Microbiology

Research output

Research output per year 1973 2007 2008 2009 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025

• 790 Journal article
• 40 Ph.D. thesis
• 33 Review
• 30 Book chapter
• 94 More
  • 28 Poster
  • 20 Conference abstract for conference
  • 9 Letter
  • 5 Compendium/lecture notes
  • 5 Report chapter
  • 4 Article in proceedings
  • 4 Conference abstract in journal
  • 3 Book
  • 3 Conference abstract in proceedings
  • 3 Comment/debate
  • 2 Report
  • 2 Conference article
  • 2 Working paper
  • 1 Encyclopedia chapter
  • 1 Memorandum
  • 1 Other contribution
  • 1 Preprint

Research output per year

Research output per year

Search results

• 2025

  A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus)

  Kliver, S., Kovacic, I., Mak, S., Sinding, M-H. S., Stagegaard, J., Petersen, B., Nesme, J. & Gilbert, M. T. P., 2025, In: The Journal of Heredity. 116, 1, p. 78-87 10 p.

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

• Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation

  Vaidya, S., Saha, D., Rode, D. K. H., Torrens, G., Hansen, M. F., Singh, P. K., Jelli, E., Nosho, K., Jeckel, H., Göttig, S., Cava, F. & Drescher, K., 2025, In: Nature Microbiology. 10, p. 144-157 14 p.

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

  Open Access

  File
  4 Downloads (Pure)

• Enzymatic exposure impacts microbial diversity and reduces biovolume of reverse osmosis membrane-associated biofilms

  Khani, M., Kiesewalter, H. T., Hansen, M. F., Ronin, D., Nesme, J., Rasekh, B., Nosrati, M. & Burmølle, M., 2025, In: Chemical Engineering Journal. 507, 14 p., 160186.

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

  Open Access

  File

• Extreme smells—microbial production of volatile organic compounds at the limits of life

  Salinas-garcía, M. Á., Fernbach, J., Rinnan, R. & Priemé, A., 2025, In: FEMS Microbiology Reviews. 49, 16 p., fuaf004.

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

  Open Access

  File

• Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues

  Matos, L., Maccarrio, L., Chung, A. P., Proença, D. N., Sørensen, S., Morais, P. V. & Francisco, R., 2025, In: International Journal of Systematic and Evolutionary Microbiology. 75, 1, 13 p., 006660.

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

• Infant Gut Microbiota and Childhood Blood Pressure: Prospective Associations and the Modifying Role of Breastfeeding

  Liu, T., Stokholm, J., Zhang, M., Vinding, R., Sørensen, S. J., Zhao, N. & Mueller, N. T., 2025, (E-pub ahead of print) In: Journal of the American Heart Association. e037447.

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

  Open Access

• Reconciling the role of mineral surfaces for bacterial evolution: Importance of minerals in the dissemination of antibiotic resistance

  Hendiani, S., Carbajo, C., Caicedo, P. N. A., Verma, T., Hansen, M. F., Agbaje, O. B. A., Mulec, I. M., Burmølle, M. & Sand, K. K., 2025, In: Science of the Total Environment. 962, 16 p., 178301.

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

• The role of noncoding RNAs in bacterial immunity

  Mayo-Muñoz, D., Li, H., Mestre, M. R. & Pinilla-Redondo, R., 2025, In: Trends in Microbiology. 33, 2, p. 208-222 15 p.

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

• The role of the early-life gut microbiome in childhood asthma

  Boulund, U., Thorsen, J., Trivedi, U., Tranæs, K., Jiang, J., Shah, S. A. & Stokholm, J., 2025, In: Gut Microbes. 17, 1, 25 p., 2457489.

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

  Open Access

  File
• 2024

  A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

  Eisenhofer, R., Nesme, J., Santos-Bay, L., Koziol, A., Sørensen, S. J., Alberdi, A. & Aizpurua, O., 2024, In: Microbiology Spectrum. 12, 4, 14 p., e03590-23.

