Microbial Ecology and Biotechnology

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  1. 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

  2. Published

    Effect of probiotic and sand filtration treatments on water quality and growth of tilapia (Oreochromis niloticus) and pangas (Pangasianodon hypophthalmus) in earthen ponds of southern Bangladesh

    Mahmud, S., Ali, M. L., Alam, M. A., Rahman, M. M. & Jørgensen, Niels O. G., 2016, In: Journal of Applied Aquaculture. 28, 3, p. 199-212 14 p.

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

  3. Published

    Effects of Intra- and Interspecific Plant Density on Rhizosphere Bacterial Communities

    Cavalieri, Andrea, Bak, Frederik, Garcia-Lemos, A. M., Weiner, Jacob, Nicolaisen, Mette Haubjerg & Nybroe, O., 2020, In: Frontiers in Microbiology. 11, 14 p., 1045.

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

  4. Published

    Effects of Metals on Antibiotic Resistance and Conjugal Plasmid Transfer in Soil Bacterial Communities

    Song, J., 2017, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 119 p.

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

  5. Published

    Effects of biochar amendments on antibiotic resistome of the soil and collembolan gut

    Ding, J., Yin, Y., Sun, A. Q., Lassen, Simon Bo, Li, G., Zhu, D. & Ke, X., 5 Sep 2019, In: Journal of Hazardous Materials. 377, p. 186-194

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

  6. Published

    Effects of reduced organic matter loading through membrane filtration on the microbial community dynamics in recirculating aquaculture systems (RAS) with Atlantic salmon parr (Salmo salar)

    Fossmark, R. O., Vadstein, O., Rosten, T. W., Bakke, I., Koseto, D., Bugten, A. V., Helberg, G. A., Nesje, J., Jørgensen, Niels O. G., Raspati, G., Azrague, K., Østerhus, S. W. & Attramadal, K. J. K., 2020, In: Aquaculture. 524, 12 p., 735268.

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

  7. Published

    Effects of sulfadiazine on soil bacterial communities

    Hangler, M., 2013, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 127 p.

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

  8. Published

    Effects of two different high-fidelity DNA polymerases on genetic analysis of the cyanobacterial community structure in a subtropical deep freshwater reservoir

    Zhen, Z., Liu, J., Rensing, C. G. T., Yan, C. & Zhang, Y., 2017, In: Archives of Microbiology. 199, 1, p. 125-134 10 p.

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

  9. Published

    Emergence and Co-selection of Antibiotic Resistance in the Environment

    Lassen, Simon Bo, 2021, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 243 p.

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

  10. Published

    Emerging Methods for Biological Control of Barley Diseases Including the Role of Endophytes

    Høyer, A. K., Jørgensen, Hans Jørgen Lyngs, Jensen, Birgit, Murphy, B. R. & Hodkinson, T. R., 2019, Endophytes for a Growing World. Hodkinson, T. R., Doohan, F. M., Saunders, M. J. & Murphy, B. R. (eds.). Cambridge University Press, p. 93-119 27 p.

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  11. Published

    Endophytes for biological control of Septoria tritici blotch of wheat

    Latz, Meike, Seeliger, M., Collinge, David B., Jensen, Birgit & Jørgensen, Hans Jørgen Lyngs, 2017.

    Research output: Contribution to conference › Poster › Research

  12. Published

    Endophytic colonisation of tomato plants by the biological control agent Clonostachys rosea

    Høyer, A. K., Jørgensen, Hans Jørgen Lyngs, Amby, Daniel Buchvaldt & Jensen, Birgit, 2016, Biological and integrated control of plant pathogens. International Organisation for Biological and Integrated Control (IOBC), p. 101-106 6 p. (IOBC-WPRS Bulletin, Vol. 115).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  13. Published

    Endophytic colonization of tomato plants by the biological control agent Clonostachys rosea

    Høyer, A. K., Jørgensen, Hans Jørgen Lyngs, Amby, Daniel Buchvaldt & Jensen, Birgit, 15 Jun 2014. 1 p.

