Microbiology

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  1. 2020
  2. Published

    Unravelling interspecies interactions across heterogeneities in complex biofilm communities

    Røder, Henriette Lyng, Olsen, N. M. C., Whiteley, M. & Burmølle, Mette, 2020, In: Environmental Microbiology. 22, 1, p. 5-16 12 p.

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

  3. Published

    Unravelling plasmidome distribution and interaction with its hosting microbiome

    Kav, A. B., Rozov, R., Bogumil, D., Sørensen, Søren Johannes, Hansen, Lars Hestbjerg, Benhar, I., Halperin, E., Shamir, R. & Mizrahi, I., 2020, In: Environmental Microbiology. 22, 1, p. 32-44

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

  4. Published

    You don’t have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts [+ correction]

    Bos, N., Guimaraes, L., Palenzuela, R., Renelies-Hamilton, J., Maccario, Lorrie, Silue, S. K., Koné, N. A. & Poulsen, Michael, 2020, In: BMC Evolutionary Biology. 20, 11 p., 163.

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

  5. 2019
  6. Published

    Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing

    Gupta, S., Mortensen, M. S., Schjørring, S., Trivedi, Urvish, Vestergaard, G., Stokholm, Jakob, Bisgaard, H., Krogfelt, K. A. & Sørensen, Søren Johannes, 2019, In: Communications Biology. 2, p. 1-7 7 p., 291.

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

  7. Published

    Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil

    Schostag, M., Priemé, Anders, Jacquiod, S., Russel, J., Ekelund, Flemming & Jacobsen, C. S., 2019, In: ISME Journal. 13, p. 1345-1359

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

  8. Published

    Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass

    Jakobsen, A. M., Bahl, M. I., Buschhardt, T., Hansen, T. B., Abu Al-Soud, W., Brejnrod, A. D., Sørensen, Søren Johannes, Nesbakken, T. & Aabo, S., 2019, In: International Journal of Food Microbiology. 295, p. 8-18 11 p.

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

  9. Published

    Big Impact of the Tiny: Bacteriophage–Bacteria Interactions in Biofilms

    Hansen, Mads Frederik, Svenningsen, Sine Lo, Røder, Henriette Lyng, Middelboe, Mathias & Burmølle, Mette, 2019, In: Trends in Microbiology. 27, 9, p. 739-752 14 p.

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

  10. Published

    Characterization of Extracellular Biosurfactants Expressed by a Pseudomonas putida Strain Isolated from the Interior of Healthy Roots from Sida hermaphrodita Grown in a Heavy Metal Contaminated Soil

    Bernat, P., Nesme, Joseph, Paraszkiewicz, K., Schloter, M. & Płaza, G., 2019, In: Current Microbiology. 76, 11, p. 1320-1329 10 p.

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

  11. Published

    Characterization of host associated microbiota under influencing factors: A case study on human gut and Brachypodium root

    Wei, S., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  12. Published

    DNA-and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

    Gülay, A., Fowler, S. J., Tatari, K., Thamdrup, B., Albrechtsen, H., Abu Al-Soud, W., Sørensen, Søren Johannes & Smets, B. F., 2019, In: mBio. 10, 6, 14 p., e01870-19.

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

  13. Published

    Deciphering links between bacterial interactions and spatial organization in multispecies biofilms

    Liu, W., Jacquiod, S., Brejnrod, A., Russel, J., Burmølle, Mette & Sørensen, Søren Johannes, 2019, In: ISME Journal. 13, 12, p. 3054-3066 13 p.

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

  14. Published

    Decomposition of an N-fixing invasive plant compared with a native species: consequences for ecosystem

    Marchante, E., Marchante, H., Freitas, H., Kjøller, Annelise Helene & Struwe, Sten, 2019, In: Applied Soil Ecology. 138, p. 19-31

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

  15. Published

    Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

    Dahl, M. B., Brejnrod, A. D., Russel, J., Sørensen, Søren Johannes & Schnittler, M., 2019, In: Microbial Ecology. 78, 3, p. 764-780

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

  16. Published

    Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce

    Paul Chowdhury, S., Babin, D., Sandmann, M., Jacquiod, S., Sommermann, L., Sørensen, Søren Johannes, Fliessbach, A., Mäder, P., Geistlinger, J., Smalla, K., Rothballer, M. & Grosch, R., 2019, In: Environmental Microbiology. 21, 7, p. 2426-2439

