Microbiology

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  1. Published

    Investigating the diversity of Pseudomonas spp. in soil using culture dependent and independent techniques

    Li, L., Abu Al-Soud, W., Bergmark, L., Riber, Leise, Hansen, Lars Hestbjerg, Magid, Jakob & Sørensen, Søren Johannes, 2013, In: Current Microbiology. 67, 4, p. 423-430 8 p.

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

  2. Published

    Deletion of the topoisomerase III gene in the hyperthermophilic archaeon Sulfolobus islandicus results in slow growth and defects in cell cycle control

    Li, X., Guo, L., Deng, Ling, Feng, D., Ren, Y., Chu, Y., She, Q. & Huang, L., 2011, In: Journal of Genetics and Genomics. 38, 6, p. 253-9 7 p.

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

  3. 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

  4. 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

  5. Published

    The microbiome of captive hamadryas baboons

    Li, Xuan Ji, Trivedi, Urvish, Brejnrod, A. D., Vestergaard, G. A., Mortensen, M. S., Bertelsen, Mads Frost & Sørensen, Søren Johannes, 2020, In: BMC Animal Microbiome. 2, 10 p., 25.

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

  6. 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

  7. Published

    The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition

    Li, Xuan Ji, Stokholm, Jakob, Brejnrod, A., Vestergaard, G. A., Russel, J., Trivedi, Urvish, Thorsen, Jonathan Jan Ilve, Gupta, S., Hjelmsø, M. H., Shah, S. A., Rasmussen, Morten Arendt, Bisgaard, H. & Sørensen, Søren Johannes, 2021, In: Cell Host & Microbe. 29, 6, p. 975–987.e4 17 p.

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

  8. Published

    Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults

    Li, Xuan Ji, Brejnrod, A., Thorsen, J., Zachariasen, Trine, Trivedi, Urvish, Russel, J., Vestergaard, G. A., Stokholm, Jakob, Rasmussen, Morten Arendt & Sørensen, Søren Johannes, 2023, In: Nature Communications. 14, 1, 16 p., 8526.

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

  9. 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

  10. Published

    Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs

    Li, Xuan Ji, Rensing, C., Vestergaard, G., Arumugam, Mani, Nesme, Joseph, Gupta, S., Brejnrod, A. D. & Sørensen, Søren Johannes, 2022, In: Environment International. 158, 10 p., 106899.

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

  11. Published

    Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

    Li, Xuan Ji, Brejnrod, A., Trivedi, Urvish, Russel, J., Thorsen, J., Shah, S. A., Vestergaard, G. A., Rasmussen, Morten Arendt, Nesme, Joseph, Bisgaard, H., Stokholm, Jakob & Sørensen, Søren Johannes, 2024, In: Microbiome. 12, 1, 18 p., 87.

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

  12. Published

    The DNA methylome of human peripheral blood mononuclear cells

    Li, Y., Zhu, J., Tian, G., Li, N., Li, Q., Ye, M., Zheng, H., Yu, J., Wu, H., Sun, J., Zhang, H., Chen, Q., Luo, R., Chen, M., He, Y., Jin, X., Zhang, Q., Yu, C., Zhou, G., Sun, J. & 17 others, Huang, Y., Zheng, H., Cao, H., Zhou, X., Guo, S., Hu, X., Li, X., Kristiansen, Karsten, Bolund, L., Xu, J., Wang, W., Yang, H., Wang, J., Li, R., Beck, S., Wang, J. & Zhang, X., 1 Jan 2010, In: PLoS - Biology. 8, 11, p. e1000533-e1000533

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

  13. Published

    Antimicrobial Activity of Metals and Metalloids

    Li, Y. P., Fekih, I. B., Fru, E. C., Moraleda-Munoz, A., Li, Xuan Ji, Rosen, B. P., Yoshinaga, M. & Rensing, C., 2021, In: Annual Review of Microbiology. 75, 23 p., 9.

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

  14. 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

  15. Published

    CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties

    Lillestøl, R. K., Shah, S. A., Brügger, K., Redder, P., Phan, Safir Hien, Christiansen, Jan & Garrett, Roger Antony, 2009, In: Molecular Microbiology. 72, 1, p. 259-272

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

  16. Published

    Up-scaling of water use efficiency from leaf to canopy as based on leaf gas exchange relationships and the modeled in-canopy light distribution

    Linderson, M., Mikkelsen, T. N., Ibrom, A., Lindroth, A., Ro-Poulsen, Helge & Pilegaard, K., 2012, In: Agricultural and Forest Meteorology. 152, p. 201-211 11 p.

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

  17. Published

    Interplay of Bacterial Interactions and Spatial Organisation in Multispecies Biofilms

    Liu, W., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

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

  18. 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

  19. 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

  20. 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

  21. Published

    Low-abundant species facilitates specific spatial organization that promotes multispecies biofilm formation

    Liu, W., Russel, J., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Burmølle, Mette & Sørensen, Søren Johannes, 2017, In: Environmental Microbiology. 19, 7, p. 2893-2905 13 p.

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

  22. Published

    Draft genome sequence of Burkholderia sordidicola S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic

    Lladó, S., Xu, Z., Sørensen, Søren Johannes & Baldrian, P., 2014, In: Genome Announcements. 2, 4, 2 p., e00810-14.

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

  23. Published

    Changes in the flora of soil fungi following oil waste application

    Llanos, C. & Kjøller, Annelise Helene, 1976, In: Oikos. 27, 3, p. 377-382 6 p.

