Microbiology

  1. 2022
  2. Published

    Trans-kingdom interactions in mixed biofilm communities

    Sadiq, F. A., Hansen, Mads Frederik, Burmølle, Mette, Heyndrickx, M., Flint, S., Lu, W., Chen, W. & Zhang, H., 2022, In: F E M S Microbiology Reviews. 46, 5, 20 p., fuac024.

    Research output: Contribution to journalReviewResearchpeer-review

  3. Published

    Unexpected diversity among small-scale sample replicates of defined plant root compartments

    Attia, S., Russel, J., Mortensen, M. S., Madsen, Jonas Stenløkke & Sørensen, Søren Johannes, 2022, In: ISME Journal. 16, 4, p. 997-1003 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Vaginal dysbiosis in pregnancy associates with risk of emergency caesarean section: a prospective cohort study

    Haahr, T., Clausen, Tine Dalsgaard, Thorsen, J., Rasmussen, Morten Arendt, Mortensen, M. S., Lehtimäki, J., Shah, S. A., Hjelmsø, M. H., Bønnelykke, Klaus, Chawes, Bo Lund Krogsgaard, Vestergaard, G., Jacobsson, B., Larsson, P., Brix, S., Sørensen, Søren Johannes, Bisgaard, H. & Stokholm, Jakob, 2022, In: Clinical Microbiology and Infection. 28, 4, p. Pages 588-595

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. 2021
  6. Published

    Extreme freeze-thaw cycles do not affect moss-associated nitrogen fixation across a temperature gradient, but affect nutrient loss from mosses

    Rousk, Kathrin, Pedersen, P., Priemé, Anders & Michelsen, Anders, Nov 2021, In: Acta Oecologica. 113, 10 p., 103796.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Deepened snow enhances gross nitrogen cycling among Pan-Arctic tundra soils during both winter and summer

    Xu, W., Priemé, Anders, Cooper, E. J., Mörsdorf, M. A., Semenchuk, P., Elberling, Bo, Grogan, P. & Ambus, Per Lennart, 1 Sep 2021, In: Soil Biology and Biochemistry. 160, 13 p., 108356.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    A community resource for paired genomic and metabolomic data mining

    Schorn, M. A., Verhoeven, S., Ridder, L., Huber, F., Acharya, D. D., Aksenov, A. A., Aleti, G., Moghaddam, J. A., Aron, A. T., Aziz, S., Bauermeister, A., Bauman, K. D., Baunach, M., Beemelmanns, C., Beman, J. M., Berlanga-Clavero, M. V., Blacutt, A. A., Bode, H. B., Boullie, A., Brejnrod, A. & 90 others, Bugni, T. S., Calteau, A., Cao, L., Carrión, V. J., Castelo-Branco, R., Chanana, S., Chase, A. B., Chevrette, M. G., Costa-Lotufo, L. V., Crawford, J. M., Currie, C. R., Cuypers, B., Dang, T., de Rond, T., Demko, A. M., Dittmann, E., Du, C., Drozd, C., Dujardin, J., Dutton, R. J., Edlund, A., Fewer, D. P., Garg, N., Gauglitz, J. M., Gentry, E. C., Gerwick, L., Glukhov, E., Gross, H., Gugger, M., Matus, D. G. G., Helfrich, E. J. N., Hempel, B., Hur, J., Iorio, M., Jensen, P. R., Kang, K. B., Kaysser, L., Kelleher, N. L., Kim, C. S., Kim, K. H., Koester, I., König, G. M., Leao, T., Lee, S. R., Lee, Y., Li, Xuan Ji, Little, J. C., Maloney, K. N., Männle, D., Martin H., C., McAvoy, A. C., Metcalf, W. W., Mohimani, H., Molina-Santiago, C., Moore, B. S., Mullowney, M. W., Muskat, M., Nothias, L., O'Neill, E. C., Parkinson, E. I., Petras, D., Piel, J., Pierce, E. C., Pires, K., Reher, R., Romero, D., Roper, M. C., Rust, M., Saad, H., Saenz, C., Sanchez, L. M., Sørensen, Søren Johannes, Sosio, M., Süssmuth, R. D., Sweeney, D., Tahlan, K., Thomson, R. J., Tobias, N. J., Trindade-Silva, A. E., van Wezel, G. P., Wang, M., Weldon, K. C., Zhang, F., Ziemert, N., Duncan, K. R., Crüsemann, M., Rogers, S., Dorrestein, P. C., Medema, M. H. & van der Hooft, J. J. J., 2021, In: Nature Chemical Biology. 17, 4, p. 363-368

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Antimicrobial Activity of Metals and Metalloids

    Li, Y. P., Fekih, I. B., Fru, E. C., Moraleda-Munoz, A., Li, Xuan Ji, Rosen, B. P., Yoshinaga, M. & Rensing, C., 2021, In: Annual Review of Microbiology. 75, 23 p., 9.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Application of wood ash leads to strong vertical gradients in soil pH changing prokaryotic community structure in forest top soil