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

  17. Published

    Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development

    Treichel, N. S., Prevorsek, Z., Mrak, V., Kostric, M., Vestergaard, G., Foesel, B., Pfeiffer, S., Stres, B., Schöler, A. & Schloter, M., 2019, In: Microbial Ecology. 78, 2, p. 517-527

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

  18. Published

    Evaluating Efficacy of Antimicrobial and Antifouling Materials for Urinary Tract Medical Devices: Challenges and Recommendations

    Ramstedt, M., Ribeiro, I. A. C., Bujdakova, H., Mergulhão, F. J. M., Jordao, L., Thomsen, P., Alm, M., Burmølle, Mette, Vladkova, T., Can, F., Reches, M., Riool, M., Barros, A., Reis, R. L., Meaurio, E., Kikhney, J., Moter, A., Zaat, S. A. J. & Sjollema, J., 2019, In: Macromolecular Bioscience. 19, 5, 26 p., 1800384.

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

  19. Published

    Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

    Voříšková, J., Elberling, Bo & Priemé, Anders, 2019, In: Environmental Microbiomes. 14, 1, 15 p., 6.

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

  20. Published

    Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli

    Anjum, M., Madsen, Jonas Stenløkke, Nesme, Joseph, Jana, B., Wiese, M., Jasinskyte, D., Nielsen, Dennis Sandris, Sørensen, Søren Johannes, Dalsgaard, Anders, Moodley, Arshnee, Bortolaia, V. & Guardabassi, Luca, 2019, In: Antimicrobial Agents and Chemotherapy. 63, 5, 13 p., e02528-18.

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

  21. Published

    Fluidic resistance control enables high-throughput establishment of mixed-species biofilms

    Hansen, Mads Frederik, Meyer Torp, A., Madsen, Jonas Stenløkke, Røder, Henriette Lyng & Burmølle, Mette, 2019, In: BioTechniques. 66, 5, p. 235-239

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

  22. Published

    Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites

    Li, Xuan Ji, Brejnrod, A. D., Ernst, M., Rykær, M., Herschend, J., Olsen, N. M. C., Dorrestein, P. C., Rensing, C. & Sørensen, Søren Johannes, 2019, In: Environment International. 126, p. 454-467 14 p.

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

  23. Published

    High throughput sequencing applied to analyze microbial communities in different animal models with an interpretation in a human health perspectives

    Li, Xuan Ji, 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  24. Published

    Human Milk Fortification with Bovine Colostrum Is Superior to Formula-Based Fortifiers to Prevent Gut Dysfunction, Necrotizing Enterocolitis, and Systemic Infection in Preterm Pigs

    Sun, Jing, Li, Y., Pan, X., Nguyen, Duc Ninh, Brunse, Anders, Bojesen, Anders Miki, Rudloff, S., Mortensen, M. S., Burrin, D. G. & Sangild, Per Torp, 2019, In: Journal of Parenteral and Enteral Nutrition. 43, 2, p. 252-262

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

  25. Published

    Impact of long-term agricultural management practices on soil prokaryotic communities

    Babin, D., Deubel, A., Jacquiod, S. J. A., Sørensen, Søren Johannes, Geistlinger, J., Grosch, R. & Smalla, K., 2019, In: Soil Biology & Biochemistry. 129, p. 17-28

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

  26. Published

    Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems

    Romero, I. A., van Dillewijn, P., Nesme, Joseph, Sørensen, Søren Johannes & Romero, E., 2019, In: Science of the Total Environment. 691, p. 749-759 11 p.

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

  27. Published

    Infant airway microbiota and topical immune perturbations in the origins of childhood asthma

    Thorsen, Jonathan Jan Ilve, Rasmussen, Morten Arendt, Waage, J., Mortensen, M., Brejnrod, A., Bønnelykke, Klaus, Chawes, Bo Lund Krogsgaard, Brix, S., Sørensen, Søren Johannes, Stokholm, Jakob & Bisgaard, H., 2019, In: Nature Communications. 10, 8 p., 5001.

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

  28. Published

    Insights into psychrotrophic bacteria in raw milk: A review

    Yuan, L., Sadiq, F. A., Burmølle, Mette, Wang, N. & He, G., 2019, In: Journal of Food Protection. 82, 7, p. 1148-1159 12 p.

