Publications

Supported by DNRF 137

 

2024

Bech PK, Jarmusch SA, Rasmussen JA, Limborg MT, Gram L, Henriksen NNSE 2024. Succession of microbial community composition and secondary metabolism during marine biofilm development. ISME Communication. 4:ycae006 https://doi.org/10.1093/ismeco/ycae006

Buijs Y, Geers AU, Nita I, Strube ML, Bentzon-Tilia M 2024. SecMet-FISH: Labeling, visualization, and enumeration of secondary metabolite producing microorganisms. FEMS Microbiology Ecology. 100:fiae038 https://doi.org/10.1093/femsec/fiae038

Clemmensen SE, Cowled MS, Kromphardt KJK, Frisvad JC, Larsen TO, Frandsen RJN 2024. The Role and Fate of Patulin in Apple-Associated Fungal-Fungal Interactions. Fungal Ecology. 69:101341 https://doi.org/10.1016/j.funeco.2024.101341

Cowled MS, Phippen CB, Kromphardt KJK, Clemmensen SE, Frandsen RJM, Frisvad JC, Larsen TO 2024. Unveiling the Microbial Diversity and Associated Secondary Metabolism on Black ApplesApplied and Environmental Microbiology  https://doi.org/10.1101/2023.11.02.565319

Hansen ML,  Denes Z,  Jarmusch SA,  Wibowo M,  Lozano-Andrade CN,  Kovacs AT,  Strube ML,  Andersen AJC,  Jelsbak L 2024. Resistance towards and biotransformation of Pseudomonas-produced secondary metabolites during community invasion. ISME Journal https://www.biorxiv.org/content/10.1101/2023.06.20.545698v1

Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT 2024. Competition for iron shapes metabolic antagonism between Bacillus subtilis and PseudomonasISME Journal 18, 1-13 https://doi.org/10.1101/2023.06.12.544649

Maleckis M, Wibowo M, Gren T, Jarmusch SA, Sterndorff EB, Booth T, Henriksen NNSE, Whitford CM, Jiang X, Jørgensen TS, Ding L, Weber T 2024. Biosynthesis of the azoxy compound azodyrecin from Streptomyces mirabilis P8-A2ACS Chemical Biology. 19:641-653  https://doi.org/10.1021/acschembio.3c00632

Maleckis M, Wibowo M, Williams SE, Gotfredsen CH, Sigrist R, Souza LDO,  Cowled MS, Charusanti P, Gren T, Saha S, Moreira JMA, Weber T, Ding L 2024. Maramycin, a cytotoxic isoquinolinequinone terpenoid produced through heterologous expression of a bifunctional indole prenyltransferase /tryptophan indole-lyase in S. albidoflavus. ACS Chemical Biology https://doi.org/10.1021/acschembio.4c00121

Mahmoud M, Abboud MM, Maleckis M, Souza L, Moreira J, Weber T, Gotfredsen CH, Ding L 2024 Pepticinnamins N, O and P, cytotoxic non-ribosomal peptides from a Soil-Derived Streptomyces mirabilis P8-A2, Journal of Natural Products. 67:1075-1083 https://doi.org/10.26434/chemrxiv-2024-4gjgb

Nuhamunada M, Mohite OS, Phaneuf PV, Palsson B, Weber T 2024. BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasetsNucleic Acids Research, gkae314 https://doi.org/10.1093/nar/gkae314

Parra J, Jarmusch SA, Duncan K Multi-Omic analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems Environmental Microbiology

Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN,  Jarmusch SA,  Wibowo M,  Kjeldgaard B,  Surabhi S, Jautzus T, Phippen CBW,  Tyc O, Arentshorst M, Wang Y,  Garbeva P,  Larsen TO,  Ram AFJ,  van den Hondel CAM,  Maróti G,  Kovács ÁT  Enhanced niche colonisation and competition during bacterial adaptation to a fungusNature Communications.  https://doi.org/10.1101/2023.03.27.534400

Roager L, Athena-Vasileiadi D, Gram L, Sonnenschein EC 2024. Antagonistic activity of Phaeobacter piscinae against the emerging fish pathogen Vibrio crassostreae in aquaculture feed algae. Applied and Environmental Microbiology 90:e01439-23 https://doi.org/10.1128/aem.01439-23

Sørensen MB, Møller JK, Strube ML, Gotfredsen CH 2024. Designing optimal experiments in metabolomics. Metabolomics

2023

Bech PK, Zhang SD, Henriksen NNSE, Bentzon-Tilia M, Strube ML, Gram L 2023 The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater. npj Biofilms and Microbiomes 9, 12 https://doi.org/10.1038/s41522-023-00379-3

Blin K, Shaw S, Medema MH, Weber T 2023. The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and moreNucleic Acid Research. 52:D586-D589 https://doi.org/10.1093/nar/gkad984

Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T 2023. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acid Research. 51. W46-W50 https://doi.org/10.1093/nar/gkad344

