Microbiology

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  1. 2016
  2. Published

    Diverse gene functions in a soil mobilome

    Luo, W., Xu, Z., Riber, Leise, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2016, In: Soil Biology & Biochemistry. 101, p. 175-183 9 p.

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

  3. Published

    Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases

    Lylloff, J. E., Hansen, L. B. S., Jepsen, M., Sanggaard, K. W., Vester, J. K., Enghild, J. J., Sørensen, Søren Johannes, Stougaard, P. & Glaring, M. A., 2016, In: Microbial Biotechnology. 9, 2, p. 245-256 12 p.

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

  4. Published

    Coexistence facilitates interspecific biofilm formation in complex microbial communities

    Madsen, Jonas Stenløkke, Røder, Henriette Lyng, Russel, J., Sørensen, Helle, Burmølle, Mette & Sørensen, Søren Johannes, 2016, In: Environmental Microbiology. 18, 8, p. 2565–2574

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

  5. Published

    Type 3 fimbriae encoded on plasmids are expressed from a unique promoter without affecting host motility, facilitating an exceptional phenotype that enhances conjugal plasmid transfer

    Madsen, Jonas Stenløkke, Riber, Leise, Kot, Witold, Basfeld, A., Burmølle, Mette, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2016, In: P L o S One. 11, 9, 19 p., e0162390.

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

  6. Published

    Metagenomic comparison of antibiotic resistance genes associated with liquid and dewatered biosolids

    McCall, C. A., Bent, E., Jørgensen, T. S., Dunfield, K. E. & Habash, M. B., 2016, In: Journal of Environmental Quality. 45, 2, p. 463-470 8 p.

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

  7. Published

    The Human Microbiota in Early Life: Initial Colonization and Development

    Mortensen, M. S., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

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

  8. Published

    The developing hypopharyngeal microbiota in early life

    Mortensen, M. S., Brejnrod, A. D., Roggenbuck, M., Abu Al-Soud, W., Balle, C., Krogfelt, K. A., Stokholm, Jakob, Thorsen, Jonathan Jan Ilve, Waage, J. E., Rasmussen, Morten Arendt, Bisgaard, H. & Sørensen, Søren Johannes, 2016, In: Microbiome. 4, 12 p., 70.

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

  9. Published

    Back to the future of soil metagenomics

    Nesme, J., Achouak, W., Agathos, S. N., Bailey, M., Baldrian, P., Brunel, D., Frostegard, A., Heulin, T., Jansson, J. K., Jurkevitch, E., Kruus, K. L., Kowalchuk, G. A., Lagares, A., Lappin-Scott, H. M., Lemanceau, P., Le Paslier, D., Mandic-Mulec, I., Murrell, J. C., Myrold, D. D., Nalin, R. & 28 others, Nannipieri, P., Neufeld, J. D., O'Gara, F., Parnell, J. J., Puehler, A., Pylro, V., Ramos, J. L., Roesch, L. F. W., Schloter, M., Schleper, C., Sczyrba, A., Sessitsch, A., Sjoeling, S., Sørensen, Jan, Sørensen, Søren Johannes, Tebbe, C. C., Topp, E., Tsiamis, G., van Elsas, J. D., van Keulen, G., Widmer, F., Wagner, M., Zhang, T., Zhang, X., Zhao, L., Zhu, Y., Vogel, T. M. & Simonet, P., 2016, In: Frontiers in Microbiology. 7, 5 p., 73.

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

  10. Published

    Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure

    Nunes, I. M., Jacquiod, S. J. A., Brejnrod, A. D., Holm, Peter Engelund, Johansen, A., Brandt, Kristian Koefoed, Priemé, Anders & Sørensen, Søren Johannes, 2016, In: F E M S Microbiology Ecology. 92, 11, 12 p., fiw175.

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

  11. Published

    Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment

    Otani, S., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes & Poulsen, Michael, 2016, In: Microbial Ecology. 71, 1, p. 207-220 14 p.

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

  12. Published

    Draft genome assembly of two Pseudoclavibacter helvolus strains, G8 and W3, isolated from slaughterhouse environments

    Raghupathi, P. K., Herschend, J., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 2, 1 p., e00077-16.