    Bang-Andreasen, T., Peltre, M., Ellegaard-Jensen, L., Hansen, Lars Hestbjerg, Ingerslev, Morten, Rønn, Regin, Jacobsen, C. S. & Kjøller, Rasmus, 2021, In: Scientific Reports. 11, 10 p., 742.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Bacterial chromosomal mobility via lateral transduction exceeds that of classical mobile genetic elements

    Humphrey, S., Fillol-Salom, A., Quiles-Puchalt, N., Ibarra Chavez, Rodrigo, Haag, A. F., Chen, J. & Penadés, J. R., 2021, In: Nature Communications. 12, 13 p., 6509.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Biofilms can act as plasmid reserves in the absence of plasmid specific selection

    Røder, Henriette Lyng, Trivedi, Urvish, Russel, J., Kragh, K. N., Herschend, J., Thalsø-Madsen, I., Tolker-Nielsen, Tim, Bjarnsholt, Thomas, Burmølle, Mette & Madsen, Jonas Stenløkke, 2021, In: npj Biofilms and Microbiomes. 7, 6 p., 78.

    Research output: Contribution to journalLetterResearchpeer-review

  13. Published

    Broad Dissemination of Plasmids across Groundwater-Fed Rapid Sand Filter Microbiomes

    Pinilla Redondo, Rafael, Olesen, Asmus Kalckar, Russel, J., de Vries, L. E., Christensen, L. D., Musovic, S., Nesme, Joseph & Sørensen, Søren Johannes, 2021, In: mBio. 12, 6, 13 p., e0306821.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments

    Mazhar, S. H., Li, Xuan Ji, Rashid, A., Su, J., Xu, J., Brejnrod, A. D., Su, J., Wu, Y., Zhu, Y., Zhou, S. G., Feng, R. & Rensing, C., 2021, In: Science of the Total Environment. 755, Part 2, 10 p., 142702.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms

    Sadiq, F. A., Burmølle, Mette, Heyndrickx, M., Flint, S., Lu, W., Chen, W., Zhao, J. & Zhang, H., 2021, In: Critical Reviews in Microbiology. 47, 3, p. 338-358 21 p.

    Research output: Contribution to journalReviewResearchpeer-review

  16. Published

    Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

    Kang, D., Shoaie, S., Jacquiod, S., Sørensen, Søren Johannes & Ledesma-Amaro, R., 2021, In: Microorganisms. 9, 5, 15 p., 1042.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

    Singh, N. K., Lavire, C., Nesme, Joseph, Vial, L., Nesme, X., Mason, C. E., Lassalle, F. & Venkateswaran, K., 2021, In: Frontiers in Microbiology. 12, 15 p., 765943.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures

    Gupta, S., Shariff, M., Chaturvedi, G., Sharma, A., Goel, N., Yadav, M., Mortensen, M. S., Sørensen, Søren Johannes, Mukerji, M. & Chauhan, N. S., 2021, In: Scientific Reports. 11, 11 p., 3963.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Declare how you are limiting your environmental impact

    Grogan, P., Buckeridge, K. M. & Priemé, Anders, 2021, In: Nature. 596, 7870, p. 35 1 p.

    Research output: Contribution to journalLetterResearchpeer-review

  20. Published

    Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

    Babin, D., Sommermann, L., Chowdhury, S. P., Behr, J. H., Sandmann, M., Neumann, G., Nesme, Joseph, Sørensen, Søren Johannes, Schellenberg, I., Rothballer, M., Geistlinger, J., Smalla, K. & Grosch, R., 2021, In: FEMS Microbiology Ecology. 97, 4, 21 p., fiab027.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Do environmental pharmaceuticals affect the composition of bacterial communities in a freshwater stream? A case study of the Knivsta river in the south of Sweden

    Hagberg, A., Gupta, S., Rzhepishevska, O., Fick, J., Burmølle, Mette & Ramstedt, M., 2021, In: Science of the Total Environment. 763, 10 p., 142991.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments

    Hassoun-Kheir, N., Stabholz, Y., Kreft, J-U., de la Cruz, R., Dechesne, A., Smets, B. F., Romalde, J. L., Lema, A., Balboa, S., García-Riestra, C., Torres-Sangiao, E., Neuberger, A., Graham, D., Quintela-Baluja, M., Stekel, D. J., Graham, J., Pruden, A., Nesme, J., Sørensen, S. J., Hough, R. & 1 others, Paul, M., 2021, In: One Health. 13, 9 p., 100339.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Efficient Production of Pyruvate Using Metabolically Engineered Lactococcus lactis

    Suo, F., Liu, J., Chen, J., Li, Xuan Ji, Solem, C. & Jensen, P. R., 2021, In: Frontiers in Bioengineering and Biotechnology. 8, 12 p., 611701.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis

    Yang, Nan, Nesme, Joseph, Røder, Henriette Lyng, Li, Xuan Ji, Zuo, Zhangli Thomsen, Petersen, Morten, Burmølle, Mette & Sørensen, Søren Johannes, 2021, In: npj Biofilms and Microbiomes. 7, 11 p., 82.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Environmental and Pathogenic Carbapenem Resistant Bacteria Isolated from a Wastewater Treatment Plant Harbour Distinct Antibiotic Resistance Mechanisms

