Microbial Ecology and Biotechnology

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  1. 2023
  2. Published

    Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance

    Forouzandeh, A., Lassen, Simon Bo, Brinck, J. E., Zhou, Y. Y., Zhu, J., Solà-Oriol, D., Monteiro, A., Hao, X., Su, J. Q., Stein, H. H., Pérez, J. F. & Brandt, Kristian Koefoed, 2023, In: Science of the Total Environment. 889, 11 p., 164183.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus

    Riber, Leise, Carstens, Alexander Byth, Dougherty, Peter Erdmann, Roy, C., Willenbücher, K., Hille, F., Franz, C. M. A. P. & Hansen, Lars Hestbjerg, 2023, In: Microorganisms. 11, 7, 17 p., 1831.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Phenotypic variation and genomic variation in insect virulence traits reveal patterns of intraspecific diversity in a locust-specific fungal pathogen

    mbs625, mbs625, Meyling, Nicolai Vitt & de Fine Licht, Henrik Hjarvard, 2023, In: Journal of Evolutionary Biology. 36, 10, p. 1438-1454 17 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II: Editorial

    Sarrocco, S., Herrera-Estrella, A. & Collinge, David B., 2023, In: Frontiers in Microbiology. 14, 3 p., 1203870.

    Research output: Contribution to journal › Editorial › Research

  6. Published

    Potential sources and producers of 2-methylisoborneol and geosmin in a river supplying a drinking water treatment plant

    Franklin, H. M., Podduturi, Raju, Jørgensen, Niels O. G., Roberts, D. T., Schlüter, L. & Burford, M. A., 2023, In: Chemical Engineering Journal Advances. 14, 12 p., 100455.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    Prediction of Cyanotoxin Episodes in Freshwater: A Case Study on Microcystin and Saxitoxin in the Lobo Reservoir, São Paulo State, Brazil

    Moraes, M. D. A. B., Rodrigues, R. D. A. M., Podduturi, Raju, Jørgensen, Niels O. G. & Calijuri, M. D. C., 2023, In: Environments. 10, 8, 16 p., 143.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Pruning Wound Protection Products Induce Alterations in the Wood Mycobiome Profile of Grapevines

    Del Frari, G., Aggerbeck, M. R., Gobbi, Alex, Ingrà, C., Volpi, L., Nascimento, T., Ferrandino, A., Hansen, Lars Hestbjerg & Ferreira, R. B., 2023, In: Journal of Fungi. 9, 4, 20 p., 488.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Relationship between fungal endophytes and plant disease: C9.3-3

    Jensen, Birgit, Collinge, David B. & Jørgensen, Hans Jørgen Lyngs, 2023, p. 280. 1 p.

    Research output: Contribution to conference › Conference abstract for conference › Research

  10. Published

    Removal of a complex VOC mixture by potted plants - effects on soil microorganisms

    Dela Cruz, Majbrit, Svenningsen, N. B., Nybroe, O., Müller, Renate & Christensen, Jan H., 2023, In: Environmental Science and Pollution Research. 30, p. 55372-55381

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Replication Protein Rep Provides Selective Advantage to Viruses in the Presence of CRISPR-Cas Immunity

    Zhang, W., Bhoobalan-Chitty, Y., Zhai, Xichuan, Hui, Y., Hansen, Lars Hestbjerg, Deng, Ling & Peng, Xu, 2023, In: CRISPR Journal. 6, 1, p. 32-42

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Response of bacterial communities to the application of sewage sludge biochar and Penicillium aculeatum in rhizosphere and bulk soil of wheat

    Efthymiou, A., Nunes, I., Jensen, Birgit & Jakobsen, Iver, 2023, In: Applied Soil Ecology. 190, 10 p., 104986.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Response of microbial taxonomic and nitrogen functional attributes to elevated nitrate in suburban groundwater

    Zhang, L., He, W., Huang, F., He, W., Zhou, P., Chen, C., Rensing, C., Brandt, Kristian Koefoed, He, J., Liu, F., Zhao, Y. & Guo, H., 2023, In: Science of the Total Environment. 874, 12 p., 162524.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Spatial controls of methane uptake in upland soils across climatic and geological regions in Greenland

    D'Imperio, Ludovica, Li, B., Tiedje, J. M., Oh, Y., Christiansen, Jesper Riis, Kepfer Rojas, Sebastian, Westergaard-Nielsen, Andreas, Brandt, Kristian Koefoed, Holm, Peter Engelund, Wang, P., Ambus, Per Lennart & Elberling, Bo, 2023, In: Communications Earth & Environment. 4, 1, 10 p., 461.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Spatiotemporal heterogeneity of nitrogen transformation potentials in a freshwater estuarine system

    Lv, Jiali, Wang, S., Liu, B. & Song, X., 2023, In: Science of the Total Environment. 859, Part 2, 160335.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Swarming of P. aeruginosa: Through the lens of biophysics

    Bru, J., Kasallis, S. J., Zhuo, Q., Høyland-Kroghsbo, Nina Molin & Siryaporn, A., 2023, In: Biophysics reviews. 4, 3, 18 p., 031305.