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

  13. Published

    Genome sequence of Kocuria varians G6 ssolated from a slaughterhouse in Denmark

    Raghupathi, P. K., Herschend, J., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 2, 2 p., e00076-16.

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

  14. Published

    Genome sequence of Psychrobacter cibarius strain W1

    Raghupathi, P. K., Herschend, J., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 3, 1 p., e00078-16.

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

  15. Published

    Bovine colostrum improves neonatal growth, digestive function, and gut immunity relative to donor human milk and infant formula in preterm pigs

    Rasmussen, S. O., Martin, L., Østergaard, M. V., Rudloff, S., Li, Y., Roggenbuck, M., Bering, S. B. & Sangild, Per Torp, 1 Sep 2016, In: American Journal of Physiology: Gastrointestinal and Liver Physiology. 311, 3, p. G480-G491 12 p.

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

  16. Published

    Enhanced plasmid loss in bacterial populations exposed to the antimicrobial compound irgasan delivered from interpenetrating polymer network silicone hydrogels

    Riber, Leise, Burmølle, Mette, Alm, M., Milani, S. M., Thomsen, P., Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2016, In: Plasmid. 87-88, p. 72-78 7 p.

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

  17. Published

    Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs

    Rinta-Kanto, J. M., Sinkko, H., Rajala, T., Abu Al-Soud, W., Sørensen, Søren Johannes, Tamminen, M. V. & Timonen, S., 2016, In: F E M S Microbiology Ecology. 92, 7, 10 p., fiw087.

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

  18. Published

    Vitamin D and allergic airway disease shape the murine lung microbiome in a sex-specific manner

    Roggenbuck, M., Anderson, D., Barfod, K. K., Feelisch, M., Geldenhuys, S., Sørensen, Søren Johannes, Weeden, C. E., Hart, P. H. & Gorman, S., 2016, In: Respiratory Research. 17, 18 p., 116.

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

  19. Published

    Studying bacterial multispecies biofilms: where to start?

    Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Trends in Microbiology. 24, 6, p. 503-513 11 p.

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

  20. Published

    Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    Thorsen, Jonathan Jan Ilve, Brejnrod, A. D., Mortensen, M. S., Rasmussen, Morten Arendt, Stokholm, Jakob, Abu Al-Soud, W., Sørensen, Søren Johannes, Bisgaard, H. & Waage, J. E., 2016, In: Microbiome. 4, 14 p., 62.

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

  21. Published

    Continuous measurements of nitrous oxide isotopomers during incubation experiments

    Winther, M. N., Balslev-Harder, D., Christensen, Søren, Priemé, Anders, Elberling, Bo, Crosson, E. & Blunier, Thomas, 2016, In: Biogeosciences. 15, p. 767-780 19 p.

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

  22. 2015
  23. Published

    Phenotypic variability in bioprocessing conditions can be tracked on the basis of on-line flow cytometry and fits to a scaling law

    Baert, J., Kinet, R., Brognaux, A., Delepierre, A., Telek, S., Sørensen, Søren Johannes, Riber, Leise, Fickers, P. & Delvigne, F., 2015, In: Biotechnology Journal. 10, 8, p. 1316-1325 10 p.

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

  24. Published

    Chlorophyll f-driven photosynthesis in a cavernous cyanobacterium

    Behrendt, L., Brejnrod, A. D., Schliep, M., Sørensen, Søren Johannes, Larkum, A. W. D. & Kühl, Michael, 2015, In: The ISME Journal. 9, 9, p. 2108-2111 4 p.

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

  25. Published

    Impacts of climate change on terrestrial ecosystem functioning: an overview

    Beier, C., Ambus, P., Arndal, M. F., Christensen, S., Holmstrup, M., Larsen, K. S., Michelsen, A., Mikkelsen, T. N., Priemé, Anders, Schmidt, Inger Kappel & Pilegaard, K., 2015, Kgs. Lyngby: DTU. 55 p.