    Oliveira, M., Leonardo, I. C., Nunes, M., Silva, A. F. & Barreto Crespo, M. T., 2021, In: Antibiotics. 10, 9, 13 p., 1118.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage

    Li, L., Nesme, Joseph, Quintela-Baluja, M., Balboa, S., Hashsham, S., Williams, M. R., Yu, Z., Sørensen, Søren Johannes, Graham, D. W., Romalde, J. L., Dechesne, A. & Smets, B. F., 2021, In: Environmental Science & Technology. 55, 9, p. 5939-5949 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    High-throughput screening alternative to crystal violet biofilm assay combining fluorescence quantification and imaging

    Amador Hierro, Cristina Isabel, Stannius, R. O., Røder, Henriette Lyng & Burmølle, Mette, 2021, In: Journal of Microbiological Methods. 190, 5 p., 106343.

    Research output: Contribution to journalLetterResearchpeer-review

  28. Published

    Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture

    Tabacchioni, S., Passato, S., Ambrosino, P., Huang, L., Caldara, M., Cantale, C., Hett, J., Del Fiore, A., Fiore, A., Schlüter, A., Sczyrba, A., Maestri, E., Marmiroli, N., Neuhoff, D., Nesme, J., Sørensen, S. J., Aprea, G., Nobili, C., Presenti, O., Giovannetti, G. & 4 others, Giovannetti, C., Pihlanto, A., Brunori, A. & Bevivino, A., 2021, In: Microorganisms. 9, 2, 23 p., 426.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root–Microbial Interactions and Plant Health of Lettuce

    Windisch, S., Sommermann, L., Babin, D., Chowdhury, S. P., Grosch, R., Moradtalab, N., Walker, F., Höglinger, B., El-Hasan, A., Armbruster, W., Nesme, Joseph, Sørensen, Søren Johannes, Schellenberg, I., Geistlinger, J., Smalla, K., Rothballer, M., Ludewig, U. & Neumann, G., 2021, In: Frontiers in Microbiology. 11, 26 p., 597745.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Impact of Tellurite on the Metabolism of Paenibacillus pabuli AL109b With Flagellin Production Explaining High Reduction Capacity

    Farias, P., Francisco, R., Maccario, Lorrie, Herschend, J., Piedade, A. P., Sørensen, Søren Johannes & Morais, P. V., 2021, In: Frontiers in Microbiology. 12, 15 p., 718963.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Importance of microbial communities at the root-soil interface for extracellular polymeric substances and soil aggregation in semiarid grasslands

    Bettermann, A., Zethof, J. H. T., Babin, D., Cammeraat, E. L. H., Solé-Benet, A., Lázaro, R., Luna, L., Nesme, Joseph, Sørensen, Søren Johannes, Kalbitz, K., Smalla, K. & Vogel, C., 2021, In: Soil Biology & Biochemistry. 159, 14 p., 108301.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis

    Stefanic, P., Belcijan, K., Kraigher, B., Kostanjšek, R., Nesme, Joseph, Madsen, Jonas Stenløkke, Kovac, J., Sørensen, Søren Johannes, Vos, M. & Mandic-Mulec, I., 2021, In: Nature Communications. 12, 11 p., 3457.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Large-scale association analyses identify host factors influencing human gut microbiome composition

    Kurilshikov, A., Medina-Gomez, C., Bacigalupe, R., Radjabzadeh, D., Wang, J., Demirkan, A., Le Roy, C. I., Raygoza Garay, J. A., Finnicum, C. T., Liu, X., Zhernakova, D. V., Bonder, M. J., Hansen, T. H., Frost, F., Rühlemann, M. C., Turpin, W., Moon, J. Y., Kim, H. N., Lüll, K., Barkan, E. & 84 others, Shah, S. A., Fornage, M., Szopinska-Tokov, J., Wallen, Z. D., Borisevich, D., Agreus, L., Andreasson, A., Bang, C., Bedrani, L., Bell, J. T., Bisgaard, H., Boehnke, M., Boomsma, D. I., Burk, R. D., Claringbould, A., Croitoru, K., Davies, G. E., van Duijn, C. M., Duijts, L., Falony, G., Fu, J., van der Graaf, A., Hansen, Torben, Homuth, G., Hughes, D. A., Ijzerman, R. G., Jackson, M. A., Jaddoe, V. W. V., Joossens, M., Jørgensen, T., Keszthelyi, D., Knight, R., Laakso, M., Laudes, M., Launer, L. J., Lieb, W., Lusis, A. J., Masclee, A. A. M., Moll, H. A., Mujagic, Z., Qibin, Q., Rothschild, D., Shin, H., Sørensen, Søren Johannes, Steves, C. J., Thorsen, Jonathan Jan Ilve, Timpson, N. J., Tito, R. Y., Vieira-Silva, S., Völker, U., Völzke, H., Võsa, U., Wade, K. H., Walter, S., Watanabe, K., Weiss, S., Weiss, F. U., Weissbrod, O., Westra, H. J., Willemsen, G., Payami, H., Jonkers, D. M. A. E., Arias Vasquez, A., de Geus, E. J. C., Meyer, K. A., Stokholm, Jakob, Segal, E., Org, E., Wijmenga, C., Kim, H. L., Kaplan, R. C., Spector, T. D., Uitterlinden, A. G., Rivadeneira, F., Franke, A., Lerch, M. M., Franke, L., Sanna, S., D’Amato, M., Pedersen, Oluf Borbye, Paterson, A. D., Kraaij, R., Raes, J. & Zhernakova, A., 2021, In: Nature Genetics. 53, p. 156-165 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community