Bradley SA, Lehka BJ, Hansson FG, Adhikari KB, Rago D, Rubaszka P, Haidar AK, Chen L, Hansen LG, Gudich O, Giannakou K, Lengger B, Gill RT, Nakamura Y, Dugé de Bernonville T, Koudounas K, Romero-Suarez D, Ding L, Qiao Y, Frimurer TM, Petersen AA, Beasseau S, Kumar S, Gautron N, Melin C, Marc J, Jeanneau R, O’Connor SE, Courdavault V, Keasling JD, Zhang J, Jensen MK 2023. Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast. : Nature Chemical Biology. 19:1551-1560

Buenrostro-Munoz, Jarmusch SA, Souza V, Martinez-Cardenas A, Fjardo-Hernandez CA, Yeverino IR, Eguiarte LE, Figueroa M 2023. Metabolomic Diversity in Microbial Mats Under Different Environmental Conditions: A Tool to Test Microbial Ecosystem Chemical Change. Chemistry and Biodiversity. e202300829  https://doi.org/10.1002/cbdv.202300829

Droumpali A, Liu Y, Ferrer-Florensa X, Sternberg C, Dimaki M, Andersen AJCStrube ML, Kempen PJ, Gram L, Taboryski R 2023. Biosynthesis Enhancement of Tropodithietic Acid (TDA) Antibacterial Compound through Biofilm Formation by Marine Bacteria Phaeobacter inhibens on Micro-Structured Polymer Surfaces RCS Advances. 13, 33159. https://doi.org/10.1039/d3ra05407a

Gallegos-Monterrosa R, Kovács ÁT 2023. Phenotypic plasticity: The role of a phosphatase family Rap in the genetic regulation of Bacilli. Molecular Microbiology. 120, 20-31 https://doi.org/10.1111/mmi.15060

Garcias-Bonet N, Roik A, Dungan A, Villela H, Garcia F, Quigley K, Sweet M, Berg G, Hoj L, Bourne DG, Ushijima B, Sogin M, Gram L, Duarte G, Hirt H, Smalla K, Rosado A, Carvalho S, Vega-Thurber R, Ziegler M, Tierney B, Mason CE, Blackall L, van Oppen MJH, Voolstra CR, Peixoto R 2023. Horizon scanning the application of probiotics for wildlife. Trends in Microbiology. 32:525-269 https://doi.org/10.1016/j.tim.2023.08.012

Geers AU, Strube ML, Bentzon-Tilia M 2023. Small spatial scale drivers of secondary metabolite biosynthetic diversity in environmental microbiomes. mSystems. 8: e00548-23 2. https://doi.org/10.1128/msystems.00724-22

Hu G, Wang Y,  Blake C, Nordgaard M, Liu X, Wang B, Kovács ÁT 2023. Parallel genetic adaptation of Bacillus subtilis to different plant species. Microbial Genomics 9, 14. https://doi.org/10.1099/mgen.0.001064

Hu G, Wang Y, Liu X, Strube ML, Wang B, Kovács AT 2023/ Species and condition dependent mutational spectrum in experimentally evolved biofilms of BacillimSystems. 8:e00548-23 https://doi.org/10.1128/msystems.00548-23 

Khatri S, Sazinas P, Strube M, Ding L, Dubey S, Shivay YS, Sharma S, Jelsbak L 2023. Pseudomonas is a key player in conferring disease suppressiveness in organic farmingPlant and Soil. https://doi.org/10.1007/s11104-023-05927-6

Lindqvist LL, Jarmusch SA, Sonnenschein EC, Strube ML, Kim J, Nielsen MW, Kempen PJ, Schoof EM, Zhang SD, Gram L 2023. Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae. mSphere 8, 1, e00517-22. https://journals.asm.org/doi/10.1128/msphere.00517-22

Lozano-Andrade CN, Nogueira CG, Wibowo M, Kovács ÁT 2023. Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. ISME Communications. 3:110 https://doi.org/10.1038/s43705-023-00318-5

Lyng M, Kovács ÁT 2023. Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions. Trends in Microbiology 31, 845-857. https://doi.org/10.1016/j.tim.2023.02.003

Murphy R, Strube ML 2023. RibDif2: Expanding amplicon analysis to full genomes. Bioinformatics Advances. 3:vbad11 https://doi.org/10.1093/bioadv/vbad111 

Shaaban M, Abdel-Razek AS, Previtali V, Clausen MH, Gotfredsen CH, Laatsch H, Ding L 2023. Sulochrins and alkaloids from a fennel endophyte Aspergillus sp. FVL2, Natural Product Research. 37, 1310-1320. https://doi.org/10.1080/14786419.2021.2005054

Su J, Wang Y, Bai M, Peng T, Li H, Xu HJ, Guo G, Bai H, Rong N, Sahu SK, He H, Liang X, Jin C, Liu W, Strube ML, Gram L, Li Y, Wang E, Liu H, Wu H 2023. Soil conditions and plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata ‘Chachi’Microbiome. 11, 61. https://doi.org/10.1186/s40168-023-01504-2

Sun X, Xie J, Zheng D, Wang W, Xia R, Wang W, Xun W, Huang Q, Zhang R, Kovács ÁT, Xu Z, Qirong S 2023. Metabolic interactions affect the biomass of synthetic bacterial biofilm communities. : mSystems. 8:e01045-23 https://doi.org/10.1128/msystems.01045-23.

