Microbial Ecology and Biotechnology

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  1. 2024
  2. 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

  3. 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

  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. E-pub ahead of print

    A data-driven genome annotation approach for cassava

    Chenna, Swetha, Ivanov, M., Nielsen, Tue Kjærgaard, Chalenko, Karina, Olsen, Evy, Jørgensen, Kirsten, Sandelin, Albin Gustav & Marquardt, Sebastian, 2024, (E-pub ahead of print) In: Plant Journal.

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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. Published

    Randomised, Placebo-Controlled Investigation of the Impact of Probiotic Consumption on Gut Microbiota Diversity and the Faecal Metabolome in Seniors

    van Zanten, G. C., Madsen, Anne Lundager, Yde, C. C., Krych, Lukasz, Yeung, N., Saarinen, M. T., Kot, Witold, Jensen, H. M., Rasmussen, Morten Arendt, Ouwehand, A. C. & Nielsen, Dennis Sandris, 2024, In: Microorganisms. 12, 4, 18 p., 796.

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

  15. 2023
  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  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

    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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

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