    Cyriaque, V., Madsen, Jonas Stenløkke, Fievez, L., Leroy, B., Hansen, Lars Hestbjerg, Bureau, F., Sørensen, Søren Johannes & Wattiez, R., 2021, In: Frontiers in Microbiology. 12, 14 p., 655903.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Metagenomic analysis of a keratin-degrading bacterial consortium provides insight into the keratinolytic mechanisms

    Kang, D., Huang, Y., Nesme, Joseph, Herschend, J., Jacquiod, S., Kot, Witold, Hansen, Lars Hestbjerg, Lange, L. & Sørensen, Søren Johannes, 2021, In: Science of the Total Environment. 761, 9 p., 143281.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas

    Fernandez-Gnecco, G., Smalla, K., Maccario, Lorrie, Sørensen, Søren Johannes, Barbieri, P., Consolo, V. F., Covacevich, F. & Babin, D., 2021, In: FEMS Microbiology Ecology. 97, 3, 14 p., fiab007.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Modeling transfer of vaginal microbiota from mother to infant in early life

    Mortensen, M. S., Rasmussen, Morten Arendt, Stokholm, Jakob, Brejnrod, A. D., Balle, C., Thorsen, J., Krogfelt, K. A., Bisgaard, H. & Sørensen, Søren Johannes, 2021, In: eLife. 10, 19 p., e57051.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Phage satellites and their emerging applications in biotechnology

    Ibarra Chavez, Rodrigo, Hansen, Mads Frederik, Pinilla Redondo, Rafael, Seed, K. D. & Trivedi, Urvish, 2021, In: FEMS Microbiology Reviews. 45, 6, 20 p., fuab031.

    Research output: Contribution to journalReviewResearchpeer-review

  39. Published

    Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems

    Cerecetto, V., Smalla, K., Nesme, Joseph, Garaycochea, S., Fresia, P., Sørensen, Søren Johannes, Babin, D. & Leoni, C., 2021, In: FEMS Microbiology Ecology. 97, 3, 14 p., fiab023.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis

    Balbín-Suárez, A., Jacquiod, S., Rohr, A. D., Liu, B., Flachowsky, H., Winkelmann, T., Beerhues, L., Nesme, Joseph, Sørensen, Søren Johannes, Vetterlein, D. & Smalla, K., 2021, In: FEMS Microbiology Ecology. 97, 4, 14 p., fiab031.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

    Meisner, A., Snoek, B. L., Nesme, Joseph, Dent, E., Jacquiod, S., Classen, A. T. & Priemé, Anders, 2021, In: The ISME Journal. 15, 4, p. 1207-1221 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Soil microorganisms decrease barley biomass uniformly across contrasting nitrogen availability

    Munkager, V., Altenburger, A., Priemé, Anders, Bang-Andreasen, T., Rønn, Regin, Vestergård, M. & Ekelund, Flemming, 2021, In: European Journal of Soil Biology. 104, 9 p., 103311.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Spatial analysis of the root system coupled to microbial community inoculation shed light on rhizosphere bacterial community assembly

    Wei, S., Jacquiod, S., Philippot, L., Blouin, M. & Sørensen, Søren Johannes, 2021, In: Biology and Fertility of Soils. 57, 7, p. 973-989 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Specialized microbiomes facilitate natural rhizosphere microbiome interactions counteracting high salinity stress in plants

    Santos, S. S., Rask, K. A., Vestergård, M., Johansen, Jesper Liengaard, Priemé, Anders, Frøslev, Tobias Guldberg, González, A. M. M., He, H. & Ekelund, Flemming, 2021, In: Environmental and Experimental Botany. 186, 12 p., 104430.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Temporal oral microbiome changes with brushing in children with cleft lip and palate

    Rodrigues, R., Chung, A. P., Mortensen, M. S., Fernandes, M. H., Monteiro, A. B., Furfuro, R., Silva, C. C., Manso, M. C., Sørensen, Søren Johannes & Morais, P. V., 2021, In: Heliyon. 7, 9 p., e06513.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    The Airway Microbiota Modulates Effect of Azithromycin Treatment for Episodes of Recurrent Asthma-like Symptoms in Preschool Children: A Randomized Clinical Trial

