Microbiology

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  1. 2016
  2. 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

  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

    Herbivory and dominance shifts among exotic and congeneric native plant species during plant community establishment

    Engelkes, T., Meisner, A., Morriën, E., Kostenko, O., van der Putten, W. H. & Macel, M., 2016, In: Oecologia. 180, 2, p. 507-517 11 p.

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

  5. Published

    High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples

    Gosalbes, M. J., Vallès, Y., Jiménez-Hernández, N., Balle, C., Riva, P., Miravet-Verde, S., de Vries, Lisbeth Elvira, Llop, S., Agersø, Y., Sørensen, Søren Johannes, Ballester, F. & Francino, M. P., 2016, In: Journal of Developmental Origins of Health and Disease. 7, 01, p. 35-44 10 p.

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

  6. Published

    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

    Knudsen, B. E., Bergmark, L., Munk, P., Lukjancenko, O., Priemé, Anders, Aarestrup, F. M. & Pamp, S. J., 2016, In: mSystems. 1, 5, p. 1-15 e00095-16.

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

  7. Published

    Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization

    Liu, W., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Bjarnsholt, Thomas, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Frontiers in Microbiology. 7, 8 p., 1366.

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

  8. 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

  9. Published

    Local diversity of heathland Cercozoa explored by in-depth sequencing

    Harder, Christoffer Bugge, Rønn, Regin, Brejnrod, A. D., Bass, D., Abu Al-Soud, W. & Ekelund, Flemming, 2016, In: The ISME Journal. 10, 10, p. 2488-2497 10 p.

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

  10. Published

    Metagenomes provide valuable comparative information on soil microeukaryotes

    Jacquiod, S. J. A., Stenbæk, J., Santos, S. S., Winding, A., Sørensen, Søren Johannes & Priemé, Anders, 2016, In: Research in Microbiology. 167, 5, p. 436-450 15 p.

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

  11. 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

  12. 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

  13. Published

    Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients

    Jitwasinkul, T., Suriyaphol, P., Tangphatsornruang, S., Hansen, M. A., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Permpikul, C., Rongrungruang, Y. & Tribuddharat, C., 2016, In: Journal of Global Antimicrobial Resistance. 6, p. 57-66 10 p.

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

  14. 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

  15. Published

    Supraglacial bacterial community structures vary across the Greenland ice sheet

    Cameron, K. A., Stibal, M., Zarsky, J. D., Gözdereliler, E., Schostag, M. D. & Jacobsen, C. S., 2016, In: F E M S Microbiology Ecology. 92, 2, 11 p.

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

  16. 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

  17. 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

  18. Published

    The legacy of climate change effects: previous drought increases short-term litter decomposition rates in a temperate mixed grass- and shrubland

    Haugwitz, M. S., Michelsen, Anders & Priemé, Anders, 2016, In: Plant and Soil. 408, 1, p. 183-193 11 p.

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

  19. 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

  20. Published

    Unravelling the mechanisms of bacterial interactions in model communities

    Herschend, J., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

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

  21. 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

  22. 2015
  23. 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

  24. 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

  25. 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

  26. 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

  27. Published

    Bio-Sustainable Control of the Blue Stain Fungi Aureobasidium pullulans on Exterior Wood Coatings

    Stenbæk, J., 2015, Department of Biology, Faculty of Science, University of Copenhagen.

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

  28. 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

  29. 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

  30. 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

  31. Published

    Colonic lesions, cytokine profiles, and gut microbiota in plasminogen-deficient mice

    Vestergaard, Bill, Krych, Lukasz, Lund, L. R., Jørgensen, B. M. P., Hansen, Lars Hestbjerg, Jensen, Henrik Elvang, Nielsen, Dennis Sandris & Hansen, Axel Kornerup, 2015, In: Comparative Medicine. 65, 5, p. 382-397 16 p.

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

  32. 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

  33. 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

  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

    Different bulk and active bacterial communities in cryoconite from the margin and interior of the Greenland ice sheet

    Stibal, M., Nielsen, M. S., Cameron, K. A., Hansen, L. H., Chandler, D. M., Wadham, J. L. & Jacobsen, C. S., 2015, In: Environmental Microbiology Reports. 7, 2, p. 293-300 8 p.

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

  36. 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

  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

    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

  39. 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

  40. 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

  41. 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

  42. Published

    Genome-wide detection of selection and other evolutionary forces

    Xu, Z. & Zhou, R., 2015, Bacterial pangenomics: methods and protocols. Mengoni, A., Galardini, M. & Fondi, M. (eds.). Springer, p. 271-287 17 p. (Methods in Molecular Biology).

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

  43. Published

    Identification of the amidase BbdA that initiates biodegradation of the groundwater micropollutant 2,6-dichlorobenzamide (BAM) in Aminobacter sp. MSH1

    T'Syen, J., Tassoni, R., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Leroy, B., Sekhar, A., Wattiez, R., De Mot, R. & Springael, D., 2015, In: Environmental Science & Technology (Washington). 49, 19, p. 11703-11713 11 p.

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

  44. 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

  45. 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

  46. 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

  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

    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

  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

    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

  51. 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

  52. 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

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