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

  29. Published

    Interactions in Biofilm Communities

    Olsen, N. M. C., 2019, Department of Biology, Faculty of Science, University of Copenhagen. 123 p.

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

  30. Published

    Interspecies interactions reduce selection for a biofilm-optimized variant in a four-species biofilm model

    Røder, Henriette Lyng, Liu, W., Sørensen, Søren Johannes, Madsen, Jonas Stenløkke & Burmølle, Mette, 2019, In: Environmental Microbiology Reports. 11, 6, p. 835-839 5 p.

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

  31. Published

    Intra- and inter-field diversity of 2,4-dichlorophenoxyacetic acid-degradative plasmids and their tfd catabolic genes in rice fields of the Mekong delta in Vietnam

    Nguyen, T. P. O., Hansen, M. A., Hansen, Lars Hestbjerg, Horemans, B., Sørensen, Søren Johannes, De Mot, R. & Springael, D., 2019, In: FEMS Microbiology Ecology. 95, 1, p. 1-11 fiy214.

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

  32. Published

    Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil

    Blau, K., Jacquiod, S., Sørensen, Søren Johannes, Su, J., Zhu, Y., Smalla, K. & Jechalke, S., 2019, In: Frontiers in Microbiology. 10, p. 1-15 725.

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

  33. Published

    Metabolism of Milk Oligosaccharides in Preterm Pigs Sensitive to Necrotizing Enterocolitis

    Rudloff, S., Kuntz, S., Rasmussen, S. O., Roggenbuck, M., Sprenger, N., Kunz, C., Sangild, Per Torp & Bering, S. B., 2019, In: Frontiers in Nutrition. 6, 11 p., 23.

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

  34. Published

    Novel Perspective on Valorization of Keratinous Materials using Microbial Consortia

    Kang, D., 2019, Department of Biology, Faculty of Science, University of Copenhagen.

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

  35. Published

    Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus

    Sáenz, J. S., Marques, T. V., Barone, R. S. C., Cyrino, J. E. P., Kublik, S., Nesme, Joseph, Schloter, M., Rath, S. & Vestergaard, G., 2019, In: Microbiome. 7, p. 1-14 24.

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

  36. Published

    Priority of Early Colonizers but No Effect on Cohabitants in a Synergistic Biofilm Community

    Olsen, N. M. C., Røder, Henriette Lyng, Russel, J., Madsen, Jonas Stenløkke, Sørensen, Søren Johannes & Burmølle, Mette, 2019, In: Frontiers in Microbiology. 10, 8 p., 1949.

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

  37. Published

    Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats

    Heins, A., Johanson, T., Han, S., Lundin, L., Carlquist, M., Gernaey, K. V., Sørensen, Søren Johannes & Lantz, A. E., 2019, In: Frontiers in Bioengineering and Biotechnology. 7, 15 p., 187.

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

  38. Published

    Soil amendment with sewage sludge affects soil prokaryotic community composition, mobilome and resistome

    Wolters, B., Fornefeld, E., Jechalke, S., Su, J., Zhu, Y., Sørensen, Søren Johannes, Smalla, K. & Jacquiod, S., 2019, In: F E M S Microbiology Reviews. 95, 1, p. 1-14 fiy193.

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

  39. Published

    Tailings microbial community profile and prediction of its functionality in basins of tungsten mine

    Chung, A. P., Coimbra, C., Farias, P., Francisco, R., Branco, R., Simão, F. V., Gomes, E., Pereira, A., Vila, M. C., Fiúza, A., Mortensen, M. S., Sørensen, Søren Johannes & Morais, P. V., 2019, In: Scientific Reports. 9, 13 p., 19596.

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

  40. Published

    The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome: Results from a Randomized Crossover Intervention Study

    Schmedes, M., Brejnrod, A. D., Aadland, E. K., Kiilerich, P., Kristiansen, Karsten, Jacques, H., Lavigne, C., Graff, I. E., Eng, Ø., Holthe, A., Mellgren, G., Young, J. F., Sundekilde, U. K., Liaset, B. & Bertram, H. C., 2019, In: Molecular Nutrition and Food Research. 63, 1, p. 1-8 1700976.

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

  41. Published

    The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures

    Heins, A., Lundin, L., Nunes, I., Gernaey, K. V., Sørensen, Søren Johannes & Eliasson Lantz, A., 2019, In: Biotechnology Progress. 35, 3, e2796.