    Thorsen, Jonathan Jan Ilve, Stokholm, Jakob, Rasmussen, Morten Arendt, Mortensen, M. S., Brejnrod, A. D., Hjelmsø, M., Shah, S., Chawes, Bo Lund Krogsgaard, Bønnelykke, Klaus, Sørensen, Søren Johannes & Bisgaard, H., 2021, In: American Journal of Respiratory and Critical Care Medicine. 204, 2, p. 149-158

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids

    Nielsen, Tue Kjærgaard, Horemans, B., Lood, C., T’Syen, J., van Noort, V., Lavigne, R., Ellegaard-Jensen, L., Hylling, Ole, Aamand, J., Springael, D. & Hansen, Lars Hestbjerg, 2021, In: Scientific Reports. 11, 12 p., 18943.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    The effect of early probiotic exposure on the preterm infant gut microbiome development

    Hui, Y., Smith, Birgitte, Mortensen, M. S., Krych, Lukasz, Sørensen, Søren Johannes, Greisen, Gorm, Krogfelt, K. A. & Nielsen, Dennis Sandris, 2021, In: Gut Microbes. 13, 1, 15 p., 1951113.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

    Li, Xuan Ji, Stokholm, Jakob, Brejnrod, A., Vestergaard, G. A., Russel, J., Trivedi, Urvish, Thorsen, Jonathan Jan Ilve, Gupta, S., Hjelmsø, M. H., Shah, S. A., Rasmussen, Morten Arendt, Bisgaard, H. & Sørensen, Søren Johannes, 2021, In: Cell Host & Microbe. 29, 6, p. 975–987.e4 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity

    Gao, C., Cao, H., Cai, P. & Sørensen, Søren Johannes, 2021, In: ISME Journal. 15, p. 29-40 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    The treasure inside barley seeds: microbial diversity and plant beneficial bacteria

    Bziuk, N., Maccario, Lorrie, Straube, B., Wehner, G., Sørensen, Søren Johannes, Schikora, A. & Smalla, K., 2021, In: Environmental Microbiomes. 16, 21 p., 20.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Tillage shapes the soil and rhizosphere microbiome of barley - but not its susceptibility towards Blumeria graminis f. sp. hordei

    Bziuk, N., Maccario, Lorrie, Douchkov, D., Lueck, S., Babin, D., Sørensen, Søren Johannes, Schikora, A. & Smalla, K., 2021, In: FEMS Microbiology Ecology. 97, 3, 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    Urbanized microbiota in infants, immune constitution and later risk of atopic diseases

    Lehtimäki, J., Thorsen, Jonathan Jan Ilve, Rasmussen, Morten Arendt, Hjelmsø, M., Shah, S., Mortensen, M. S., Trivedi, Urvish, Vestergaard, G., Bønnelykke, Klaus, Chawes, Bo Lund Krogsgaard, Brix, S., Sørensen, Søren Johannes, Bisgaard, H. & Stokholm, Jakob, 2021, In: Journal of Allergy and Clinical Immunology. 148, 1, p. 234-243 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. 2020
  55. Published

    Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms

    Schierstaedt, J., Jechalke, S., Nesme, Joseph, Neuhaus, K., Sørensen, Søren Johannes, Grosch, R., Smalla, K. & Schikora, A., 2020, In: Environmental Microbiology. 22, 7, p. 2639-2652 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. Published

    A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

    Song, J., Klümper, U., Riber, Leise, Dechesne, A., Smets, B. F., Sørensen, Søren Johannes & Brandt, Kristian Koefoed, 2020, In: FEMS Microbiology Ecology. 96, 11, 10 p., fiaa200.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    AgNO3 sterilizes grains of barley (Hordeum vulgare) without inhibiting germination - a necessary tool for plant–microbiome research

    Munkager, V., Vestergård, M., Priemé, Anders, Altenburger, A., de Visser, E., Johansen, Jesper Liengaard & Ekelund, Flemming, 2020, In: Plants. 9, 3, 16 p., 372.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies

    Marino, N. D., Pinilla Redondo, Rafael, Csörgő, B. & Bondy-Denomy, J., 2020, In: Nature Methods. 17, 5, p. 471-479 9 p.

    Research output: Contribution to journalReviewResearchpeer-review

  59. Published

    Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm

    Vandeplassche, E., Sass, A., Ostyn, L., Burmølle, Mette, Kragh, K. N., Bjarnsholt, Thomas, Coenye, T. & Crabbé, A., 2020, In: Biofilm. 2, 9 p., 100031.

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    Azo dying of α-keratin material improves microbial keratinase screening and standardization

    Gonzalo, M., Espersen, R., Al-Soud, W. A., Cristiano Falco, F., Hägglund, Per Mårten, Sørensen, Søren Johannes, Svensson, B. & Jacquiod, S., 2020, In: Microbial Biotechnology. 13, 4, p. 984-996

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and Ralstonia solanacearum

    Elsayed, T. R., Jacquiod, S., Nour, E. H., Sørensen, Søren Johannes & Smalla, K., 2020, In: Frontiers in Microbiology. 10, 15 p., 2835.