    Research output: Contribution to journal › Review › Research › peer-review

  17. Published

    The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data

    Pakkir Shah, A. K., Walter, A., Ottosson, F., Russo, F., Navarro-Díaz, M., Boldt, J., Kalinski, J-C., Kontou, E. E., Elofson, J., Polyzois, A., González-Marín, C., Farrell, S., Aggerbeck, M. R., Pruksatrakul, T., Chan, N., Wang, Y., Pöchhacker, M., Brungs, C., Cámara, B., Caraballo-Rodríguez, A. M. & 37 others, Cumsille, A., de Oliveira, F., Dührkop, K., El Abiead, Y., Geibel, C., Graves, L. G., Hansen, M., Heuckeroth, S., Knoblauch, S., Kostenko, A., Kuijpers, M. C., Mildau, K., Papadopoulos Lambidis, S., Portal Gomes, P. W., Schramm, T., Steuer-Lodd, K., Stincone, P., Tayyab, S., Vitale, G. A., Wagner, B. C., Xing, S., Yazzie, M. T., Zuffa, S., de Kruijff, M., Beemelmanns, C., Link, H., Mayer, C., van der Hooft, J. J., Damiani, T., Pluskal, T., Dorrestein, P. C., Stanstrup, Jan, Schmid, R., Wang, M., Aron, A. T., Ernst, M. & Petras, D., 2023, ChemRxiv, 83 p.

    Research output: Working paper › Preprint › Research

  18. Published

    The Role of Cyclic Lipopeptides in Bacterial-Plant Interactions

    Guan, Ying, 2023, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 205 p.

    Research output: Book/Report › Ph.D. thesis › Research

  19. Published

    The great divide: rhamnolipids mediate separation between P. aeruginosa and S. aureus

    Bru, J., Kasallis, S. J., Chang, R., Zhuo, Q., Nguyen, J., Pham, P., Warren, E., Whiteson, K., Høyland-Kroghsbo, Nina Molin, Limoli, D. H. & Siryaporn, A., 2023, In: Frontiers in Cellular and Infection Microbiology. 13, 16 p., 1245874.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses

    Zhai, Xichuan, Castro-Mejía, J. L., Gobbi, Alex, Aslampaloglou, A., Kot, Witold, Nielsen, Dennis Sandris & Deng, Ling, 2023, In: Microbiome. 11, 12 p., 193.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Three novel Erwinia billingiae phages isolated from organic waste represent three new genera

    Alanin, K. W. S., Olsen, Nikoline S., Djurhuus, Amaru Miranda, Carstens, Alexander Byth, Nielsen, Tue Kjærgaard, Wagner, N., Lametsch, Rene, Bak, Frederik, Hennessy, Rosanna Catherine, Nicolaisen, Mette Haubjerg, Kot, Witold & Hansen, Lars Hestbjerg, 2023, In: Archives of Virology. 168, 7 p., 71.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Understanding the mechanisms underlying biological control of Fusarium diseases in cereals

    Petrucci, A., Khairullina, A., Sarrocco, S., Jensen, Dan Funck, Jensen, Birgit, Jørgensen, Hans Jørgen Lyngs & Collinge, David B., 2023, In: European Journal of Plant Pathology. 167, p. 453-476

    Research output: Contribution to journal › Review › Research › peer-review

  23. Published

    Used Nasogastric Feeding Tubes from Neonates Contain Infant-Specific Bacterial Profiles

    Meinich Juhl, S., Angeliki Krogfelt, K., Kot, Witold, Nielsen, Dennis Sandris & Krych, Lukasz, 2023, In: Microorganisms. 11, 6, 11 p., 1365.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria

    Dougherty, Peter Erdmann, Nielsen, Tue Kjærgaard, Riber, Leise, Lading, H. H., Forero Junco, Laura Milena, Kot, Witold, Raaijmakers, J. M. & Hansen, Lars Hestbjerg, 2023, In: ISME Journal. 17, 12, p. 2415-2425

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    “Impacts of treated wastewater on soil properties with special reference to the soil microbiome and resistome in irrigated Tunisian agricultural soils”.

    Chamekh, Anissa, 2023, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 159 p.