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

  42. Published

    The human milk microbiota is modulated by maternal diet

    Padilha, M., Danneskiold-Samsøe, Niels Banhos, Brejnrod, A., Hoffmann, C., Cabral, V. P., Iaucci, J. D. M., Sales, C. H., Fisberg, R. M., Cortez, R. V., Brix, S., Taddei, C. R., Kristiansen, Karsten & Saad, S. M. I., 2019, In: Microorganisms. 7, 11, 18 p., 502.

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

  43. Published

    The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits

    Würth, D. G., Dahl, M. B., Trouillier, M., Wilmking, M., Unterseher, M., Scholler, M., Sørensen, Søren Johannes, Mortensen, M. & Schnittler, M., 2019, In: Fungal Ecology. 41, p. 177-186 10 p.

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

  44. Published

    The scent of symbiosis: gut bacteria may affect social interactions in leaf-cutting ants

    Teseo, S., van Zweden, J. S., Pontieri, L., Kooij, P. W., Sørensen, Søren Johannes, Wenseleers, T., Poulsen, Michael, Boomsma, Jacobus J. & Sapountzis, P., 2019, In: Animal Behaviour. 150, p. 239-254

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

  45. Published

    To assemble or not to resemble - A validated Comparative Metatranscriptomics Workflow (CoMW)

    Anwar, M. Z., Lanzen, A., Bang-Andreasen, T. & Jacobsen, C. S., 2019, In: GigaScience. 8, 8, 10 p., giz096.

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

  46. 2018
  47. Published

    Staphylococcus aureus coagulases are exploitable yet stable public goods in clinically relevant conditions

    Trivedi, Urvish, Madsen, Jonas Stenløkke, Everett, J., Fell, C., Russel, J., Haaber, J., Crosby, H. A., Horswill, A. R., Burmølle, Mette, Rumbaugh, K. P. & Sørensen, Søren Johannes, 11 Dec 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 50, p. E11771-E11779

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

  48. Published

    Papio spp. Colon microbiome and its link to obesity in pregnancy

    Li, Xuan Ji, Rensing, C., Taylor, W. L., Costelle, C., Brejnrod, A. D., Ferry, R. J. ,. J., Higgins, P. B., Folli, F., Kottapalli, K. R., Hubbard, G. B., Dick, E. J. ,. J., Yooseph, S., Nelson, K. E. & Schlabritz-Loutsevitch, N., Dec 2018, In: Journal of Medical Primatology. 47, 6, p. 393-401

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

  49. Published

    Enhanced bacterial mutualism through an evolved biofilm phenotype

    Røder, Henriette Lyng, Herschend, J., Russel, J., Andersen, M. F., Madsen, Jonas Stenløkke, Sørensen, Søren Johannes & Burmølle, Mette, 1 Nov 2018, In: I S M E Journal. 12, p. 2608-2618 11 p.

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

  50. Published

    A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities

    Anjum, M., Madsen, Jonas Stenløkke, Espinosa-Gongora, C., Jana, B., Wiese, M., Nielsen, Dennis Sandris, Sørensen, Søren Johannes, Moodley, Arshnee, Bortolaia, V. & Guardabassi, Luca, Sep 2018, In: Journal of Microbiological Methods. 152, p. 18-26 9 p.

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

  51. Published

    Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community

    Li, L., Dechesne, A., He, Z., Madsen, Jonas Stenløkke, Nesme, Joseph, Sørensen, Søren Johannes & Smets, B. F., 8 May 2018, In: Environmental Science & Technology Letters. 5, 5, p. 260-265 6 p.

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

  52. Published

    Emissions of biogenic volatile organic compounds from arctic shrub litter are coupled with changes in the bacterial community composition

    Svendsen, S. H., Priemé, Anders, Voriskova, J., Kramshoj, M., Schostag, M. D., Jacobsen, C. S. & Rinnan, Riikka, May 2018, In: Soil Biology & Biochemistry. 120, p. 80-90 11 p.

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

  53. Published

    Genetic barcoding of dark-spored myxomycetes (Amoebozoa): identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

    Dahl, M. B., Brejnrod, A. D., Unterseher, M., Hoppe, T., Feng, Y., Novozhilov, Y., Sørensen, Søren Johannes & Schnittler, M., Mar 2018, In: Molecular Ecology Resources. 18, 2, p. 306-318 13 p.