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

  14. Published

    Endophytic fungi as biocontrol agents: elucidating mechanisms in disease suppression

    Latz, Meike, Jensen, Birgit, Collinge, David B. & Jørgensen, Hans Jørgen Lyngs, 2 Nov 2018, In: Plant Ecology and Diversity. 11, 5-6, p. 555-567

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

  15. Published

    Engraftment of strictly anaerobic oxygen-sensitive bacteria in irritable bowel syndrome patients following fecal microbiota transplantation does not improve symptoms

    Browne, Patrick Denis, Cold, F., Petersen, Andreas Munk, Halkjær, S. I., Christensen, A. H., Günther, S. & Hansen, Lars Hestbjerg, 2021, In: Gut Microbes. 13, 1, 16 p.

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

  16. Published

    Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae

    Olsen, Nikoline S., Nielsen, K. J., Plöger, M., Kot, Witold & Hansen, Lars Hestbjerg, 2021, In: Archives of Virology. 166, p. 593-599 7 p.

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

  17. 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

  18. Published

    Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?

    Riber, Leise & Hansen, Lars Hestbjerg, 2021, In: Trends in Microbiology. 29, 3, p. 190-194 5 p.

    Research output: Contribution to journal › Editorial › Research

  19. Published

    Epigenetic effects of short-chain fatty acids from the large intestine on host cells

    Stein, R. A. & Riber, Leise, 2023, In: microLife. 4, 16 p.

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

  20. Published

    Evaluating the microbial effects of stocking freshwater snails (Physa gyrina) in water reuse systems culturing rainbow trout (Oncorhynchus mykiss)

    Davidson, J., Plautz, C. Z., Grimm, C., Jørgensen, Niels O. G., Podduturi, Raju, Raines, C., Snader, R., Summerfelt, S. & Good, C., 2019, In: Journal of Applied Aquaculture. 31, 2, p. 97-120

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

  21. Published

    Evaluation of dimethyl sulfoxide (DMSO) as a co-solvent for toxicity testing of hydrophobic organic compounds

    Modrzyński, J. J., Christensen, Jan H. & Brandt, Kristian Koefoed, 2019, In: Ecotoxicology. 28, p. 1136-1141

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

  22. Published

    Evaluation of pH-Dependent Metal Speciation Artifacts in Whole-Cell Bioreporter Analysis

    Hansen, M. G., Marcussen, H., Holm, Peter Engelund & Brandt, Kristian Koefoed, 1 Jan 2019, In: Journal of Environmental Quality. 48, 1, p. 199-204 6 p.

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

  23. Published

    Evaluation of the leucine incorporation technique for detection of pollution-induced community tolerance to copper in a long-term agricultural field trial with urban waste fertilizers

    Lekfeldt, J. D. S., Magid, Jakob, Holm, Peter Engelund, Nybroe, O. & Brandt, Kristian Koefoed, 2014, In: Environmental Pollution. 194, p. 78-85 8 p.

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

  24. Published

    Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban soils

    Zhao, Y., Cocerva, T., Cox, S., Tardif, S., Su, J. Q., Zhu, Y. G. & Brandt, Kristian Koefoed, 15 Mar 2019, In: Science of the Total Environment. 656, p. 512-520

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

  25. Published

    Evidence that linamarin and lotaustralin, the two cyanogenic glucosides of Trifolium repens L., are synthesized by a single set of microsomal enzymes controlled by the Ac/ac locus

    Collinge, David B. & Hughes, M. A., 1 Jan 1984, In: Plant Science Letters. 34, 1-2, p. 119-125 7 p.

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

  26. Published

    Evolution of the bacterial Cu resistome as revealed by comparative genomics

    Qin, Y., 2018, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen.