Yang Z, Strøbech E, Qiao Y, Konakall NG, Harris P, Peschel G, Agler-Rosenbaum M, Weber T, Andreasson E, Ding L 2023 Streptomyces alleviate abiotic stress in plant by producing pteridic acidsNature Communications. 14:article #7398 https://doi.org/10.1038/s41467-023-43177-3 

Xu A, Nielsen LJD, Song L, Maróti G, Strube ML, Kovács ÁT 2023. Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach. bioRχiv. https://doi.org/10.1101/2023.05.28.542609

2022

Christiansen JV, Isbrandt T, Asferg R, Jarmusch SA, Larsen TO, Frisvad JC 2022. Phoenicin Switch: Discovering the Trigger for Radical Phoenicin Production in Multiple Wild-Type Penicillium Species. Applied and Environmental Microbiology. 88, 16. https://doi.org/10.1128/aem.00302-22

Clemmensen SE, Kromphardt KJK, Frandsen RJN 2022. Marker-free CRISPR-Cas9 based genetic engineering of the phytopathogenic fungus, Penicillium expansum. Fungal Genetics and Biology. 160, 103689. https://doi.org/10.1016/j.fgb.2022.103689

Geers AU, Buijs Y,  Strube ML, Gram L, Bentzon-Tilia M 2022. The natural product biosynthesis potential of the microbiomes of Earth – bioprospecting for novel anti-microbial agents in the meta-omics era. Computational and Structural Biotechnology Journal. 20, 343-352. https://doi.org/10.1016/j.csbj.2021.12.024

Hansen ML, Wibowo M, Jarmusch SA, Larsen TO, Jelsbak L 2022. Sequential interspecies interactions affect production of antimicrobial secondary metabolites in Pseudomonas protegens DTU9.1. ISME Journal. https://doi.org/10.1038/s41396-022-01322-8

Henriksen NNSE, Schostag MD, Balder SR, Bech PK, Strube ML, Sonnenschein E, Gram L 2022. The ability of Phaeobacter inhibens to produce tropodithietic acid influences the community dynamics of a microalgal microbiome. ISME Communicationshttps://doi.org/10.1038/s43705-022-00193-6

Henriksen NNSE, Lindqvist LL, Wibowo M, Sonnenschein EC, Bentzon-Tilia M, Gram L 2022. Role is in the eye of the beholder – the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae. FEMS Microbiology Review. 46(3) fuac007. https://doi.org/10.1093/femsre/fuac007

Jakab Á, Kovács F, Balla N, Tóth Z, Ragyák Á, Sajtos Z, Csillag K, Nagy-Köteles C, Nemes D,  Pócsi I, Majoros L, Kovács ÁT,  Kovács R 2022 Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans. Biomedicine & Pharmacotherapy. 152, 113220 https://doi.org/10.1016/j.biopha.2022.113220

Jautzus T, van Gestel J, Kovács ÁT 2022. Complex extracellular biology drives surface competition in Bacillus subtilis. ISME Journal. 16: 2320-2328. https://doi.org/10.1038/s41396-022-01279-8

Khatri S, Dubey S, Shivay YS, Jelsbak L, Sharma S 2022. Organic farming induces changes in bacterial community and disease suppressiveness against fungal phytopathogens. Applied Soil Ecology. 181, 104658. https://doi.org/10.1016/j.apsoil.2022.104658

Kjeldgaard B, Neves AR, Fonseca C,  Kovács ÁT, Domínguez-Cuevas P 2022. Quantitative high-throughput screening methods designed for identification of bacterial biocontrol strains with antifungal properties. Microbiology Spectrum. 10, 2, e01433-21. https://doi.org/10.1128/spectrum.01433-21

Lin Y, Xu X, Maróti G, Strube ML, Kovács ÁT 2022. Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes. npj Biofilms and Microbiomes. 8, 27. https://doi.org/10.1038/s41522-022-00292-1

Nordgaard M, Blake C, Maróti G, Strube ML, Kovács ÁT 2022. Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization. iScience. 25, 6, 104406. https://doi.org/10.1016/j.isci.2022.104406

Peixoto R, Voolstra CR, Sweet M, Duarte C, Carvalho S, Villela H, Lunshof JE, Gram L, Woodhams DC, Walter J, Roik A, Hentschel U, Vega Thurber R, Daisley B, Ushijima B, Daffonchio D,  Costa R, Keller-Costa T, Bowman J, Rosado AS, Reid G, Mason C, Walke JB, Thomas T, Berg G 2022. Harnessing the microbiome to prevent global biodiversity loss. Nature Microbiology. 7, 1726-1735.https://doi.org/10.1038/s41564-022-01173-1