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

  54. Published

    Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

    Jacquiod, S. J. A., Cyriaque, V., Riber, Leise, Al-Soud, W. A., Gillan, D. C., Wattiez, R. & Sørensen, Søren Johannes, 15 Feb 2018, In: Journal of Hazardous Materials. 344, p. 299-307 9 p.

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

  55. Published

    Soil bacteria show different tolerance ranges to an unprecedented disturbance

    Nunes, I. M., Jurburg, S., Jacquiod, S. J. A., Brejnrod, A. D., Falcão Salles, J., Priemé, Anders & Sørensen, Søren Johannes, Feb 2018, In: Biology and Fertility of Soils. 54, 2, p. 189–202 14 p.

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

  56. Published

    The origin of king crabs: hermit crab ancestry under the magnifying glass

    Noever, C. & Glenner, Henrik, 19 Jan 2018, In: Zoological Journal of the Linnean Society. 182, 2, p. 300-318

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

  57. Published

    Microbial indicators for soil quality

    Schloter, M., Nannipieri, P., Sørensen, Søren Johannes & van Elsas, J. D., Jan 2018, In: Biology and Fertility of Soils. 54, 1, p. 1-10 10 p.

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

  58. Published

    Rifaximin has minor effects on bacterial composition, inflammation and bacterial translocation in cirrhosis: a randomized trial

    Kimer, N., Pedersen, J. S., Tavenier, J., Christensen, J. E., Busk, T. M., Hobolth, L., Krag, A., Abu Al-Soud, W., Mortensen, M. S., Sørensen, Søren Johannes, Møller, Søren & Bendtsen, Flemming, Jan 2018, In: Journal of Gastroenterology and Hepatology. 33, 1, p. 307-314 8 p.

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

  59. Published

    In Vitro Community Synergy between Bacterial Soil Isolates Can Be Facilitated by pH Stabilization of the Environment

    Herschend, J., Koren, K., Røder, Henriette Lyng, Brejnrod, A., Kühl, Michael & Burmølle, Mette, 2018, In: Applied and Environmental Microbiology. 84, 21, e01450.

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

  60. Published

    In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina

    Behrendt, L., Raina, J., Lutz, A., Kot, W., Albertsen, M., Nielsen, P. H., Sørensen, Søren Johannes, Larkum, A. W. D. & Kühl, Michael, 2018, In: I S M E Journal. 12, p. 556–567 12 p.

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

  61. Published

    In vitro community synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment.

    Herschend, J., Koren, K., Røder, Henriette Lyng, Brejnrod, A. D., Kühl, Michael & Burmølle, Mette, 2018, In: Applied and Environmental Microbiology. 84, 21, p. 1-15 e01450-18.

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

  62. Published

    An intriguing relationship between the cyclic diguanylate signaling system and horizontal gene transfer

    Madsen, Jonas Stenløkke, Hylling, Ole, Jacquiod, S. J. A., Pécastaings, S., Hansen, L. H., Riber, Leise, Vestergaard, G. A. & Sørensen, Søren Johannes, 2018, In: ISME Journal. 12, 9, p. 2330-2334 5 p.

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

  63. Published

    Bacterial social interactions and the emergence of community-intrinsic properties

    Madsen, Jonas Stenløkke, Sørensen, Søren Johannes & Burmølle, Mette, 2018, In: Current Opinion in Microbiology. 42, p. 104-109 6 p.

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

  64. Published

    Biofouling on RO-membranes used for water recovery in the dairy industry

    Stoica, I., Vitzilaiou, E., Røder, Henriette Lyng, Burmølle, Mette, Thaysen, D., Knoechel, Susanne & van der Berg, Franciscus Winfried J, 2018, In: Journal of Water Process Engineering. 24, p. 1-10 10 p.

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

  65. Published

    Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization

    Wolters, B., Jacquiod, S. J. A., Sørensen, Søren Johannes, Widyasari-Mehta, A., Bech, T. B., Kreuzig, R. & Smalla, K., 2018, In: F E M S Microbiology Ecology. 94, 4, 13 p., fiy027.