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

  24. Published

    Proportionally more deleterious genetic variation in European than in African populations

    Lohmueller, K. E., Indap, A. R., Schmidt, S., Boyko, A. R., Hernandez, R. D., Hubisz, M. J., Sninsky, J. J., White, T. J., Sunyaev, S. R., Nielsen, Rasmus, Clark, A. G. & Bustamante, C. D., 2008, In: Nature. 451, 7181, p. 994-7 3 p.

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

  25. Published

    High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

    Lorenzen, Eline, Arctander, P. & Siegismund, Hans Redlef, 2008, In: Molecular Ecology. 17, 12, p. 2812-2824 12 p.

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

  26. Published

    Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression

    Lorenzen, Eline, Simonsen, Bo Thisted, Kat, P. W., Arctander, P. & Siegismund, Hans Redlef, 2006, In: Molecular Ecology. 15, 12, p. 3787-99 12 p.

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

  27. Published

    Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant's gazelles

    Lorenzen, Eline, Arctander, P. & Siegismund, Hans Redlef, 2008, In: Conservation Genetics. 9, 3, p. 593-601

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

  28. Published

    Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob)

    Lorenzen, E. D., De Neergaard, R., Arctander, P. & Siegismund, Hans Redlef, 2007, In: Molecular Ecology. 16, 15, p. 3241-52 11 p.

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

  29. 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

  30. 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

  31. Published

    Beringian paleoecology inferred from permafrost-preserved fungal DNA

    Lydolph, M. C., Jacobsen, J., Arctander, P., Gilbert, M Thomas P, Gilichinsky, D. A., Hansen, Anders Johannes, Willerslev, Eske & Lange, L., 2005, In: Applied and Environmental Microbiology. 71, 2, p. 1012-7 5 p.

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

  32. 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

  33. 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

  34. Published

    Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea

    Maccario, Lorrie, Silva, A. F., Nesme, Joseph, Amador Hierro, Cristina Isabel, Sørensen, Søren Johannes, Cooper, V. S. & Røder, Henriette Lyng, 2023, In: Microbiology resource announcements. 12, 12, 4 p.

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

  35. 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

  36. Published

    Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

    Macedo, G., Olesen, Asmus Kalckar, Maccario, Lorrie, Leal, L. H., v. d. Maas, P., Heederik, D., Mevius, D., Sørensen, Søren Johannes & Schmitt, H., 2022, In: Environmental Science & Technology. 56, 16, p. 11398-11408 11 p.

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

  37. 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

  38. Published

    A spatiotemporal view of plasmid loss in biofilms and planktonic cultures: [plus] Erratum

    Madsen, Jonas Stenløkke, Burmølle, Mette & Sørensen, Søren Johannes, 2013, In: Biotechnology and Bioengineering (Print). 110, 12, p. 3071-3074 4 p.

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

  39. 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

  40. 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

  41. Published

    When it makes sense to socialize whilst being on the move: A small EAL-domain containing protein, encoded on natural biofilm-promoting plasmids, triggers motility

    Madsen, Jonas Stenløkke, Riber, Leise, Burmølle, Mette, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2012.

    Research output: Contribution to conference › Poster › Research

  42. 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

  43. Published

    The interconnection between biofilm formation and horizontal gene transfer

    Madsen, Jonas Stenløkke, Burmølle, Mette, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2012, In: F E M S Immunology and Medical Microbiology. 65, 2, p. 183-195 13 p.

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

  44. 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

  45. Published

    Characterization of pIC13_78, a biofilm enabling plasmid

    Madsen, Jonas Stenløkke, Norman, A., Burmølle, Mette, Hansen, Lars Hestbjerg & Sørensen, Søren Johannes, 2011.

    Research output: Contribution to conference › Poster › Research

  46. Published

    Horizontal Transfer of Cyclic di-GMP Associated Genes: Theoretical Underpinnings and Future Perspectives

    Madsen, Jonas Stenløkke, 2020, Microbial Cyclic Di-Nucleotide Signaling. Chou, S-H., Guiliani, N., Lee, V. T. & Römling, U. (eds.). Springer, p. 641-652 12 p.

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

  47. Published

    Sociomicrobiology: Bacterial Interactions and Biofilm Formation

    Madsen, Jonas Stenløkke, 2014, Department of Biology, Faculty of Science, University of Copenhagen. 165 p.

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

  48. Published

    Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer

    Mahendra, C., Christie, K. A., Osuna, B. A., Pinilla Redondo, Rafael, Kleinstiver, B. P. & Bondy-Denomy, J., 2020, In: Nature Microbiology. 5, 4, p. 620-629 10 p.

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

  49. Published

    Investigation of the relationship between lactococcal host cell wall polysaccharide genotype and 936 phage receptor binding protein phylogeny

    Mahony, J., Kot, Witold, Murphy, J., Ainsworth, S., Neve, H., Hansen, Lars Hestbjerg, Heller, K. J., Sørensen, Søren Johannes, Hammer, K., Cambillau, C., Vogensen, Finn Kvist & Sinderen, D. V., 2013, In: Applied and Environmental Microbiology. 79, 14, p. 4385-4392 8 p.

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

  50. Published

    Influence of sewage sludge stabilization method on microbial community and the abundance of antibiotic resistance genes

    Major, N., Jechalke, S., Nesme, Joseph, Goreta Ban, S., Černe, M., Sørensen, Søren Johannes, Ban, D., Grosch, R., Schikora, A. & Schierstaedt, J., 2022, In: Waste Management. 154, p. 126-135 10 p.

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

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