Perini L, Gostincar C, Lilov M, Frisvad JC, Kostansek R, Nicoles M, Williamson C, Anesio, M., Zalar P, Gunde-Cimerman N 2022. Interactions of Fungi and Algae from the Greenland Ice Sheet. Environmental Microbiology. https://link.springer.com/article/10.1007/s00248-022-02033-5

Sanchez-Navarro R, Nuhamunada M, Mohite O, Wasmund K, Albertsen M, Gram L, Nielsen PH, Weber T, Singleton C 2022.  Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem. mSystems. 20, 7, 6. https://doi.org/10.1128/msystems.00632-22

Schostag MD,  Gobbi A,  Fini MN, Ellegaard-Jensen L, Aamand J, Hansen LH, Muff J, Albers CN 2022. Combining reverse osmosis and microbial degradation for remediation of drinking water contaminated with recalcitrant pesticide residue. Water Research. 216, 118352. https://doi.org/10.1016/j.watres.2022.118352

Shaaban M, Abdel-Razek AS, Previtali V, Hartvig CM, Gotfredsen CH, Laatsch H, Ding L 2022. Sulochrins and alkaloids from a fennel endophyte Aspergillus sp. FVL2. Natural Product Researchhttps://doi.org/10.1080/14786419.2021.2005054

Sun X, Xu Z, Xie J, Hesselberg-Thomsen V, Tan T, Zheng D, Strube ML, Dragoš A, Shen Q, Zhang R, Kovács ÁT 2022. Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME Journal. 16, 3, 774–787. https://doi.org/10.1038/s41396-021-01125-3

Terlouw BR, Blin K, Navarro-Muñoz JC,  Avalon N, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJJ, Reitz ZL, van Santen JA, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SAA, Augustijn HE, Avelar-Rivas JA, Avitia-Domínguez LA, Barona-Gomez F, Bernaldo-Agüero J, Bielinski VA, Biermann F,  Booth TJ, Carrion Bravo VJ, Castelo-Branco R, Chagas FO, Cruz-Morales P, Du C, Duncan KR, Gavriilidou A, Gayrard D, Gutiérrez-García K, Haslinger K, Helfrich EJN, van der Hooft JJJ, Jati AP, Kalkreuter E, Kalyvas N, Kang KB, Kautsar S, Kim W, Kunjapur A, Li YX, Lin GM, Loureiro C, Louwen JJR, Louwen NL, Lund G, Parra J, Philmus B, Pourmohsenin B, Pronk LJU, Rego A, Rex DAB, Robinson S, Rosas-Becerra LR, Roxborough ET, Schorn MA, Scobie DJ, Singh KS, Sokolova N, Tang X, Udwary D, Vigneshwari A, Vind K, Vromans SPJM, Waschulin V, Williams SE, Winter J, Witte TE, Xie H, Yang D, Yu J, Zdouc M, Zhong Z, Collemare J, Linington RG, Weber T, Medema MH 2022. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac1049

Tesdorpf JE, Geers AU,  Strube ML, Gram L, Bentzon-Tilia M 2022. Roseobacter Group Probiotics Exhibit Differential Killing of Fish Pathogenic Tenacibaculum Species. Applied and Environmental Microbiology. 88, 6. https://doi.org/10.1128/aem.02418-21

Wang X, Jarmusch SA, Frisvad JC, Larsen TO 2022. Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri. Natural Product Reviewshttps://doi.org/10.1039/D1NP00074H

Wang X, Serrano R, González-Menéndez V, Mackenzie TA, Ramos MC, Frisvad JC, Larsen TO 2022.  A Molecular Networking Based Discovery of Diketopiperazine Heterodimers and Aspergillicins from Aspergillus caelatus. Journal of Natural Products. 85, 1, 25-33. https://doi.org/10.1021/acs.jnatprod.1c00526 

Wang Y, Wang X,  Sun S, Jin C, Su J, Wei J, Luo X, Wen J, Wei T, Sahu SK, Zou H, Chen H, Zhang G, Liu X, Xu X, Gram L, Yang H, Wang E, Liu H 2022.  GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet. Nature Communications. 13, 5913. https://doi.org/10.1038/s41467-022-33238-4 

Zhang SD, Lindqvist LL, Isbrandt T, Borre I, Wibowo M, Wennekers Nielsen M, Ding L, Larsen TO, Gram L 2022. Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753. Applied and Environmental Microbiology. 88, 17. https://doi.org/10.1128/aem.01105-22 

2021

Ardalani H, Anam S, Kromphardt KJK, Staerk D, Kongstad KT 2021. Coupling microplate‐based antibacterial assay with liquid chromatography for high‐resolution growth inhibition profiling of crude extracts: validation and proof‐of‐concept study with Staphylococcus aureus. Molecules 26, 6. https://doi.org/10.3390/molecules26061550