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

  27. Published

    Evolutionary conserved nitric oxide synthesis proteins responding to bacterial MAMPs are located to the endoplasmic reticulum and are also involved in secondary metabolite synthesis and sterol production

    Zheng, W., Li, H., Ipcho, S., Fang, W., Hennessy, Rosanna Catherine, Hansen, B. Ø., Lu, G., Wang, Z., Newman, M. & Olsson, S., 2021, Cold Spring Harbor Laboratory, 43 p. (bioRxiv).

    Research output: Working paper › Preprint › Research

  28. Published

    Evolutionary genomic patterns of diversity and adaptability in the host-specificentomopathogenic fungus, Metarhizium acridum

    mbs625, mbs625, 2023, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 212 p.

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

  29. Published

    Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum - A Novel Lineage of Lactobacillus Phages Comprising Five New Members

    Kyrkou, I., Carstens, Alexander Byth, Ellegaard-Jensen, L., Kot, Witold, Zervas, A., Djurhuus, Amaru Miranda, Neve, H., Hansen, M. & Hansen, Lars Hestbjerg, 2019, In: Viruses. 11, 7, 20 p.

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

  30. Published

    Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

    Olsen, Nikoline S., Forero Junco, Laura Milena, Kot, Witold & Hansen, Lars Hestbjerg, 2020, In: Viruses. 12, 9, 21 p., 986.

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

  31. Published

    Exploring the endophytic fungal microbiome of tomato roots: The role of phytohormones in plant-endophyte interactions

    Manzotti, A., 2019, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen.

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

  32. Published

    Exposing Deep Roots: A Rhizobox Laboratory

    Thorup-Kristensen, Kristian, Halberg, N., Nicolaisen, Mette Haubjerg, Olesen, J. E. & Dresbøll, Dorte Bodin, 2020, In: Trends in Plant Science. 25, 4, p. 418-419

    Research output: Contribution to journal › Journal article › Research

  33. Published

    Exposure of CuO nanoparticles and their metal counterpart leads to change in the gut microbiota and resistome of collembolans

    Ding, J., Liu, J., Chang, X. B., Zhu, D. & Lassen, Simon Bo, 2020, In: Chemosphere. 258, 10 p., 127347.

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

  34. Published

    Exposure to heavy metal and antibiotic enriches antibiotic resistant genes on the tire particles in soil

    Ding, J., Zhu, D., Wang, Y., Wang, H., Liang, A., Sun, H., Chen, Q., Lassen, Simon Bo, Lv, M. & Chen, L., 2021, In: Science of the Total Environment. 792, 9 p., 148417.

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

  35. Published

    Expression of a defence-related intercellular barley peroxidase in transgenic tobacco

    Kristensen, B. K., Brandt, J., Bojsen, K., Thordal-Christensen, Hans, Kerby, K. B., Collinge, David B., Mikkelsen, J. D. & Rasmussen, S. K., 28 Feb 1997, In: Plant Science. 122, 2, p. 173-182 10 p.

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

  36. Published

    Expression profiling and functional analyses of BghPTR2, a peptide transporter from Blumeria graminis f. sp hordei

    Droce, A., Holm, K. B., Olsson, S., Frandsen, R. J. N., Sondergaard, T. E., Sørensen, J. L. & Giese, H., 2015, In: Fungal Biology. 119, 7, p. 551-559 9 p.

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

  37. Published

    Extension of Plant Phenotypes by the Foliar Microbiome

    Hawkes, C. V., Kjøller, Rasmus, Raaijmakers, J. M., Riber, Leise, Christensen, Svend, Rasmussen, Simon, Christensen, Jan H., Dahl, A. B., Westergaard, Jesper Cairo, Nielsen, Mads, Brown-Guedira, G. & Hansen, Lars Hestbjerg, 2021, In: Annual Review of Plant Biology. 72, p. 823-846 24 p.