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. Published

    Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer

    Mahendra, C., Christie, K. A., Osuna, B. A., Pinilla Redondo, Rafael, Kleinstiver, B. P. & Bondy-Denomy, J., 2020, In: Nature Microbiology. 5, 4, p. 620-629 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci

    Russel, J., Pinilla Redondo, Rafael, Mayo-Muñoz, D., Shah, S. A. & Sørensen, Søren Johannes, 2020, In: CRISPR Journal. 3, 6, p. 462-469 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus

    Zadel, U., Nesme, Joseph, Michalke, B., Vestergaard, G., Płaza, G. A., Schröder, P., Radl, V. & Schloter, M., 2020, In: Science of the Total Environment. 711, 10 p., 134433.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    Community-intrinsic properties enhance keratin degradation from bacterial consortia

    Nasipuri, P., Herschend, J., Brejnrod, A. D., Madsen, Jonas Stenløkke, Espersen, R., Svensson, B., Burmølle, Mette, Jacquiod, S. & Sørensen, Søren Johannes, 2020, In: PLoS ONE. 15, 1, 26 p., e0228108.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review

    Hassoun-Kheir, N., Stabholz, Y., Kreft, J., de la Cruz, R., Romalde, J. L., Nesme, Joseph, Sørensen, Søren Johannes, Smets, B. F., Graham, D. & Paul, M., 2020, In: Science of the Total Environment. 743, 11 p., 140804.

    Research output: Contribution to journalReviewResearchpeer-review

  67. Published

    Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities

    Ganther, M., Yim, B., Ibrahim, Z., Bienert, M. D., Lippold, E., Maccario, Lorrie, Sørensen, Søren Johannes, Bienert, G. P., Vetterlein, D., Heintz-Buschart, A., Blagodatskaya, E., Smalla, K. & Tarkka, M. T., 2020, In: Journal of Experimental Botany. 71, 18, p. 5603-5614 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  68. Published

    Composted sewage sludge influences the microbiome and persistence of human pathogens in soil

    Major, N., Schierstaedt, J., Jechalke, S., Nesme, Joseph, Ban, S. G., Černe, M., Sørensen, Søren Johannes, Ban, D. & Schikora, A., 2020, In: Microorganisms. 8, 7, 14 p., 1020.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

    Kang, D., Jacquiod, S., Herschend, J., Wei, S., Nesme, Joseph & Sørensen, Søren Johannes, 2020, In: Frontiers in Microbiology. 10, 10 p., 3010.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma

    Stokholm, Jakob, Thorsen, Jonathan Jan Ilve, Blaser, M. J., Rasmussen, Morten Arendt, Hjelmsø, M., Shah, S., Christensen, E. D., Chawes, Bo Lund Krogsgaard, Bønnelykke, Klaus, Brix, S., Mortensen, M. S., Brejnrod, A., Vestergaard, G., Trivedi, Urvish, Sørensen, Søren Johannes & Bisgaard, H., 2020, In: Science Translational Medicine. 12, 569, 14 p., eaax9929.

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements

    Pinilla Redondo, Rafael, Shehreen, S., Marino, N. D., Fagerlund, R. D., Brown, C. M., Sørensen, Søren Johannes, Fineran, P. C. & Bondy-Denomy, J., 2020, In: Nature Communications. 11, 11 p., 5652.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    Do Mixed-Species Biofilms Dominate in Chronic Infections? Need for in situ Visualization of Bacterial Organization

    Kvich, Lasse Andersson, Burmølle, Mette, Bjarnsholt, Thomas & Lichtenberg, Mads, 2020, In: Frontiers in Cellular and Infection Microbiology. 10, 12 p., 396.

    Research output: Contribution to journalReviewResearchpeer-review

  73. Published

    Ecological succession in the vaginal microbiota during pregnancy and birth

    Rasmussen, Morten Arendt, Thorsen, Jonathan Jan Ilve, Dominguez-Bello, M. G., Blaser, M. J., Mortensen, M. S., Brejnrod, A. D., Shah, S. A., Hjelmsø, M. H., Lehtimäki, J., Trivedi, Urvish, Bisgaard, H., Sørensen, Søren Johannes & Stokholm, Jakob, 2020, In: The ISME Journal. 14, 9, p. 2325-2335 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    Enrichment of endophytic Actinobacteria in roots and rhizomes of Miscanthus × giganteus plants exposed to diclofenac and sulfamethoxazole

    Sauvêtre, A., Węgrzyn, A., Yang, L., Vestergaard, G., Miksch, K., Schröder, P. & Radl, V., 2020, In: Environmental Science and Pollution Research. 27, 11, p. 11892-11904 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota

    Gupta, S., Hjelmsø, M. H., Lehtimäki, J., Li, Xuan Ji, Mortensen, M. S., Russel, J., Trivedi, Urvish, Rasmussen, Morten Arendt, Stokholm, Jakob, Bisgaard, H. & Sørensen, Søren Johannes, 2020, In: Microbiome. 8, 16 p., 115.