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

  66. Published

    Catch Crop Residues Stimulate N2O Emissions During Spring, Without Affecting the Genetic Potential for Nitrite and N2O Reduction

    Duan, Y., Hallin, S., Jones, C. M., Priemé, Anders, Labouriau, R. & Petersen, S. O., 2018, In: Frontiers in Microbiology. 9, p. 1-13 2629.

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

  67. Published

    Changes in rumen bacterial and archaeal communities over the transition period in primiparous Holstein dairy cows

    Zhu, Z., Kristensen, L., Difford, G. F., Poulsen, M., Noel, S. J., Abu Al-Soud, W., Sørensen, Søren Johannes, Lassen, J., Løvendahl, P. & Højberg, O., 2018, In: Journal of Dairy Science. 101, 11, p. 9847-9862

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

  68. Published

    Disease-induced assemblage of a plant-beneficial bacterial consortium

    Berendsen, R. L., Vismans, G., Yu, K., Song, Y., de Jonge, R., Burgman, W. P., Burmølle, Mette, Herschend, J., Bakker, P. A. H. M. & Pieterse, C. M. J., 2018, In: I S M E Journal. 12, p. 1496-1507 12 p.

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

  69. Published

    Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates

    Müller, O., Bang-Andreasen, T., White, R. A., Elberling, Bo, Taş, N., Kneafsey, T., Jansson, J. K. & Øvreås, L., 2018, In: Environmental Microbiology. 20, 12, p. 4328-4342 15 p.

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

  70. Published

    Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities

    Meisner, A., Jacquiod, S., Snoek, B. L., ten Hooven, F. C. & van der Putten, W. H., 2018, In: Frontiers in Microbiology. 9, 12 p., 294.

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

  71. Published

    Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity

    Kang, D., Herschend, J., Abu Al-Soud, W., Mortensen, M. S., Gonzalo, M., Jacquiod, S. J. A. & Sørensen, Søren Johannes, 2018, In: Bioresource Technology. 270, p. 303-310

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

  72. Published

    Fluorescence recovery allows theimplementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments

    Pinilla Redondo, Rafael, Riber, Leise & Sørensen, Søren Johannes, 2018, In: Applied and Environmental Microbiology. 84, 6, 9 p., e02507-17.

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

  73. Published

    Free-Living Nematodes Together With Associated Microbes Play an Essential Role in Apple Replant Disease

    Kanfra, X., Liu, B., Beerhues, L., Sørensen, Søren Johannes & Heuer, H., 2018, In: Frontiers in Plant Science. 9, p. 1-13 1666.

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

  74. Published

    How Microbial Aggregates Protect against Nanoparticle Toxicity

    Tang, J., Wu, Y., Esquivel-Elizondo, S., Sørensen, Søren Johannes & Rittmann, B. E., 2018, In: Trends in Biotechnology. 36, 11, p. 1171-1182

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

  75. Published

    Impact of free living protozoa and bacterial interactions on multispecies biofilm

    Raghupathi, P. K., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  76. Published

    Insights into Bacterial Milk Spoilage with Particular Emphasis on the Roles of Heat-Stable Enzymes, Biofilms, and Quorum Sensing

    Yuan, L., Sadiq, F. A., Burmølle, Mette, Liu, T. & He, G., 2018, In: Journal of Food Protection. 81, 10, p. 1651-1660

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

  77. Published

    Interactions in Microbial Community Assembly - from Patterns to Processes and Back

    Russel, J., 2018, Department of Biology, Faculty of Science, University of Copenhagen.

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

  78. Published

    Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk

    Yuan, L., Burmølle, Mette, Sadiq, F. A., Wang, N. & He, G., 2018, In: Food Control. 91, p. 47-57 11 p.

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

  79. Published

    Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches

    Muhammed, Musemma Kedir, Olsen, M. L., Kot, Witold, Neve, H., Castro Mejia, J. L., Janzen, T., Hansen, L. H., Nielsen, Dennis Sandris, Sørensen, Søren Johannes, Heller, K. J. & Vogensen, Finn Kvist, 2018, In: International Journal of Food Microbiology. 272, p. 61-72 12 p.

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

  80. Published

    Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

    Jacquiod, S., Nunes, I., Brejnrod, A., Hansen, M. A., Holm, Peter Engelund, Johansen, A., Brandt, Kristian Koefoed, Priemé, Anders & Sørensen, Søren Johannes, 2018, In: Microbiome. 6, p. 1-14 223.