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

  38. Published

    External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

    Kalle, E., Gulevich, A. & Rensing, C. G. T., 2013, In: Journal of Microbiological Methods. 95, 2, p. 285-294 10 p.

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

  39. Published

    Factors governing the solid phase distribution of Cr, Cu and As in contaminated soil after 40 years of ageing

    Tardif, S., Cipullo, S., Sø, H. U., Wragg, J., Holm, Peter Engelund, Coulon, F., Brandt, Kristian Koefoed & Cave, M., 20 Feb 2019, In: Science of the Total Environment. 652, p. 744-754

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

  40. Published

    Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model

    Rasmussen, Torben Sølbeck, Mentzel, Caroline M. Junker, Kot, Witold, Castro-Mejiá, J. L., Zuffa, S., Swann, J. R., Hansen, Lars Hestbjerg, Vogensen, Finn Kvist, Hansen, Axel Kornerup & Nielsen, Dennis Sandris, 2020, In: Gut. 69, 12, p. 2122-2130 9 p.

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

  41. 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

  42. Published

    Fate and activity of fungal BCAs delivered to strawberry flowers and their potential for integration with fungicides

    Jensen, Birgit, Andersen, B., Thrane, U., Jensen, Dan Funck, Nielsen, K. F. & Larsen, J., 2013, IPM in Nordic and Baltic berry crops. Nordic Association of Agricultural Scientists (NJF), p. 11-12 2 p. (NJF Seminar, Vol. 465).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research

  43. 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

  44. Published

    Fate of arsenate following arsenite oxidation in Agrobacterium tumefaciens GW4

    Wang, Q., Qin, D., Zhang, S., Wang, L., Li, J., Rensing, C. G. T., McDermott, T. R. & Wang, G., 2015, In: Environmental Microbiology. 17, 6, p. 1926-1940 15 p.

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

  45. Published

    Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review

    Cold, F., Kousgaard, S. J., Halkjaer, S. I., Petersen, Andreas Munk, Nielsen, H. L., Thorlacius-Ussing, O. & Hansen, Lars Hestbjerg, 2020, In: Microorganisms. 8, 9, 17 p., 1433.

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

  46. 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

  47. Published

    Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice

    Rasmussen, Torben Sølbeck, Mentzel, Caroline M. Junker, Danielsen, M. R., Jakobsen, Rasmus Riemer, Zachariassen, L. S. F., Castro Mejia, J. L., Brunse, Anders, Hansen, Lars Hestbjerg, Hansen, Camilla Hartmann Friis, Hansen, Axel Kornerup & Nielsen, Dennis Sandris, 2023, In: Gut Microbes. 15, 1, 21 p., 2208504.

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

  48. Published

    Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut

    Zhao, Y., Su, J., An, X., Huang, F., Rensing, C., Brandt, Kristian Koefoed & Zhu, Y., 15 Apr 2018, In: Science of the Total Environment. 621, p. 1224-1232 9 p.

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

  49. Published

    Fermentable Dietary Fiber Promotes Helminth Infection and Exacerbates Host Inflammatory Responses

    Myhill, L. J., Stolzenbach, S., Mejer, Helena, Jakobsen, S. R., Hansen, Tina Vicky Alstrup, Andersen, D., Brix, S., Hansen, Lars Hestbjerg, Krych, Lukasz, Nielsen, Dennis Sandris, Nejsum, P., Thamsborg, Stig Milan & Williams, Andrew Richard, 2020, In: The Journal of Immunology. 204, 11, p. 3042-3055 14 p.

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

  50. Published

    Fertilising effect of sewage sludge ash inoculated with the phosphate-solubilising fungus Penicillium bilaiae under semi-field conditions

    Raymond, Nelly Sophie, Jensen, Lars Stoumann, van der Bom, Frederik, Nicolaisen, Mette Haubjerg & Müller-Stöver, Dorette Sophie, 1 Jan 2019, In: Biology and Fertility of Soils. 55, 1, p. 43-51 9 p.

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

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