    Research output: Contribution to journalJournal articleResearchpeer-review

  76. Published

    Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age

    Morin, A., McKennan, C. G., Pedersen, C. T., Stokholm, Jakob, Chawes, Bo Lund Krogsgaard, Schoos, A. M., Naughton, K. A., Thorsen, Jonathan Jan Ilve, Mortensen, M. S., Vercelli, D., Trivedi, Urvish, Sørensen, Søren Johannes, Bisgaard, H., Nicolae, D. L., Bønnelykke, Klaus & Ober, C., 2020, In: Journal of Allergy and Clinical Immunology. 146, 6, p. 1358-1366

    Research output: Contribution to journalJournal articleResearchpeer-review

  77. Published

    Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design

    Balbín-Suárez, A., Lucas, M., Vetterlein, D., Sørensen, Søren Johannes, Winkelmann, T., Smalla, K. & Jacquiod, S., 2020, In: FEMS Microbiology Ecology. 96, 12, 12 p., fiaa211.

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Exposure of consumers to substandard antibiotics from selected authorised and unauthorised medicine sales outlets in Ghana

    Bekoe, S. O., Ahiabu, M. A., Orman, E., Tersbøl, Britt Pinkowski, Adosraku, R. K., Hansen, M., Frimodt-Møller, N. & Styrishave, Bjarne, 2020, In: Tropical Medicine and International Health. 25, 8, p. 962-975 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum

    Tan, D., Hansen, Mads Frederik, de Carvalho, L. N., Røder, Henriette Lyng, Burmølle, Mette, Middelboe, Mathias & Svenningsen, Sine Lo, 2020, In: The ISME Journal. 14, 7, p. 1731-1742 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  80. Published

    Horizontal Transfer of Cyclic di-GMP Associated Genes: Theoretical Underpinnings and Future Perspectives

    Madsen, Jonas Stenløkke, 2020, Microbial Cyclic Di-Nucleotide Signaling. Chou, S-H., Guiliani, N., Lee, V. T. & Römling, U. (eds.). Springer, p. 641-652 12 p.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  81. Published

    Interspecific interactions in dual-species biofilms of soil bacteria: effects of fertilization practices

    Sun, X., Cai, P., Sørensen, Søren Johannes, Mortimer, M., Gao, C., Huang, Q., Wang, Y., Lin, X., Wu, Y., Zhu, D. & Chen, R., 2020, In: Journal of Soils and Sediments. 20, 3, p. 1494-1501 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    Jagten på den gode opgave: Identifikation af kriterier og implementering af peer feedback i praksis

    Mark Jensen, L., Burmølle, Mette, Johannsen, B. F., Bruun, Jesper & Ellegaard, M., 2020, In: Dansk universitetspædagogisk tidsskrift [online]. 15, 28, p. 16-30 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    Low Turnover of Soil Bacterial rRNA at Low Temperatures

    Schostag, M. D., Albers, C. N., Jacobsen, C. S. & Priemé, Anders, 2020, In: Frontiers in Microbiology. 11, 5 p., 962.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    Metal-induced bacterial interactions promote diversity in river-sediment microbiomes

    Cyriaque, V., Géron, A., Billon, G., Nesme, Joseph, Werner, J., Gillan, D. C., Sørensen, Søren Johannes & Wattiez, R., 2020, In: F E M S Microbiology Ecology. 96, 6, 12 p., fiaa076.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Mixed-species biofilms in the food industry: current knowledge and novel control strategies

    Yuan, L., Hansen, Mads Frederik, Røder, Henriette Lyng, Wang, N., Burmølle, Mette & He, G., 2020, In: Critical Reviews in Food Science and Nutrition. 60, 13, p. 2277-2293

    Research output: Contribution to journalReviewResearchpeer-review

  86. Published

    Patterns and Processes of the Microbiome Assembly at a Small-Scale of the Plant Root Microenvironments: Study Case on the Wheat and Faba Bean Root Systems

    Attia, S. M. H., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 132 p.

    Research output: Book/ReportPh.D. thesisResearch

  87. Published

    Persistence and progression of staphylococcal infection in the presence of public goods

    Trivedi, Urvish, Fell, C., Madsen, Jonas Stenløkke, Everett, J., Burmølle, Mette, Rumbaugh, K. P. & Sørensen, Søren Johannes, 2020, In: npj Biofilms and Microbiomes. 6, 5 p., 55.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

    Li, L., Dechesne, A., Madsen, Jonas Stenløkke, Nesme, Joseph, Sørensen, Søren Johannes & Smets, B. F., 2020, In: I S M E Journal. 14, 5, p. 1170-1181 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    Plasmids, CRISPR-Cas and Anti-CRIPSRs: Uncovering the secret lives of mobile genetic elements

    Pinilla Redondo, Rafael, 2020, Department of Biology, Faculty of Science, University of Copenhagen. 217 p.