    Research output: Book/Report › Report › Research

  26. Published

    The effect of Lactobacillus paracasei subsp. paracasei L. casei W8® on blood levels of triacylglycerol is independent of colonisation

    Bjerg, A. T., Sørensen, M. B., Krych, Lukasz, Hansen, Lars Hestbjerg, Astrup, A., Kristensen, M. B. & Nielsen, Dennis Sandris, 2015, In: Beneficial Microbes. 6, 3, p. 263-269 7 p.

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

  27. Published

    Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

    Castro Mejia, J. L., Muhammed, Musemma Kedir, Kot, Witold, Neve, H., Franz, C. M. A. P., Hansen, L. H., Vogensen, Finn Kvist & Nielsen, Dennis Sandris, 2015, In: Microbiome. 3, 14 p., 64.

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

  28. Published

    Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments

    De Vries, M., Schöler, A., Ertl, J., Xu, Z. & Schloter, M., 2015, In: FEMS Microbiology Ecology. 91, 7, p. 1-10 10 p.

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

  29. Published

    Natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields

    Farias, P., Santo, C. E., Branco, R., Francisco, R., Santos, S., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes & Morais, P. V., 2015, In: Applied and Environmental Microbiology. 81, 7, p. 2534-2543 10 p.

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

  30. Published

    Microbial diversity in a permanently cold and alkaline environment in Greenland

    Glaring, M. A., Vester, J. K., Lylloff, J. E., Abu Al-Soud, W., Sørensen, Søren Johannes & Stougaard, P., 2015, In: PLoS ONE. 10, 4, 22 p., e0124863.

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

  31. Published

    Context dependency and saturating effects of loss of rare soil microbes on plant productivity

    Hol, W. H. G., de Boer, W., de Hollander, M., Kuramae, E. E., Meisner, A. & van der Putten, W. H., 2015, In: Frontiers in Plant Science. 6, 10 p., 485.

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

  32. Published

    Presence of Pathogenic bacteria and viruses in the daycare environment

    Ibfelt, T., Engelund, E. H., Permin, A., Madsen, Jonas Stenløkke, Schultz, A. C. & Andersen, Leif Percival, 2015, In: Journal of Environmental Health. 78, 3, p. 24-29 6 p.

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

  33. Published

    Characterization of the Mobilome and Microbiome of Rat Cecum

    Jørgensen, T. S., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 174 p.

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

  34. Published

    Current strategies for mobilome research

    Jørgensen, T. S., Kiil, A. S., Hansen, M. A., Sørensen, Søren Johannes & Hansen, Lars Hestbjerg, 2015, In: Frontiers in Microbiology. 5, 6 p., 750.

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

  35. Published

    Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    Klümper, U., Riber, Leise, Dechesne, A., Sannazzaro, A. I., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes & Smets, B. F., 2015, In: I S M E Journal. 9, p. 934-945 12 p.

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

  36. Published

    The potential for bioaugmentation of sand filter materials from waterworks using bacterial cultures degrading 4-chloro-2-methylphenoxyacetic acid

    Krüger, U. S., Johnsen, A. R., Burmølle, Mette, Aamand, J. & Sørensen, S. R., 1 Feb 2015, In: Pest Management Science. 71, 2, p. 257-265 9 p.

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

  37. Published

    Draft Genome Sequence of Se(IV)-Reducing Bacterium Pseudomonas migulae ES3-33

    Li, Xuan Ji, Kot, W., Wang, D., Zheng, S., Wang, G., Hansen, L. H. & Rensing, C., 2015, In: Genome Announcements. 3, 3, p. 1-2 2 p., e00406-15.

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

  38. Published

    Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

    Liberti, J., Sapountzis, P., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Adams, R. M. M. & Boomsma, Jacobus J., 2015, In: Molecular Ecology. 24, 12, p. 3151-3169 19 p.

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

  39. Published

    The Soil Mobilome: A Direct Approach to Study Plasmid Functional Responses to Long-Term Copper Contamination

    Luo, W., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 166 p.