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

  81. Published

    Maturation of the gut microbiome and risk of asthma in childhood

    Stokholm, Jakob, Blaser, M. J., Thorsen, Jonathan Jan Ilve, Rasmussen, Morten Arendt, Waage, J. E., Vinding, R. K., Schoos, A. M., Kunøe, A., Fink, N. R., Chawes, Bo Lund Krogsgaard, Bønnelykke, Klaus, Brejnrod, A. D., Mortensen, M. S., Abu Al-Soud, W., Sørensen, Søren Johannes & Bisgaard, H., 2018, In: Nature Communications. 9, 10 p., 141.

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

  82. Published

    Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm

    Liu, W., Russel, J., Burmølle, Mette, Sørensen, Søren Johannes & Madsen, Jonas Stenløkke, 2018, In: I S M E Journal. 12, p. 1940-1951 12 p.

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

  83. Published

    Microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities

    Raghupathi, P. K., Zupančič, J., Brejnrod, A. D., Jacquiod, S. J. A., Houf, K., Burmølle, Mette, Gunde-Cimerman, N. & Sørensen, Søren Johannes, 2018, In: Applied and Environmental Microbiology. 84, 5, 17 p., e02755-17.

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

  84. Published

    Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives

    Pinilla Redondo, Rafael, Cyriaque, V., Jacquiod, S., Sørensen, Søren Johannes & Riber, Leise, 2018, In: Plasmid. 99, p. 56-67

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

  85. Published

    Nutrient Fortification of Human Donor Milk Affects Intestinal Function and Protein Metabolism in Preterm Pigs

    Sun, Jing, Li, Y., Nguyen, Duc Ninh, Mortensen, M. S., van den Akker, C. H. P., Skeath, T., Pors, S. E., Pankratova, Stanislava, Rudloff, S., Sørensen, Søren Johannes, Burrin, D. G., Thymann, Thomas & Sangild, Per Torp, 2018, In: Journal of Nutrition. 148, 3, p. 336-347 12 p.

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

  86. Published

    Short and Long-Term Controls on Active Layer and Permafrost Carbon Turnover Across the Arctic

    Faucherre, S., Jørgensen, C. J., Blok, D., Weiss, N., Siewert, M. B., Bang-Andreasen, T., Hugelius, G., Kuhry, P. & Elberling, Bo, 2018, In: Journal of Geophysical Research: Biogeosciences. 123, 2, p. 372-390 19 p.

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

  87. Published

    Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: a double-blind, randomized, placebo-controlled trial

    Wei, S., Mortensen, M. S., Stokholm, Jakob, Brejnrod, A. D., Thorsen, Jonathan Jan Ilve, Rasmussen, Morten Arendt, Trivedi, Urvish, Bisgaard, H. & Sørensen, Søren Johannes, 2018, In: EBioMedicine. 38, p. 265-272

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

  88. Published

    Stability and resilience of the intestinal microbiota in children in daycare - a 12 month cohort study

    Mortensen, M. S., Jensen, Betina Hebbelstrup, Williams, J., Brejnrod, A. D., Andersen, L. O., Röser, D., Andreassen, B. U., Petersen, Andreas Munk, Stensvold, C. R., Sørensen, Søren Johannes & Krogfelt, K. A., 2018, In: BMC Microbiology. 18, 11 p., 223.

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

  89. Published

    Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers

    Zupancic, J., Raghupathi, P. K., Houf, K., Burmølle, Mette, Sørensen, Søren Johannes & Gunde-Cimerman, N., 2018, In: Frontiers in Microbiology. 9, 13 p., 21.

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

  90. Published

    Synergistic Interactions within a Multispecies Biofilm Enhance Individual Species Protection against Grazing by a Pelagic Protozoan

    Raghupathi, P. K., Liu, W., Sabbe, K., Houf, K., Burmølle, Mette & Sørensen, Søren Johannes, 2018, In: Frontiers in Microbiology. 8, 11 p., 2649.

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

  91. Published

    Synergistic Removal of Static and Dynamic Staphylococcus aureus Biofilms by Combined Treatment with a Bacteriophage Endolysin and a Polysaccharide Depolymerase

    Olsen, N. M. C., Thiran, E., Hasler, T., Vanzieleghem, T., Belibasakis, G. N., Mahillon, J., Loessner, M. J. & Schmelcher, M., 2018, In: Viruses. 10, 8, p. 1-17 438.