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

  Open Access

  File
  8 Citations (Scopus)

  27 Downloads (Pure)

• Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase-Cas1 fusion proteins

  Molina-Sánchez, M. D., Martínez-Abarca, F., Millán, V., Mestre, M. R., Stehantsev, P., Stetsenko, A., Guskov, A. & Toro, N., 2024, In: Nucleic Acids Research. 52, 22, p. 14229-14243 15 p.

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

  Open Access

  File
  2 Downloads (Pure)

• Antibiotic implant irrigation and deep infection: A retrospective study of 1508 patients undergoing breast reconstruction with implants

  Hemmingsen, M. N., Bennedsen, A. K., Kullab, R. B., Weltz, T. K., Ørholt, M., Norlin, C. B., Kalstrup, J., Bredgaard, R., Sørensen, S. J., Bjarnsholt, T., Hölmich, L. R., Damsgaard, T. E., Vester-Glowinski, P. & Herly, M., 2024, In: Plastic and Reconstructive Surgery. 154, 1, 9 p.

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

  Open Access

  File
  4 Citations (Scopus)

  16 Downloads (Pure)

• Artificially selected rhizosphere microbiota modify plant growth in a soil-independent and species-dependent way

  Jacquiod, S., Nesme, J., Ducourtieux, C., Pimet, E. & Blouin, M., 2024, (Accepted/In press) In: Plant and Soil.

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

• Bacteria isolated from Arctic soil crust and permafrost produce volatile sulfur and nitrogen compounds in vitro

  Roslund, K. E., Salinas García, M. A., Rinnan, R. & Bygum Risom, M., 2024, p. 42. 1 p.

  Research output: Contribution to conference › Conference abstract for conference › Research

  File

• Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages

  Parra, B., Lutz, V. T., Brøndsted, L., Carmona, J. L., Palomo, A., Nesme, J., Le, V. V. H., Smets, B. F. & Dechesne, A., 2024, In: Microbial Ecology. 87, 11 p., 85.

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

  Open Access

  File
  1 Citation (Scopus)

  5 Downloads (Pure)

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

  Li, X., Brejnrod, A., Trivedi, U., Russel, J., Thorsen, J., Shah, S. A., Vestergaard, G. A., Rasmussen, M. A., Nesme, J., Bisgaard, H., Stokholm, J. & Sørensen, S. J., 2024, In: Microbiome. 12, 1, 18 p., 87.

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

  Open Access

  File
  1 Citation (Scopus)

  20 Downloads (Pure)

• Crispr-Cas Repurposed: Defense and Counter-defense on Mobile Genetic Elements

  Camara, S., 2024, Department of Biology, Faculty of Science, University of Copenhagen. 186 p.

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

  File

• Cross-feeding während der Ausbreitung auf Oberflächen

  Kovács, Á. T. & Kiesewalter, H. T., 2024, In: BioSpektrum. 30, 1, p. 71 1 p.

  Research output: Contribution to journal › Comment/debate › Research › peer-review

• Deciphering the Key Players of the Bacterial Microbiota Associated with Aerial Crown Gall Tumors on Rhododendron: Insights into the Gallobiome

  Kuzmanović, N., Nesme, J., Wolf, J., Neumann-Schaal, M., Petersen, J., Fernandez-Gnecco, G., Spröer, C., Bunk, B., Overmann, J., Sørensen, S. J., Idczak, E. & Smalla, K., 2024, In: Phytobiomes Journal. 8, 3, p. 401-415 15 p.

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

  Open Access

  File
  1 Citation (Scopus)

  3 Downloads (Pure)

• Early-life microbiome dynamics: Initial colonization, development and influencing factors

  Peng, S., 2024, Department of Biology, Faculty of Science, University of Copenhagen. 149 p.

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

  File

• Effects of temperature, chloride and perchlorate salt concentration on the metabolic activity of Deinococcus radiodurans

  Symeonidou, E., Jørgensen, U. G., Madsen, M. B. & Priemé, A., 2024, In: Extremophiles. 28, 3, 8 p., 34.

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

  Open Access

  File
  10 Downloads (Pure)

• Extreme smells: Volatile Organic Compounds from Greenlandic bacteria as biomarkers

  Salinas García, M. A., Roslund, K. E., Bygum Risom, M., Rinnan, R. & Priemé, A., 2024. 2 p.

  Research output: Contribution to conference › Conference abstract for conference › Research

  Open Access

  File
  1 Downloads (Pure)

• Fertilizer regime and cultivar affect barley growth and rhizobiome composition

  Kindtler, N. L., Sheikh, S., Richardy, J., Krogh, E., Maccario, L., Vestergård, M., da Fonseca, R. R., Ekelund, F. & Laursen, K. H., 2024, In: Applied Soil Ecology. 198, 13 p., 105384.

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

  Open Access

  File
  17 Downloads (Pure)

• Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study

  Røder, H. L., Christidi, E., Amador, C. I., Music, S., Olesen, A. K., Svensson, B., Madsen, J. S., Herschend, J., Kreft, J-U. & Burmølle, M., 2024, In: Applied and Environmental Microbiology. 90, 1, 15 p., e01510-23.

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

  Open Access

• Genome Insights into Beneficial Microbial Strains Composing SIMBA Microbial Consortia Applied as Biofertilizers for Maize, Wheat and Tomato

  Cangioli, L., Tabacchioni, S., Visca, A., Fiore, A., Aprea, G., Ambrosino, P., Ercole, E., Sørensen, S., Mengoni, A. & Bevivino, A., 2024, In: Microorganisms. 12, 12, 13 p., 2562.

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

  Open Access

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  1 Downloads (Pure)

• Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater

  Yu, Z., Wang, Q., Pinilla-Redondo, R., Madsen, J. S., Clasen, K. A. D., Ananbeh, H., Olesen, A. K., Gong, Z., Yang, N., Dechesne, A., Smets, B., Nesme, J. & Sørensen, S. J., 2024, In: Ecotoxicology and Environmental Safety. 271, 12 p., 115971.

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

  Open Access

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  26 Downloads (Pure)

• Infantile colic is associated with development of later constipation and atopic disorders

  Stokholm, J., Thorsen, J., Schoos, A-M. M., Rasmussen, M. A., Brandt, S., Sørensen, S. J., Vahman, N., Chawes, B. & Bønnelykke, K., 2024, In: Allergy: European Journal of Allergy and Clinical Immunology. 79, 12, p. 3360–3372 13 p.

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

  Open Access

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• Inhibitors of bacterial immune systems: discovery, mechanisms and applications

  Mayo-Muñoz, D., Pinilla-Redondo, R., Camara-Wilpert, S., Birkholz, N. & Fineran, P. C., 2024, In: Nature Reviews Genetics. 25, 4, p. 237-254 18 p.

  Research output: Contribution to journal › Review › Research › peer-review
  18 Citations (Scopus)

• Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

  Yu, Z., He, W., Klincke, F., Madsen, J. S., Kot, W., Hansen, L. H., Quintela-Baluja, M., Balboa, S., Dechesne, A., Smets, B., Nesme, J. & Sørensen, S. J., 2024, In: Environment International. 183, 12 p., 108351.

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

  Open Access

  File
  4 Citations (Scopus)

  35 Downloads (Pure)

• Insights into the ecology of the infant gut plasmidome

  He, W., Russel, J., Klincke, F., Nesme, J. & Sørensen, S. J., 2024, In: Nature Communications. 15, 1, 13 p., 6924.

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

  Open Access

  File
  2 Citations (Scopus)

  4 Downloads (Pure)

• Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study

  Yang, Q. E., Ma, X., Zeng, L., Wang, Q., Li, M., Teng, L., He, M., Liu, C., Zhao, M., Wang, M., Hui, D., Madsen, J. S., Liao, H., Walsh, T. R. & Zhou, S., 2024, In: The Lancet Microbe. 5, 1, p. e13-e23 11 p.

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

  Open Access

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  25 Citations (Scopus)

  20 Downloads (Pure)

• Interspecies interactions in dairy biofilms drive community structure and response against cleaning and disinfection

  Sadiq, F. A., De Reu, K., Yang, N., Burmølle, M. & Heyndrickx, M., 2024, In: Biofilm. 7, 13 p., 100195.

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

  Open Access

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  2 Citations (Scopus)

  29 Downloads (Pure)

• Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth

  Yang, N., Røder, H. L., Wicaksono, W. A., Wassermann, B., Russel, J., Li, X., Nesme, J., Berg, G., Sørensen, S. J. & Burmølle, M., 2024, In: The ISME Journal. 18, 1, 15 p.

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

  Open Access

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  4 Citations (Scopus)

  37 Downloads (Pure)

• L-asparaginase-driven antibiosis in Pseudomonas fluorescens EK007: A promising biocontrol strategy against fire blight

  Habibi, R., Zibaee, I., Talebi, R., Behravan, J., Tarighi, S., Brejnrod, A., Kjøller, A. H., Sørensen, S. J. & Madsen, J. S., 2024, In: International Journal of Biological Macromolecules. 281, Part 2, 11 p., 136402.

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

• Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant–microorganism feedback in the rhizosphere

  Behr, J. H., Kuhl-Nagel, T., Sommermann, L., Moradtalab, N., Chowdhury, S. P., Schloter, M., Windisch, S., Schellenberg, I., Maccario, L., Sørensen, S. J., Rothballer, M., Geistlinger, J., Smalla, K., Ludewig, U., Neumann, G., Grosch, R. & Babin, D., 2024, In: FEMS Microbiology Ecology. 100, 2, 18 p., fiae003.

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

  Open Access

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  4 Citations (Scopus)

  19 Downloads (Pure)

• MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies

  Zachariasen, T., Russel, J., Petersen, C., Vestergaard, G. A., Shah, S., Atienza Lopez, P., Passali, M., Turvey, S. E., Sørensen, S. J., Lund, O., Stokholm, J., Brejnrod, A. & Thorsen, J., 2024, In: Nature Communications. 15, 1, 10 p., 5734.

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

  Open Access

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  5 Downloads (Pure)

• Microbial landscapes in Trinervitermes trinervoides termite colonies are affected by mound compartments and soil properties but not by symbiotic Podaxis fungi

  Bodawatta, K. H., Maccario, L., Peereboom, N., Conlon, B. H., Li, G., Plaszkó, T., Vinagre-Izquierdo, C., Jønsson, K. A., Vesala, R. M., de Beer, Z. W., Priemé, A. & Poulsen, M., 2024, In: Science of the Total Environment. 957, 13 p., 177015.

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

  Open Access

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  2 Downloads (Pure)

• Modelling soil prokaryotic traits across environments with the trait sequence database ampliconTraits and the R package MicEnvMod

  Donhauser, J., Doménech-Pascual, A., Han, X., Jordaan, K., Ramond, J. B., Frossard, A., Romaní, A. M. & Priemé, A., 2024, In: Ecological Informatics. 83, 13 p., 102817.

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

  Open Access

  File
  1 Citation (Scopus)

  4 Downloads (Pure)

• Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly

  Tao, K., Jensen, I. T., Zhang, S., Villa-Rodríguez, E., Blahovska, Z., Salomonsen, C. L., Martyn, A., Björgvinsdóttir, Þ. N., Kelly, S., Janss, L., Glasius, M., Waagepetersen, R. & Radutoiu, S., 2024, In: Nature Communications. 15, 1, 15 p., 3436.

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

  Open Access

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  1 Citation (Scopus)

  7 Downloads (Pure)

• No association between the early-life gut microbiota and childhood body mass index and body composition

  Poulsen, C. E., Vinding, R., Rasmussen, M. A., Shah, S., Trivedi, U., Rodriguez, C. L., Widdowson, M. L., Jiang, J., Poulsen, C. S., Eliasen, A., Chawes, B., Bønnelykke, K., Hansen, C. H. F., Sørensen, S. J., Thorsen, J. & Stokholm, J., 2024, (Accepted/In press) In: Med.

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

• Optimizing cleaning strategies for biofouling in reverse osmosis membrane systems: A comparative study using a self-formed instrument

  Khani, M., Hansen, M. F., Rasekh, B., Nosrati, M., Burmølle, M., Ghasemipanah, K. & Zamir, S. M., 2024, In: Journal of Industrial and Engineering Chemistry. 132, p. 448-460 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  5 Citations (Scopus)

• Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer

  Verma, T., Hendiani, S., Carbajo, C., Andersen, S. B., Hammarlund, E. U., Burmølle, M. & Sand, K. K., 2024, In: Frontiers in Microbiology. 15, 11 p., 1449094.

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

  Open Access

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  1 Citation (Scopus)

• Retron-Eco1 assembles NAD⁺-hydrolyzing filaments that provide immunity against bacteriophages

  Carabias, A., Camara-Wilpert, S., Mestre, M. R., Lopéz-Méndez, B., Hendriks, I. A., Zhao, R., Pape, T., Fuglsang, A., Luk, S. H. C., Nielsen, M. L., Pinilla-Redondo, R. & Montoya, G., 2024, In: Molecular Cell. 84, 11, p. 2185-2202.e12 31 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  10 Citations (Scopus)

• Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

  Cyriaque, V., Ibarra-Chávez, R., Kuchina, A., Seelig, G., Nesme, J. & Madsen, J. S., 2024, In: Nature Communications. 15, 1, 10 p., 5853.

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

  Open Access

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  2 Citations (Scopus)

  5 Downloads (Pure)

• Soil organic matter properties drive microbial enzyme activities and greenhouse gas fluxes along an elevational gradient

  Han, X., Doménech-Pascual, A., Pere Casas-Ruiz, J., Donhauser, J., Jordaan, K., Ramond, J. B., Priemé, A., Romaní, A. M. & Frossard, A., 2024, In: Geoderma. 449, 14 p., 116993.

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

  Open Access

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  1 Citation (Scopus)

  4 Downloads (Pure)

• Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference

  Čepaitė, R., Klein, N., Mikšys, A., Camara-Wilpert, S., Ragožius, V., Benz, F., Skorupskaitė, A., Becker, H., Žvejytė, G., Steube, N., Hochberg, G. K. A., Randau, L., Pinilla-Redondo, R., Malinauskaitė, L. & Pausch, P., 2024, In: Nature Communications. 15, 1, 18 p., 9306.

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

  Open Access

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  2 Citations (Scopus)

  1 Downloads (Pure)

• Supramolecular assemblies in bacterial immunity: an emerging paradigm

  Payne, L., Jackson, S. & Pinilla-Redondo, R., 2024, In: Trends in Microbiology. 32, 9, p. 828-831 4 p.

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

  Open Access

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  4 Citations (Scopus)

  3 Downloads (Pure)

• The feather moss Hylocomium splendens affects the transcriptional profile of a symbiotic cyanobacterium in relation to acquisition and turnover of key nutrients

  Alvarenga, D. O., Priemé, A. & Rousk, K., 2024, In: Microbial Ecology. 87, 11 p., 49.

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

  Open Access

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  1 Citation (Scopus)

  17 Downloads (Pure)

• The Role of Matrix Components in Multispecies Coexistence in Biofilms

  Hansen, M. F., Ronin, D., Kiesewalter, H. T., Amador Hierro, C. I. & Burmølle, M., 2024, Biofilm Matrix. Springer, p. 187-214 28 p. (Springer Series on Biofilms, Vol. 13).

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

  File

• The use of biomimetic surfaces to reduce single- and dual-species biofilms of Escherichia coli and Pseudomonas putida

  Teixeira-Santos, R., Azevedo, A., Romeu, M. J., Amador, C. I., Gomes, L. C., Whitehead, K. A., Sjollema, J., Burmølle, M. & Mergulhão, F. J., 2024, In: Biofilm. 7, 13 p., 100185.

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

  Open Access

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  1 Citation (Scopus)

  9 Downloads (Pure)