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

  40. Published

    Draft genome sequences of two protease-producing strains of Arsukibacterium, isolated from two cold and alkaline environments

    Lylloff, J. E., Hansen, L. B. S., Jepsen, M., Hallin, P. F., Sørensen, Søren Johannes, Stougaard, P. & Glaring, M. A., 2015, In: Genome Announcements. 3, 3, 2 p., e00585-15.

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

  41. Published

    Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment

    Macdonald, C. A., Crawley, M. J., Wright, D. J., Kuczynski, J., Robinson, L., Knight, R., Abu Al-Soud, W., Sørensen, Søren Johannes, Deng, Y., Zhou, J. & Singh, B. K., 2015, In: Environmental Microbiology. 17, 3, p. 841-854 14 p.

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

  42. Published

    Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models

    Madsen, Jonas Stenløkke, Lin, Y. C., Squyres, G. R., Price-Whelan, A., Torio, A. D. S., Song, A., Cornell, W. C., Sørensen, Søren Johannes, Xavier, J. B. & Dietrich, L. E. P., 2015, In: Applied and Environmental Microbiology. 81, 24, p. 8414-8426 13 p.

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

  43. Published

    Extrachromosomal circular DNA is common in yeast

    Møller, H. D., Parsons, L., Jørgensen, T. S., Botstein, D. & Regenberg, Birgitte, 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 24, p. E3114–E3122 9 p.

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

  44. Published

    Shifts in the microbial community structure explain the response of soil respiration to land-use change but not to climate warming

    Nazaries, L., Tottey, W., Robinson, L., Khachane, A., Abu Al-Soud, W., Sørensen, Søren Johannes & Singh, B. K., 2015, In: Soil Biology & Biochemistry. 89, p. 123-134 12 p.

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

  45. Published

    Draft genome sequence of MCPA-degrading Sphingomonas sp. strain ERG5, isolated from a groundwater aquifer in Denmark

    Nielsen, Tue Kjærgaard, Kot, Witold, Sørensen, S. R. & Hansen, Lars Hestbjerg, 2015, In: Genome Announcements. 3, 1, 2 p., e01529-14.

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

  46. Published

    Coping with Stress: Exploring the Use of RNA-Based Approaches for the Study of Soil Microbial Communities

    Nunes, I. M., 2015, Department of Biology, Faculty of Science, University of Copenhagen. 206 p.

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

  47. Published

    Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere

    Pathan, S. I., Ceccherini, M. T., Hansen, M. A., Giagnoni, L., Ascher, J., Arenella, M., Sørensen, Søren Johannes, Pietramellara, G., Nannipieri, P. & Renella, G., 2015, In: Biology and Fertility of Soils. 51, 8, p. 995-1004 10 p.

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

  48. Published

    High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

    Ren, D., Madsen, Jonas Stenløkke, Sørensen, Søren Johannes & Burmølle, Mette, 11 Jan 2015, In: ISME Journal. 9, p. 81-89 9 p.

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

  49. Published

    Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques

    Ryssel, M., Johansen, P., Abu Al-Soud, W., Sørensen, Søren Johannes, Arneborg, Nils & Jespersen, Lene, 2015, In: International Journal of Food Microbiology. 215, p. 124-30 7 p.

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

  50. Published

    Interspecies interactions result in enhanced biofilm formation by co-cultures of bacteria isolated from a food processing environment

    Røder, Henriette Lyng, Raghupathi, P. K., Herschend, J., Brejnrod, A. D., Knoechel, Susanne, Sørensen, Søren Johannes & Burmølle, Mette, 2015, In: Food Microbiology. 51, p. 18-24 7 p.

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

  51. Published

    Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential

    Sapountzis, P., Zhukova, M., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Schiøtt, M. & Boomsma, Jacobus J., 2015, In: Applied and Environmental Microbiology. 81, 16, p. 5527-5537 11 p.

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

  52. Published

    Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    Schostag, M. D., Stibal, M., Jacobsen, C. S., Bælum, J., Tas, N., Elberling, Bo, Jansson, J., Semenchuk, P. & Priemé, Anders, 2015, In: Frontiers in Microbiology. 6, 13 p., 399.

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

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