    Research output: Book/Report › Ph.D. thesis › Research

  26. 2022
  27. Published

    2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem

    Qian, P., Gardiner, A. T., Šímová, I., Naydenova, K., Croll, T. I., Jackson, P. J., Nupur, Kloz, M., Čubáková, P., Kuzma, M., Zeng, Y., Castro-Hartmann, P., van Knippenberg, B., Goldie, K. N., Kaftan, D., Hrouzek, P., Hájek, J., Agirre, J., Siebert, C. A., Bína, D. & 7 others, Sader, K., Stahlberg, H., Sobotka, R., Russo, C. J., Polívka, T., Hunter, C. N. & Koblížek, M., 2022, In: Science Advances. 8, 7, 12 p., eabk3139.

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs

    Gobbi, Alex, Acedo, A., Imam, N., Santini, R. G., Ortiz-Alvarez, R., Ellegaard-Jensen, L., Belda, I. & Hansen, Lars Hestbjerg, 2022, In: Communications Biology . 5, 9 p., 241.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics

    Li, H. Z., Yang, K., Liao, H., Lassen, Simon Bo, Su, J. Q., Zhang, X., Cui, L. & Zhu, Y. G., 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 40, 10 p., e2201473119.

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    Antibiotic resistance genes are differentially mobilized according to resistance mechanism

    Nielsen, Tue Kjærgaard, Browne, Patrick Denis & Hansen, Lars Hestbjerg, 2022, In: GigaScience. 11, 17 p., giac072.

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    Assessment of heavy metals from pangasius and tilapia aquaculture in Bangladesh and human consumption risk

    Ahsan, M. E., Islam, S. R., Razzak, M. A., Ali, M. L. & Haque, M. M., 2022, In: Aquaculture International. 30, 3, p. 1407-1434 28 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    Back to our roots: exploring the role of root morphology as a mediator of beneficial plant–microbe interactions

    Herms, Courtney Horn, Hennessy, Rosanna Catherine, Bak, Frederik, Dresbøll, Dorte Bodin & Nicolaisen, Mette Haubjerg, 2022, In: Environmental Microbiology. 24, 8, p. 3264-3272

    Research output: Contribution to journal › Review › Research › peer-review

  33. Published

    Bacterial composition associated with different traditions of salted and dried fish across countries

    Bahrndorff, S., Menanteau-Ledouble, S., Stidsborg, S., Jørgensen, Niels O. G., Hoque, M. S. & Nielsen, J. L., 2022, In: Food Bioscience. 50, 7 p., 101991.

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Bacteriophages Roam the Wheat Phyllosphere

    Forero Junco, Laura Milena, Alanin, K. W. S., Djurhuus, Amaru Miranda, Kot, Witold, Gobbi, Alex & Hansen, Lars Hestbjerg, 2022, In: Viruses. 14, 2, 13 p., 244.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Biological control of plant diseases – what has been achieved and what is the direction?

    Collinge, David B., Jensen, Dan Funck, Rabiey, M., Sarrocco, S., Shaw, M. W. & Shaw, R., 2022, In: Plant Pathology. 71, 5, p. 1024-1047

    Research output: Contribution to journal › Review › Research › peer-review

  36. Published

    Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil

    Gómez-Muñoz, B., Efthymiou, A., Dubey, M., Sølve, Jonathan, Nicolaisen, Mette Haubjerg, Jensen, Dan Funck, Nybroe, O. & Larsen, J., 2022, In: Fungal Biology. 126, 5, p. 356-365 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Characterization of five marine family 29 glycoside hydrolases reveals an α-l-fucosidase targeting specifically Fuc(α1,4)GlcNAc

    Schultz-Johansen, M., Stougaard, P., Svensson, B. & Teze, D., 2022, In: Glycobiology. 32, 6, p. 529-539

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. Published

    Combining reverse osmosis and microbial degradation for remediation of drinking water contaminated with recalcitrant pesticide residue

    Schostag, M. D., Gobbi, Alex, Fini, M. N., Ellegaard-Jensen, L., Aamand, J., Hansen, Lars Hestbjerg, Muff, J. & Albers, C. N., 2022, In: Water Research. 216, 12 p., 118352.

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. Published

    Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes

    Bista, P. K., Pillai, D., Roy, C., Scaria, J. & Narayanan, S. K., 2022, In: Microbiology Spectrum. 10, 6, 18 p., e00297-22.

    Research output: Contribution to journal › Journal article › Research › peer-review

  40. Published

    Complete Genome Sequence and Benzophenone-3 Mineralisation Potential of Rhodococcus sp. USK10, A Bacterium Isolated from Riverbank Sediment

    Martin, J. D., Krüger, U. S., Zervas, A., Schostag, M., Nielsen, Tue Kjærgaard, Aamand, J., Hansen, Lars Hestbjerg & Ellegaard-Jensen, L., 2022, In: Applied Microbiology. 2, p. 104-112 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. Published

    Computational Tools for the Analysis of Uncultivated Phage Genomes

    Andrade-Martínez, J. S., Camelo Valera, L. C., Chica Cárdenas, L. A., Forero Junco, Laura Milena, López-Leal, G., Moreno-Gallego, J. L., Rangel Piñeros, Guillermo Andres & Reyes, A., 2022, In: Microbiology and Molecular Biology Reviews. 86, 2, e0000421.