Arnaouteli S, Bamford NC,  Stanley-Wall NR, Kovács ÁT 2021 Bacillus subtilis biofilm formation and social interactions. Nature Reviews Microbiology. 19. https://doi.org/10.1038/s41579-021-00540-9

Blin K,  Shaw S, Kautsar SA. Medema MH, Weber T 2021 The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. Nucleic Acids Research. 49. https://doi.org/10.1093/nar/gkaa978

Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, Weber T 2021. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Research. 49 https://doi.org/10.1093/nar/gkab335

Borre I, Sonnenschein EC.2021. Draft genome sequences of nine environmental bacterial isolates colonizing plastic. In: Microbiology Resource Announcements. 10, 11. https://doi.org/10.1128/MRA.01485-20

Buijs Y, Zhang S, Jørgensen KM, Isbrandt T, Larsen TO, Gram L 2021 Enhancement of antibiotic production by co-cultivation of two antibiotic producing marine Vibrionaceae strains. FEMS Microbiology Ecology 97. https://doi.org/10.1093/femsec/fiab041.

Ding L, Zhang  SD,  Haidar A.K.,  Bajimaya M,  Guo Y,  Larsen TO, Gram L 2021 Polycyclic tetramate macrolactams–a group of natural bioactive metallophores. Frontiers in Chemistry.  9: 772858. https://doi.org/10.3389/fchem.2021.772858

Dragoš A, Andersen AJC, Lozano-Andrade CN, Kempen PJ, Kovács ÁT, Strube ML 2021. Phages carry interbacterial weapons encoded by biosynthetic gene clusters. Current Biology. 31, 1-11. https://doi.org/10.1016/j.cub.2021.05.046

Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT 2021 Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME Journal. 15. https://doi.org/10.1038/s41396-020-00854-1

Eelderink-Chen Z, Bosman J, Sartor F, Dodd A, Kovács ÁT, Merrow M 2021 A circadian clock in a nonphotosynthetic prokaryote. Science Advances. 7. https://doi.org/10.1126/sciadv.abe2086

Hansen J, Melchiorsen J, Mateiu RV, Ciacotich N, Gram L, Sonnenschein EC 2021 Effect of polymer type on the colonization of plastic pellets by marine bacteria. FEMS Microbiology Letters. 368. https://doi.org/10.1093/femsle/fnab026

Hansen ML, He Z, Wibowo M, Jelsbak L  2021 A whole-cell biosensor for detection of 2,4-diacetylphloroglucinol (DAPG)-producing bacteria from grassland soil. Applied and Environmental Microbiology. 87, 3. https://doi.org/10.1128/AEM.01400-20

Jarmusch, SA, van der Hooft, JJJ, Dorrestein P, Jarmusch AK  2021 Advancements in Capturing and Mining Mass Spectrometry Data Are Transforming Natural Products Research. Natural Product Reports.38. https://doi.org/10.1039/D1NP00040C

Kautsar SA, Blin K, Shaw S, Weber T, Medema MH 2021 BiG-FAM: the biosynthetic gene cluster families database. Nucleic Acids Research. 49. https://doi.org/10.1093/nar/gkaa812

Kiesewalter HT, Lozano-Andrade CN, Wibowo M, Strube ML, Maróti G, Snyder D, Jørgensen TS, Larsen TO, Cooper VS, Weber T, Kovács ÁT 2021 Genomic and chemical diversity of Bacillus subtilis secondary metabolites against plant pathogenic fungi. mSystems. 6, 1. https://doi.org/10.1128/mSystems.00770-20

Lauritsen JG, Hansen ML, Bech PK, Jelsbak L, Gram L, Strube ML 2021 Identification and differentiation of Pseudomonas species in field samples using an rpoD amplicon sequencing methodology. mSystems. 6, 4. https://doi.org/10.1128/mSystems.00704-21

Li L, Wang H, Wang S, Xu Y, Liang H, Liu H, and Sonnenschein EC 2021The Draft Genome of the Centric Diatom Conticribra weissflogii (Coscinodiscophyceae, Ochrophyta). Protist. 172 (5-6): 125845 (1-6). https://doi.org/10.1016/j.protis.2021.125845

Lozano-Andrade CN, Strube ML, Kovács ÁT  2021 Complete Genome Sequences of Four Soil-Derived Isolates for Studying Synthetic Bacterial Community Assembly. Microbiology Resource Announcements. 10, 46. https://doi.org/10.1128/MRA.00848-21

Sonnenschein EC, Jiménez G, Castex M, Gram L 2021 The Roseobacter-group bacterium Phaeobacter as safe probiotic solution for aquaculture. Applied Environmental Microbiology. 87, 5. https://doi.org/10.1128/AEM.02581-20

