenburg H (2017); Front. Microbiol., 8:485. doi: 10.3389/fmicb.2017.00485
2017
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Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology.
Ott S J, Waetzig G H, Rehman A, Moltzau-Anderson J, Bharti R, Grasis J A, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S (2017); Gastroenterology, 152(4):799-811.e7. doi: 10.1053/j.gastro.2016.11.010
2016
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Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose.
Treitz C, Enjalbert B, Portais J C, Letisse F, Tholey A (2016); Proteomics., 16(21):2742-2746. doi: 10.1002/pmic.201600303
2016
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Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei.
Cassidy L, Prasse D, Linke D, Schmitz R A, Tholey A (2016)
J Proteome Res., 15(10):3773-3783. doi: 10.1021/acs.jproteome.6b00569
2016
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The native microbiome of the nematode Caenorhabditis elegans: Gateway to a new host-microbiome model.
Dirksen P, Marsh SA, Braker I, Heitland N, Wagner S, Nakad R, Mader S, Petersen C, Kowallik V, Rosenstiel P C, Felix M A, Schulenburg H (2016); BMC Biology, 14:38. doi:10.1186/s12915-016-0258-1
2016
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Antimicrobial effectors in the nematode C. elegans – an outgroup to the Arthropoda.
Dierking K, Yang W, Schulenburg H (2016); Phil Trans R Soc Lond B., 371. doi: