Microbial Ecology and Biotechnology

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  1. 2024
  2. Published

    A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea

    Latz, Meike, Andersson, A., Brugel, S., Hedblom, M., Jurdzinski, K. T., Karlson, B., Lindh, M., Lycken, J., Torstensson, A. & Andersson, A. F., 2024, In: Scientific Data. 11, 9 p., 18.

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

  3. Published

    Challenges and opportunities for increasing the use of low-risk plant protection products in sustainable production. A review

    Lankinen, Å., Witzell, J., Aleklett, K., Furenhed, S., Green, K. K., Latz, Meike, Liljeroth, E., Larsson, R., Löfkvist, K., Meijer, J., Menkis, A., Ninkovic, V., Olson, Å. & Grenville-Briggs, L., 2024, In: Agronomy for Sustainable Development. 44, 22 p., 21.

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

  4. Published

    Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment

    Bünemann, E. K., Reimer, M., Smolders, E., Smith, S. R., Bigalke, M., Palmqvist, A., Brandt, Kristian Koefoed, Möller, K., Harder, R., Hermann, L., Speiser, B., Oudshoorn, F., Løes, A. K. & Magid, Jakob, 2024, In: Science of the Total Environment. 912, 18 p., 168901.

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

  5. Published

    Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology?

    Zhou, L., Höfte, M. & Hennessy, Rosanna Catherine, 2024, In: Frontiers in Bioengineering and Biotechnology. 12, 28 p., 1363183.

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

  6. E-pub ahead of print

    Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

    Aizpurua Arrieta, Ostaizka, Dunn, Rob, Hansen, Lars Hestbjerg, Gilbert, M Thomas P & Alberdi, Antton, 2024, (E-pub ahead of print) In: Critical Reviews in Biotechnology.

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

  7. Published

    Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

    Yu, Z., He, Wanli, Klincke, F., Madsen, Jonas Stenløkke, Kot, Witold, Hansen, Lars Hestbjerg, Quintela-Baluja, M., Balboa, S., Dechesne, A., Smets, B., Nesme, Joseph & Sørensen, Søren Johannes, 2024, In: Environment International. 183, 12 p., 108351.

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

  8. Published

    Multifaceted photoreceptor compositions in dual phototrophic systems – A genomic analysis

    Ihalainen, J. A., Dogan, B., Kurttila, M., Zeng, Y., van Elsas, J. D. & Nissinen, R., 2024, In: Journal of Molecular Biology. 436, 5, 13 p., 168412.

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

  9. Published

    Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China

    Yi, Xingyun, Brandt, Kristian Koefoed, Xue, S., Peng, J., Wang, Y., Li, M., Deng, Y. & Duan, G., 2024, In: Environmental Microbiome. 19, 12 p., 13.

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

  10. Published

    The coffee leaf rust pandemic: An ever-present danger to coffee production

    Koutouleas, Tina, Collinge, David B. & Boa, E., 2024, In: Plant Pathology. 73, 3, p. 522-534

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

  11. Published

    The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

    Xie, Zhuqing, He, W., Gobbi, Alex, Bertram, H. C. & Nielsen, Dennis Sandris, 2024, In: BMC Microbiology. 24, 13 p., 83.

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

  12. Published

    Wine Yeast as Potential Biological Control Agent Against Downy Mildew of Grapevine (Plasmopara viticola)

    Behrendt, R. A., Toldam-Andersen, Torben, Arneborg, Nils, Collinge, David B. & Jensen, Birgit, 2024, Proceedings of the 21st International Conference on Organic Fruit- Growing. p. 51-57 7 p.

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

  13. 2023
  14. Published

    Universiteterne har brug for en reformpause

    Kropp, K., Vallgårda, Karen Asta Arnfred, Hougaard Laustsen-Kiel, A., Albrechtsen, Nicolai Jacob Wewer, Sylow, Lykke, Damgaard, R. B., Kristensen, Line Burholt, Hansen, N. C., Uusimäki, E., Jønsson, A. B., Høyland-Kroghsbo, Nina Molin, Eriksen, J. J., Rasmussen, Laura Vang, Andersen, P. E., Jensen, Louise Kruse, Lomborg, Stine, Morueta-Holme, Naia, Simonsen, K. B., Zetterberg-Nielsen, S. & Autzen, A., 29 Jan 2023, In: Berlingske Tidende.

    Research output: Contribution to journal › Contribution to newspaper - Comment/debate › Communication

  15. Published

    Pseudomonas nunensis sp. nov. isolated from a suppressive potato field in Greenland

    Ntana, F., Hennessy, Rosanna Catherine, Zervas, A. & Stougaard, P., 2023, In: International Journal of Systematic and Evolutionary Microbiology. 73, 2, 8 p., 005700.

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

  16. Published

    A novel Queuovirinae lineage of Pseudomonas aeruginosa phages encode dPreQ0 DNA modifications with a single GA motif that provide restriction and CRISPR Cas9 protection in vitro

    Olsen, Nikoline S., Nielsen, Tue Kjærgaard, Cui, L., Dedon, P., Neve, H., Hansen, Lars Hestbjerg & Kot, Witold, 2023, In: Nucleic Acids Research. 51, 16, 14 p.

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

  17. Published

    Activity of root-knot nematodes associated with composition of a nematode-attached microbiome and the surrounding soil microbiota

    Topalovic, Olivera, Bak, Frederik, Santos, S., Sikder, M. M., Sapkota, R., Ekelund, Flemming, Nicolaisen, Mette Haubjerg & Vestergård, M., 2023, In: FEMS Microbiology Ecology. 99, 9, 11 p., fiad091.

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

  18. Published

    Airborne methicillin-resistant Staphylococcus aureus, other bacteria, fungi, endotoxin, and dust in a pigeon exhibition

    Madsen, A. M., Zhang, F., Zeng, Y. & Frederiksen, M. W., 2023, In: Environmental Research. 216, 7 p., 114642.

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

  19. Published

    Alternative plant protection strategies for tomorrow's coffee

    Koutouleas, Tina, Collinge, David B. & Ræbild, Anders, 2023, In: Plant Pathology. 72, 3, p. 409-429

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

  20. Published

    An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette

    Mikkelsen, K., Bowring, Janine Zara, Ng, Y. K., Svanberg Frisinger, Frida, Maglegaard, J. K., Li, Q., Sieber, R. N., Petersen, A., Andersen, P. S., Rostøl, J. T., Høyland-Kroghsbo, Nina Molin & Ingmer, Hanne, 2023, In: Microbiology Spectrum. 11, 4, e01277-23.

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

  21. Published

    Bacterial dual phototrophy was demystified

    Zeng, Y., 2023, In: Trends in Microbiology. 31, 4, p. 326-328 3 p.

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

  22. Published

    Bacteriophages Targeting both Pathogenic and Commensal Plant-Associated Bacteria

    Djurhuus, Amaru Miranda, 2023, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 132 p.

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

  23. Published

    Biochar assisted soil quality recovery in chromated copper arsenate contaminated soil

    Tang, Yinqi, 2023, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 268 p.

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

  24. Published

    Biocontrol effect of Clonostachys rosea on Fusarium graminearum infection and mycotoxin detoxification in oat (Avena sativa)

    Khairullina, A., Micic, Nikola, Jørgensen, Hans Jørgen Lyngs, Bjarnholt, Nanna, Bülow, L., Collinge, David B. & Jensen, Birgit, 2023, In: Plants. 12, 3, 16 p., 500.

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

  25. Published

    Biological control of Zymoseptoria tritici in wheat

    Jørgensen, Hans Jørgen Lyngs, Jensen, Birgit, Latz, Meike, Jørgensen, L., Heick, T. M. & Collinge, David B., 2023. 1 p.

    Research output: Contribution to conference › Poster › Research

  26. Published

    CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice

    Rasmussen, Torben Sølbeck, Koefoed, A. K., Deng, Ling, Muhammed, Musemma Kedir, Rousseau, G. M., Kot, Witold, Sprotte, S., Neve, H., Franz, C. M. A. P., Hansen, Axel Kornerup, Vogensen, Finn Kvist, Moineau, S. & Nielsen, Dennis Sandris, 2023, In: ISME Journal. 17, p. 432–442

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

  27. Published

    Cessation of grazing causes biodiversity loss and homogenization of soil food webs

    Schrama, M., Quist, C. W., Arjen De Groot, G., Cieraad, E., Ashworth, D., Laros, I., Hansen, Lars Hestbjerg, Leff, J., Fierer, N. & Bardgett, R. D., 2023, In: Proceedings of the Royal Society B: Biological Sciences. 290, 2011, 12 p., 20231345.

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

  28. Published

    Characterization and finding the origin of off-flavor compounds in Nile tilapia cultured in net cages in hydroelectric reservoirs, São Paulo State, Brazil

    Podduturi, Raju, da Silva David, G., da Silva, R. J., Hyldig, G., Jørgensen, Niels O. G. & Petersen, Mikael Agerlin, 2023, In: Food Research International. 173, 15 p., 113375.

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

  29. Published

    Collaborations Between Microbes and those who Love Them

    Høyland-Kroghsbo, Nina Molin, 2023, In: Israel Journal of Chemistry. 63, 3 p., e202200082.

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

  30. Published

    Complete Genome Sequence of Sphingopyxis sp. Strain PET50, a Potential Polyethylene Terephthalate (PET)-Degrading Bacterium Isolated from Compost

    Lago-Maciel, A., Nielsen, Tue Kjærgaard, Jensen, K., Nicolaisen, Mette Haubjerg & Hennessy, Rosanna Catherine, 2023, In: Microbiology Resource Announcements. 12, 1, 2 p., e0097022.

    Research output: Contribution to journal › Journal article › Research

  31. Published

    Complete Genome Sequences of Three Lactiplantibacillus plantarum Strains Isolated from Traditional Iranian Raw Milk Motal Cheese

    Fatemizadeh, S. S., Krych, Lukasz, Castro-Mejía, J. L., Stefanova, Denitsa Vladimirova, Kot, Witold, Najafi, M. B. H. & Nielsen, Dennis Sandris, 2023, In: Microbiology Resource Announcements. 12, 1, 3 p., e0047922.

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

  32. Published

    Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software

    Nielsen, Tue Kjærgaard, Forero Junco, Laura Milena, Kot, Witold, Moineau, S., Hansen, Lars Hestbjerg & Riber, Leise, 2023, In: Molecular Ecology. 32, 6, p. 1236-1247 12 p.

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

  33. Published

    Development of a high-throughput chip technology to monitor water quality, off-flavour and diseases in recirculated aquaculture systems (RAS)

    Li, H., Larsen, H., Heegaard, P., Jørgensen, Niels O. G. & Jørgensen, Louise von Gersdorff, 2023, p. 40. 1 p.

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

  34. Published

    Dietary non-starch polysaccharides impair immunity to enteric nematode infection

    Valente, Angela Hørdum, Jensen, K. M. R., Myhill, Laura Jessica, Zhu, L., Mentzel, Caroline M. Junker, Krych, Lukasz, Simonsen, H. T., Castro-Mejía, J. L., Gobbi, Alex, Bach Knudsen, K. E., Nielsen, Dennis Sandris, Thamsborg, Stig Milan & Williams, Andrew Richard, 2023, In: BMC Biology. 21, 16 p., 138.

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

  35. Published

    Differential impacts of sewage sludge and biochar on phosphorus-related processes: An imaging study of the rhizosphere

    Bornø, Marie Louise, Zervas, A., Bak, Frederik, Merl, T., Koren, K., Nicolaisen, Mette Haubjerg, Jensen, Lars Stoumann & Müller-Stöver, Dorette Sophie, 2023, In: Science of the Total Environment. 905, 13 p., 166888.

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

  36. Published

    Draft Genome Sequences of Phytase Active Endophytic and Epiphytic Erwinia gerundensis Isolated from Wheat (Triticum aestivum) Seeds

    Sølve, Jonathan, Nielsen, Tue Kjærgaard, Nicolaisen, Mette Haubjerg & Bak, Frederik, 2023, In: Microbiology Resource Announcements. 12, 1, 3 p., e0107322.

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

  37. 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

  38. 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

  39. 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

  40. Published

    Four novel Curtobacterium phages isolated from environmental samples

    Alanin, K. W. S., Olsen, Nikoline S., Djurhuus, Amaru Miranda, Carstens, Alexander Byth, Nielsen, Tue Kjærgaard, Rothgardt, M. M., Russel, A. M., Wagner, N., Lametsch, Rene, Bak, Frederik, Hennessy, Rosanna Catherine, Nicolaisen, Mette Haubjerg, Hansen, Lars Hestbjerg & Kot, Witold, 2023, In: Archives of Virology. 168, 3

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

  41. Published

    From BCA discovery in cereals to biological control of Fusarium head blight

    Collinge, David B., Khairoullina, A., Jørgensen, Hans Jørgen Lyngs & Jensen, Birgit, 2023, p. 58-59. 1 p.

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

  42. Published

    Genetic rearrangements in Pseudomonas amygdali pathovar aesculi shape coronatine plasmids

    Nielsen, Tue Kjærgaard, Winther-Have, Caroline Sophie W, Thomsen, Iben Margrete, Jackson, R. W., Rabiey, M., Hennessy, Rosanna Catherine, Bak, Frederik, Kot, Witold, Nicolaisen, Mette Haubjerg, Carstens, Alexander Byth & Hansen, Lars Hestbjerg, 2023, In: Infection, Genetics and Evolution. 113, 10 p., 105486.

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

  43. Published

    Global biogeographic distribution of Bathyarchaeota in paddy soils

    Xue, S. D., Yi, Xingyun, Cui, H. L., Li, M., Peng, J. J., Zhu, Y. G. & Duan, G. L., 2023, In: mSystems. 8, 3, 15 p., e0014323.

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

  44. Published

    Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes

    Fu, Y., Dou, Q., Smalla, K., Wang, Y., Johnson, T. A., Brandt, K. K., Mei, Z., Liao, M., Hashsham, S. A., Schäffer, A., Smidt, H., Zhang, T., Li, H., Stedtfeld, R., Sheng, H., Chai, B., Virta, M., Jiang, X., Wang, F., Zhu, Y. G. & 1 others, Tiedje, J. M., 2023, In: mLife. 2, 4, p. 350-364 15 p.

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

  45. Published

    Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil

    Tang, Yinqi, Wang, Chen, Holm, Peter Engelund, Hansen, Hans Chr. Bruun & Brandt, Kristian Koefoed, 2023, In: Journal of Hazardous Materials. 459, 14 p., 132067.

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

  46. Published

    Impacts of dietary copper on the swine gut microbiome and antibiotic resistome

    Brinck, J. E., Lassen, Simon Bo, Forouzandeh, A., Pan, T., Wang, Y. Z., Monteiro, A., Blavi, L., Solà-Oriol, D., Stein, H. H., Su, J. Q. & Brandt, Kristian Koefoed, 2023, In: Science of the Total Environment. 857, 11 p., 159609.

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

  47. Published

    Insights into abundance, adaptation and activity of prokaryotes in arctic and Antarctic environments

    Holmberg, S. M. & Jørgensen, Niels O. G., 2023, In: Polar Biology. 46, p. 381-396

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

  48. Published

    Insights on strain 115 plant growth-promoting bacteria traits and its contribution in lead stress alleviation in pea (Pisum sativum L.) plants

    Chamekh, Anissa, Kharbech, O., Fersi, C., Driss Limam, R., Brandt, Kristian Koefoed, Djebali, W. & Chouari, R., 2023, In: Archives of Microbiology. 205, 12 p., 1.

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

  49. Published

    Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition

    Hansen, Søren Blikdal, Bozzi, D., Mak, Sarah Siu Tze, Clausen, C. G., Nielsen, Tue Kjærgaard, Kodama, M., Hansen, Lars Hestbjerg, Gilbert, M Thomas P & Limborg, Morten Tønsberg, 2023, In: Genomics. 115, 3, 9 p., 110629.

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

  50. Published

    Isothiazolinone inhibition of soil microbial activity persists despite biocide dissipation

    Fernández-Calviño, D., Rousk, J., Bååth, E., Bollmann, U. E., Bester, K. & Brandt, Kristian Koefoed, 2023, In: Soil Biology and Biochemistry. 178, 9 p., 108957.

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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. 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

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 2022
  76. 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

  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 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

  85. 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

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. Published

    Fungal Endophytes Isolated from Elymus repens, a Wild Relative of Barley, Have Potential for Biological Control of Fusarium culmorum and Pyrenophora teres in Barley

    Høyer, A. K., Jørgensen, Hans Jørgen Lyngs, Hodkinson, T. R. & Jensen, Birgit, 2022, In: Pathogens. 11, 14 p., 1097.

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

  103. Published

    Fungal endophytes in plants and their relationship to plant disease

    Collinge, David B., Jensen, Birgit & Jørgensen, Hans Jørgen Lyngs, 2022, In: Current Opinion in Microbiology. 69, 6 p., 102177.

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

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