Steinke K, Mohite OS, Weber T, Kovács ÁT 2021 Phylogenetic distribution of secondary metabolites in the Bacillus subtilis species complex. mSystems. 6, 2. https://doi.org/10.1128/mSystems.00057-21

Strube ML 2021 RibDif: can individual species be differentiated by 16S sequencing?. Bioinformatics Advances. 1, 1. https://doi.org/10.1093/bioadv/vbab020

Visagie CM, Frisvad JC, Visagie A, Houbraken, J, Seifert KA, Samson RA, Jacobs K 2021 A re-evaluation of Penicillium section Canescentia, including the description of five new species. Persoonia. 46. https://doi.org/10.3767/persoonia.2021.46.06

Wang X, Isbrand T, Christensen EØ, Melchiorsen J,  Larsen TO,  Zhang S-D, Gram L  2021 Identification and verification of the prodigiosin biosynthetic gene cluster (BGC) in Pseudoalteromonas rubra S4059. Microbiology Spectrum. 9, 2. https://doi.org/10.1128/Spectrum.01171-21

Wang X, Isbrandt T, Strube ML, Paulsen SS, Nielsen MW, Buijs Y, Schoof EM, Larsen TO, Gram L, Zhang SD 2021 Chitin degradation machinery and secondary metabolite profiles in the marine bacterium Pseudoalteromonas rubra S4059. Marine Drugs 19. https://doi.org/10.3390/md19020108

Wang X, Subko K, Kildgaard S, Frisvad JC and Larsen TO 2021 Mass Spectrometry-Based Network Analysis Reveals New Insights Into the Chemodiversity of 28 Species in Aspergillus section Flavi. Frontiers in Fungal Biology.  2: 719420 (1-13). https://doi.org/10.3389/ffunb.2021.719420

Wang Y, Shuilin L, Gai Y, Liu G, Jin T, Liu H, Gram L, Strube ML, Fan G, Sahu S, Liu S, Gan S, Xie ZZ, Kong LF, Zhang P, Liu X, Wang D 2021 Metagenomic analysis reveals community structure and their metabolic potential for nitrogen acquisition in the oligotrophic surface waters of the Indian Ocean. Frontiers Microbiology. 12. https://doi.org/10.3389/fmicb.2021.518865

Zhang SD, Isbrandt T, Lindqvist LL, Larsen TO, Gram L  2021 Holomycin, an Antibiotic Secondary Metabolite, Is Required for Biofilm Formation by the Native Producer Photobacterium galatheae S2753. Applied Environmental Microbiology. 87. https://doi.org/10.1128/AEM.00169-21

2020

Barret, K Jensen K, Meyer AS Frisvad JC, Lange L 2020 Fungal secretome profle categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium. Scientific Reports, 10. https://doi.org/10.1038/s41598-020-61907-1

Bech PK, Lysdal KL, Gram L, Bentzon-Tilia M, Strube ML 2020 Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity. mSystems, 5, 5. https://doi.org/10.1128/mSystems.00782-20

Buijs Y, Isbrandt T, Zhang SD, Larsen TO,  Gram L 2020. The Antibiotic Andrimid Produced by Vibrio coralliilyticus Increases Expression of Biosynthetic Gene Clusters and Antibiotic Production in Photobacterium galatheae. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.622055

Contesini FJ, Frandsen RJN, Damasio A 2020. Editorial: CAZymes in Biorefinery: From Genes to Application. Frontiers in Bioengineering and Biotechnology, .9. https://doi.org/10.3389/fbioe.2021.622817

Dittmann KK, Rasmussen BB, Melchiorsen J, Sonnenschein EC, Gram L, Bentzon-Tilia M 2020. Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens. Applied and Environmental Microbiology. 86, e00499-20. https://doi.org/10.1128/aem.00499-20

Frisvad JC, Isbrandt T, and Ostenfeld Larsen T 2020. Fungal Partially Reducing Polyketides and Related Natural Products From AspergillusPenicillium, and Talaromyces. Comprehensive Natural Products III: Chemistry and Biology, 1:313-332. https://doi.org/10.1016/B978-0-12-409547-2.14731-6

García CF, Kretschmer M, Lozano-Andrade CN, Schönleitner M, Dragoŝ A, Kovács ÁT, Lieleg O 2020. Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms. npj biofilms and microbiomes. 6. https://doi.org/10.1038/s41522-019-0111-8

Houbraken J, Kocsubé S, Visagie CM, Yilmaz N, Wang  X-C, Meijer M, Kraak B, Hubka V, Bensch K, Samson RA, Frisvad JC 2020.  Classification of AspergillusPenicilliumTalaromyces and related genera (Eurotiales): An overview of families, genera, subgenera, sections, series and species. Studies in Mycology,  95. https://doi.org/10.1016/j.simyco.2020.05.002