    Research output: Contribution to journal › Review › Research › peer-review

  42. Published

    Critical Assessment of Metagenome Interpretation: the second round of challenges

    Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P. T. L. C., Cristian, A., Dabrowski, P. W. & 83 others, Darling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, Lars Hestbjerg, Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, Jakob Nybo, Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, Simon, Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H. J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, Søren Johannes, Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C., 2022, In: Nature Methods. 19, 4, p. 429-440

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Deep-rooted perennial crops differ in capacity to stabilize C inputs in deep soil layers

    Peixoto, L., Olesen, J. E., Elsgaard, L., Lønne Enggrob, K., C. Banfield, C., Dippold, M. A., Nicolaisen, Mette Haubjerg, Bak, Frederik, Zang, H., Dresbøll, Dorte Bodin, Thorup-Kristensen, Kristian & Rasmussen, J., 2022, In: Scientific Reports. 12, 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. Published

    Deep-rooted plant species recruit distinct bacterial communities in subsoil than in topsoil

    Bak, Frederik, Lyhne-Kjærbye, A., Tardif, S., Dresbøll, Dorte Bodin, Nybroe, O. & Nicolaisen, Mette Haubjerg, 2022, In: Phytobiomes Journal. 6, 3, p. 236-246 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Diversity and Structure of Bacterial Communities in Different Rhizocompartments (Rhizoplane, Rhizosphere, and Bulk) at Flag Leaf Emergence in Four Winter Wheat Varieties

    Zervas, A., Ellegaard-Jensen, L., Hennessy, Rosanna Catherine, Bak, Frederik, Guan, Ying, Herms, Courtney Horn, Molina Zamudio, Kitzia Yashvelt, Thybo Ganzhorn, D., Müller-Stöver, Dorette Sophie, Ahmad, J., Grunden, A., Jacobsen, C. S. & Nicolaisen, Mette Haubjerg, 2022, In: Microbiology resource announcements. 11, 5, 3 p., e0022222.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. Published

    Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs

    Hui, Y., Vestergaard, G., Deng, Ling, Kot, Witold, Thymann, Thomas, Brunse, Anders & Nielsen, Dennis Sandris, 2022, In: npj Biofilms and Microbiomes. 8, 1, 12 p., 48.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Published

    Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination

    Kihl, Pernille, Krych, Lukasz, Deng, Ling, Hansen, Lars Hestbjerg, Buschard, K., Skov, Søren, Nielsen, Dennis Sandris & Hansen, Axel Kornerup, 2022, In: Plos One. 17, 4, 21 p., e0266719.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Published

    Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses

    Jammer, A., Akhtar, S. S., Amby, Daniel Buchvaldt, Pandey, Chandana, Mekureyaw, M. F., Bak, Frederik, Roth, P. M. & Roitsch, Thomas Georg, 2022, In: Journal of Experimental Botany. 73, 15, p. 5170-5198

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Published

    Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data

    Mas-Sandoval, A., Pope, N. S., Nielsen, Knud Nor, Altinkaya, Isin, Fumagalli, M. & Korneliussen, Thorfinn Sand, 2022, In: GigaScience. 11, 9 p., giac032.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Fate of Saxitoxins in Lake Water: Preliminary Testing of Degradation by Microbes and Sunlight

    Jørgensen, Niels O. G., Podduturi, Raju, Michelsen, C. F., Jepsen, T. & Moraes, M. D. A. B., 2022, In: Water. 14, 21, 18 p., 3556.

    Research output: Contribution to journal › Journal article › Research › peer-review

  51. Published

    Fecal filtrate transplantation protects against necrotizing enterocolitis

    Brunse, Anders, Deng, Ling, Pan, X., Hui, Y., Castro Mejia, J. L., Kot, Witold, Nguyen, Duc Ninh, Secher, Jan Bojsen-Møller, Nielsen, Dennis Sandris & Thymann, Thomas, 2022, In: The ISME Journal. 16, p. 686–694

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    From Alpha Diversity to Zzz: Interactions among sleep, the brain, and gut microbiota in the first year of life

    Schoch, S. F., Castro-Mejía, J. L., Krych, Lukasz, Leng, B., Kot, Witold, Kohler, M., Huber, R., Rogler, G., Biedermann, L., Walser, J. C., Nielsen, Dennis Sandris & Kurth, S., 2022, In: Progress in Neurobiology. 209, 11 p., 102208.

    Research output: Contribution to journal › Journal article › Research › peer-review

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