    Research output: Book/ReportPh.D. thesisResearch

  90. Published

    Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial

    Hjelmsø, M. H., Shah, S. A., Thorsen, Jonathan Jan Ilve, Rasmussen, Morten Arendt, Vestergaard, G., Mortensen, M. S., Brejnrod, A., Brix, S., Chawes, Bo Lund Krogsgaard, Bønnelykke, Klaus, Sørensen, Søren Johannes, Stokholm, Jakob & Bisgaard, H., 2020, In: Nature Communications. 11, 10 p., 426.

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. Published

    Prokaryotic Community Composition and Extracellular Polymeric Substances Affect Soil Microaggregation in Carbonate Containing Semiarid Grasslands

    Zethof, J. H. T., Bettermann, A., Vogel, C., Babin, D., Cammeraat, E. L. H., Solé-Benet, A., Lázaro, R., Luna, L., Nesme, Joseph, Woche, S. K., Sørensen, Søren Johannes, Smalla, K. & Kalbitz, K., 2020, In: Frontiers in Environmental Science. 8, 19 p., 51.

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    Rhizosphere microbial communities associated to rose replant disease: links to plant growth and root metabolites

    Yim, B., Baumann, A., Grunewaldt-Stöcker, G., Liu, B., Beerhues, L., Zühlke, S., Sapp, M., Nesme, Joseph, Sørensen, Søren Johannes, Smalla, K. & Winkelmann, T., 2020, In: Horticulture Research. 7, 16 p., 144.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

    Rose replant disease: detailed analyses of plant reactions, root endophytes and rhizosphere microbial communities

    Baumann, A., Yim, B., Grunewaldt-Stöcker, G., Liu, B., Beerhues, L., Sapp, M., Nesme, Joseph, Sørensen, Søren Johannes, Smalla, K. & Winkelmann, T., 2020, In: Acta Horticulturae. 1283, p. 97-104 8 p.

    Research output: Contribution to journalConference articleResearchpeer-review

  94. Published

    Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments

    Cyriaque, V., Jacquiod, S. J. A., Riber, Leise, Abu Al-Soud, W., Gillan, D. C., Sørensen, Søren Johannes & Wattiez, R., 2020, In: Journal of Hazardous Materials. 382, 10 p., 121173.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds

    Zhu, C., Miller, M., Lusskin, N., Bergk Pinto, B., Maccario, Lorrie, Häggblom, M., Vogel, T., Larose, C. & Bromberg, Y., 2020, In: MicrobiologyOpen. 9, 9, e1100.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    Soil bacterial community response to long-term land use conversion in Yellow River Delta

    He, H., Miao, Y., Gan, Y., Wei, S., Tan, S., Rask, K. A., Wang, L., Dai, J., Chen, W. & Ekelund, Flemming, 2020, In: Applied Soil Ecology. 156, 14 p., 103709.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    The T-shirt microbiome is distinct between individuals and shaped by washing and fabric type

    Sterndorff, E. B., Russel, J., Jakobsen, J., Mortensen, M. S., Gori, K., Herschend, J. & Burmølle, Mette, 2020, In: Environmental Research. 185, 9 p., 109449.

    Research output: Contribution to journalJournal articleResearchpeer-review

  98. Published

    The environmental contribution to the dissemination of carbapenem and (fluoro)quinolone resistance genes by discharged and reused wastewater effluents: The role of cellular and extracellular DNA

    Oliveira, M., Nunes, M., Barreto Crespo, M. T. & Silva, A. F., 2020, In: Water Research. 182, 13 p., 116011.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    The evolution of virulence in Pseudomonas aeruginosa during chronic wound infection

    Vanderwoude, J., Fleming, D., Azimi, S., Trivedi, Urvish, Rumbaugh, K. P. & Diggle, S. P., 2020, In: Proceedings of the Royal Society B: Biological Sciences. 287, 1937, 10 p., 20202272.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    The human microbiome: one step forward

    Gupta, S., 2020, Department of Biology, Faculty of Science, University of Copenhagen. 120 p.

    Research output: Book/ReportPh.D. thesisResearch

  101. Published

    The microbiome of captive hamadryas baboons

    Li, Xuan Ji, Trivedi, Urvish, Brejnrod, A. D., Vestergaard, G. A., Mortensen, M. S., Bertelsen, Mads Frost & Sørensen, Søren Johannes, 2020, In: BMC Animal Microbiome. 2, 10 p., 25.

    Research output: Contribution to journalJournal articleResearchpeer-review

  102. Published

    Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil

    Bang-Andreasen, T., Anwar, M. Z., Lanzén, A., Kjøller, Rasmus, Rønn, Regin, Ekelund, Flemming & Jacobsen, C. S., 2020, In: FEMS Microbiology Ecology. 96, 3, 13 p., fiaa016.

    Research output: Contribution to journalJournal articleResearchpeer-review

  103. Published

    Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

    Pinilla Redondo, Rafael, Mayo-Muñoz, D., Russel, J., Garrett, Roger Antony, Randau, L., Sørensen, Søren Johannes & Shah, S. A., 2020, In: Nucleic Acids Research. 48, 4, p. 2000-2012 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

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