Khatri S, Sazinas P, Shivay YS, Sharma S, Jelsbak L 2020. Complete Genome Sequence of Pseudomonas sp. Strain SK, Isolated from Organic Wheat Rhizosphere. Microbiology Resource Announcements, 9, 26. https://doi.org/10.1128/MRA.00510-20

Kiesewalter HT, Lozano-Andrade CN, Maróti G, Snyder D, Jørgensen TS, Weber T, Kovács ÁT  2020. Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity. Microbiology Resource Announcements, 9, 2 https://doi.org/10.1128/mra.01406-19

Kiesewalter  HT, Lozano-Andrade CN, Strube, ML, Kovács ÁT 2020. Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities. Beilstein Journal of Organic Chemistry. 16:2983-2998. https://doi.org/10.3762/bjoc.16.248

Kjærbølling I,  Vesth TC, Frisvad JC, Nybo JL, Theobald S, Kildgaard S, Petersen TI, Kuo A, Sato A, Lyhne EK, Kogle ME, Wiebenga A, Kun  RS, Lubbers RJM, Mäkelä MR, Barry K, Chovatia M, Clum A, Daum C, Haridas S, He G, LaButti K, Lipzen A, Mondo S, Pangilinan J, Riley R, Salamov A, Simmons BA, Magnuson JK, Henrissat B, Mortensen UH, Larsen TO, de Vries RP, Grigoriev IV, Machida M, Baker SE, Andersen MR 2020. A comparative genomics study of 23 Aspergillus species from section Flavi. Nature Communications, 11, 1. https://doi.org/10.1038/s41467-019-14051-y

Kovács ÁT 2020 A fungal scent from the cheese. Environmental Microbiology. 22, 11: 4524-4526. https://doi.org/10.1111/1462-2920.15267

Liao S, Wang Y, Liu H, Fan G, Sahu SK, Jin T, Chen J, Zhang P, Gram L, Strube ML, Shi Q, Lee SMY, Liu X 2020. Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds. mSystems, 5, 5. https://doi.org/10.1128/mSystems.00851-19

Malik A, Ardalani H, Anam S, McNair LM, Kromphardt KJK, Normand Frandsen RJ, Franzyk H, Staerk D, Kongstad KT 2020. Antidiabetic xanthones with α-glucosidase inhibitory activities from an endophytic Penicillium canescens. Fitoterapia, 142. https://doi.org/10.1016/j.fitote.2020.104522

Martin M, Dragoš A, Otto SB, Schäfer D, Brix, S, Maróti G, Kovács ÁT 2020. Cheaters shape the evolution of phenotypic heterogeneity in Bacillus subtilis biofilms. ISME Journal, 14. https://doi.org/10.1038/s41396-020-0685-4

Otto SB, Martin M, Schäfer D, Hartmann R, Drescher K, Brix S, Dragoš A, Kovács ÁT 2020. Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms. mSystems, 5, 4. https://doi.org/10.1128/mSystems.00425-20

Paulsen SS, Petersen TI, Kirkegaard M, Buijs Y, Strube ML, Sonnenschein EC, Larsen TO, Gram L 2020. Production of the antimicrobial compound tetrabromopyrrole and the Pseudomonas quinolone system precursor, 2-heptyl-4-quinolone, by a novel marine species Pseudoalteromonas galatheae sp. nov.. Scientific Reports, 10. https://doi.org/10.1038/s41598-020-78439-3

Thérien M, Kiesewalter HT, Auria  E, Charron-Lamoreux V, Wibowo M, Maróti G, Kovács ÁT, Beuregard PB 2020. Surfactin production is not essential for pellicle and root-associated biofilmdevelopment of Bacillus subtilis. Biofilm, 2. https://doi.org/10.1016/j.bioflm.2020.100021

Wibowo M, Ding L 2020. Chemistry and Biology of Natural Azoxy Compounds. Journal of Natural Products, 83, 11. https://doi.org/10.1021/acs.jnatprod.0c00725

Wibowo M, Gotfredsen CH, Sassetti E, Melchiorsen J, Clausen MH, Gram L, Ding L 2020. Azodyrecins A-C: Azoxides from a Soil-Derived Streptomyces Species. Journal of Natural Products, 83, 12 https://doi.org/10.1021/acs.jnatprod.0c00339 

2019

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee, Sang Y, Medema MH, Weber T 2019.  antiSMASH 5.0: updates to the secondary metabolite genome mining pipelineNucleic acids research, 87. https://doi.org/10.1093/nar/gkz310

Buijs Y, Bech PK, Vazquez Albacete D,  Bentzon-Tilia M, Sonnenschein EC, Gram L, Zhang SD 2019. Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies. Natural Product Reports, 36. https://doi.org/10.1039/c9np00020h

de Reus E, Nielsen MR, Frandsen RJN 2019. Metabolic and regulatory insights from the experimental Horizontal Gene Transfer of the aurofusarin and bikaverin gene clusters to Aspergillus nidulans. Molecular Microbiology, 112, 6. https://doi.org/10.1111/mmi.14376