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

  92. Published

    The Genome of BAM-degrading Aminobacter sp. MSH1 with Several Low Copy Plasmids

    Nielsen, Tue Kjærgaard, Hylling, Ole & Ellegaard-Jensen, L., 2018, 12 p.

    Research output: Working paper › Preprint › Research

  93. Published

    The bacterial microbiota in first-void urine from men with and without idiopathic urethritis

    Frølund, M., Wikström, A., Lidbrink, P., Abu Al-Soud, W., Larsen, N., Harder, C. B., Sørensen, Søren Johannes, Jensen, J. S. & Ahrens, P., 2018, In: PLoS ONE. 13, 7, p. 1-19 e0201380.

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

  94. Published

    The impact of exercise training and resveratrol supplementation on gut microbiota composition in high-fat diet fed mice

    Brandt, N., Kotowska, D., Kristensen, C. M., Olesen, J., Lützhøft, Ditte Olsen, Halling, Jens Frey, Hansen, M., Al-Soud, W. A., Hansen, Lars Hestbjerg, Kiilerich, P. & Pilegaard, Henriette, 2018, In: Physiological Reports. 6, 20, p. 1-11 e13881.

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

  95. Published

    Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota

    Bradford, L. M., Vestergaard, G., Táncsics, A., Zhu, B., Schloter, M. & Lueders, T., 2018, In: Frontiers in Microbiology. 9, 13 p., 2696.

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

  96. 2017
  97. Published

    Hot spots of N2O emission move with the seasonally mobile oxic-anoxic interface in drained organic soils

    Lee, A. J., Winther, M. N., Priemé, Anders, Blunier, Thomas & Christensen, Søren Tvorup, 1 Dec 2017, In: Soil Biology & Biochemistry. 115, p. 178-186 9 p.

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

  98. Published

    A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community

    Herschend, J., Damholt, Z. B. V., Marquard, A. M., Svensson, B., Sørensen, Søren Johannes, Hägglund, Per Mårten & Burmølle, Mette, 28 Nov 2017, In: Scientific Reports. 7, 13 p., 16483.

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

  99. Published

    Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity

    Dahl, M. B., Priemé, Anders, Brejnrod, A. D., Brusvang, P., Lund, M., Nymand, J., Kramshøj, M., Ro-Poulsen, Helge & Haugwitz, M. S., 22 Nov 2017, In: Scientific Reports. 7, 13 p., 16035.

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

  100. Published

    Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period

    Zhu, Z., Noel, S. J., Difford, G. F., Abu Al-Soud, W., Brejnrod, A. D., Sørensen, Søren Johannes, Lassen, J., Løvendahl, P. & Højberg, O., 8 Nov 2017, In: PLoS ONE. 12, 11, 24 p., e0187858.

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

  101. Published

    A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil

    Ghodsalavi, B., Svenningsen, N. B., Hao, X., Olsson, S., Nicolaisen, Mette Haubjerg, Al-Soud, W. A., Sørensen, Søren Johannes & Nybroe, O., 27 Oct 2017, In: PLOS ONE. 12, 10, 14 p., e0187116.

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

  102. Published

    Antagonism correlates with metabolic similarity in diverse bacteria

    Russel, J., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Burmølle, Mette & Sørensen, Søren Johannes, 3 Oct 2017, In: Proceedings of the National Academy of Science of the United States of America. 114, 40, p. 10684-10688 5 p.

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

  103. Published

    Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season

    Holmsgaard, P. N., Dealtry, S., Dunon, V., Heuer, H., Hansen, Lars Hestbjerg, Springael, D., Smalla, K., Riber, Leise & Sørensen, Søren Johannes, Oct 2017, In: Environmental Pollution. 229, p. 854-862 9 p.

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

  104. Published

    Effects of soil pre-treatment with Basamid© granules, Brassica juncea, Raphanus sativus, and Tagetes patula on bacterial and fungal communities at two apple replant disease sites

    Yim, B., Nitt, H., Wrede, A., Jacquiod, S. J. A., Sørensen, Søren Johannes, Winkelmann, T. & Smalla, K., 1 Sep 2017, In: Frontiers in Microbiology. 8, 15 p., 1604.

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

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