Devi S, Kiesewalter HT, Kovács R, Frisvad JC, Weber T, Larsen TO, Kovács ÁT, Ding L 2019. Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001. Synthetic and Systems Biotechnology, 4, 3. https://doi.org/10.1016/j.synbio.2019.08.002

Dittmann KK, Sonnenschein EC, Egan S, Gram L, Bentzon-Tilia M 2019. Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities. Environmental Microbiology Reports. 11, 3. https://doi.org/10.1111/1758-2229.12698

Frisvad JC, Hubka V, Ezekiel CN, Hong S-B, Nováková A, Chen AJ, Arzanlou M, Larsen TO, Sklenár F, Mahakarnchanakul W, Samson RA, Houbraken J 2019. Taxonomy of Aspergillus section Flavi and their production of aflatoxins, ochratoxins and other mycotoxins. Studies in Mycology, 1 -63. https://doi.org/10.1016/j.simyco.2018.06.001

Kjeldgaard B, Listian SA, Ramaswamhi V, Richter A, Kiesewalter HT, Kovács ÁT 2019. Fungal hyphae colonization by Bacillus subtilis relies on biofilm matrix components. Biofilm, 1. https://doi.org/10.1016/j.bioflm.2019.100007

Kovács ÁT 2019 Bacillus subtilis. Trends in Microbiology, 27, 8. https://doi.org/10.1016/j.tim.2019.03.008

Kovács ÁT, Dragoš A 2019. Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles. Journal of Molecular Biology, 431, 23. https://doi.org/10.1016/j.jmb.2019.02.005

Palazzotto E, Tong Y, Lee SY, Weber T 2019. Synthetic biology and metabolic engineering of actinomycetes for natural product discovery. Biotechnology Advances, 37, 6. https://doi.org/10.1016/j.biotechadv.2019.03.005

Phippen CBW, Jørgensen CM, Bentzon-Tilia M, Gotfredsen CH, Larsen TO, Gram L, Sonnenschein EC 2019. Isolation of Methyl Troposulfenin from Phaeobacter inhibens. Journal of Natural Products, 82, 1387-1390. https://doi.org/10.1021/acs.jnatprod.8b01097

Sartor F, Eelderink-Chen Z, Aronson B, Bosman J, Hibbert LE, Dodd AN, Kovács AT, Merrow M 2019. Are There Circadian Clocks in Non-Photosynthetic Bacteria?. MDPI Biology, 8, 8. http://dx.doi.org/10.3390/biology8020041

Sazinas P, Hansen ML, Aune MI, Fischer MH, Jelsbak L 2019. A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1. Genome Biology and Evolution, 11.  https://doi.org/10.1093/gbe/evz267

Sazinas P, Aune MI, Fischer MH,  Lauritsen JG, Gram L, Jelsbak L 2019. Complete Genome Sequence of a Bioactive Pseudomonas sp. Strain, DTU12.3, Isolated from Soil in DenmarkMicrobiology Resource Announcements, 8, 16. https://doi.org/10.1128/mra.00121-19 

2018

Dragos A, Kiesewalter HT, Martin M, Hsu CY, Hartmann R, Wechsler T, Eriksen C, Brix S, Drescher K, Stanley-Wall N, Kümmerli R, Kovács ÁT 2018. Division of Labor during Biofilm Matrix Production. Current Biology, 28, 12. https://doi.org/10.1016/j.cub.2018.04.046

Frisvad JC 2019. A critical review of producers of small lactone mycotoxins: patulin, penicillic acid and moniliformin. World Mycotoxin Journal, 11, 1. https://doi.org/10.3920/WMJ2017.2294

Kjærbølling I, Vesth TC, Frisvad JC,  Nybo JL, Theobald S,  Kuo A,  Bowyer P, Matsuda Y,  Mondo S, Lyhne EK, Kogle ME, Clum A, Lipzen A, Salamov A, Ngan CE, Daum C, Chiniquy J, Barry K, LaButti K, Haridas S, Simmons BA, Magnuson JK, Mortensen UH, Larsen TO, Grigoriev IV, Baker SE, Andersen MR  2018. Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proceedings of the National Academy of Sciences of the United States of America, 115, 4. https://doi.org/10.1073/pnas.1715954115

Palazzotto E, Weber T 2018. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Current Opinion in Microbiology, 45. https://doi.org/10.1016/j.mib.2018.03.004

Richter A, Hoelscher T, Pausch P, Sehrt T, Brockhaus F, Bange G, Kovács ÁT 2018. Hampered motility promotes the evolution of wrinkly phenotype in Bacillus subtilis. BMC Evolutionary Biology, 18, 1. https://doi.org/10.1186/s12862-018-1266-2

Vesth TC, Nybo JL, Theobald S, Frisvad, JC, Larsen, TO, Nielsen KF, Hoof, JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen, MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti  K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M,  Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR 2018.  Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics. 50. https://doi.org/10.1038/s41588-018-0246-1