Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.

Autor: Pakkir Shah AK; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Walter A; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.; Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany., Ottosson F; Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark., Russo F; Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark., Navarro-Diaz M; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Boldt J; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.; German Center for Infection Research, Partner Site Braunschweig-Hannover, Braunschweig, Germany., Kalinski JJ; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa., Kontou EE; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark., Elofson J; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA., Polyzois A; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA., González-Marín C; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Universidad EAFIT, Medellín, Antioquia, Colombia., Farrell S; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.; School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, USA., Aggerbeck MR; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Environmental Science, Aarhus University, Roskilde, Denmark., Pruksatrakul T; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand., Chan N; Department of Computer Science, University of California Riverside, Riverside, CA, USA., Wang Y; Department of Computer Science, University of California Riverside, Riverside, CA, USA., Pöchhacker M; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria., Brungs C; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Cámara B; Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile., Caraballo-Rodríguez AM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Cumsille A; Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Centro de Biotecnología DAL, Universidad Técnica Federico Santa María, Valparaíso, Chile., de Oliveira F; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil., Dührkop K; Department of Bioinformatics, University of Jena, Jena, Germany., El Abiead Y; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Geibel C; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Graves LG; Department of Environmental Systems Analysis, University of Tübingen, Tübingen, Germany.; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany., Hansen M; Department of Environmental Science, Aarhus University, Roskilde, Denmark., Heuckeroth S; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Knoblauch S; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Kostenko A; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA., Kuijpers MCM; Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA., Mildau K; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Analytical Chemistry, University of Vienna, Vienna, Austria.; Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands., Papadopoulos Lambidis S; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Portal Gomes PW; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Schramm T; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.; Department of Biochemistry, University of California Riverside, Riverside, CA, USA., Steuer-Lodd K; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany.; Department of Biochemistry, University of California Riverside, Riverside, CA, USA., Stincone P; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Tayyab S; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Vitale GA; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Wagner BC; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Xing S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Yazzie MT; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA., Zuffa S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., de Kruijff M; Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany., Beemelmanns C; Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany.; Saarland University, Saarbrücken, Germany., Link H; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., Mayer C; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany., van der Hooft JJJ; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands.; Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa., Damiani T; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Pluskal T; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Dorrestein P; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Stanstrup J; Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark., Schmid R; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic., Wang M; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Computer Science, University of California Riverside, Riverside, CA, USA., Aron A; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA.; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA., Ernst M; Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen S, Denmark. MAET@ssi.dk., Petras D; Virtual Multi-Omics Laboratory, The Internet, Riverside, CA, USA. dpetras@ucr.edu.; University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine, Tübingen, Germany. dpetras@ucr.edu.; Department of Biochemistry, University of California Riverside, Riverside, CA, USA. dpetras@ucr.edu.

Publikováno v: Nature protocols [Nat Protoc] 2024 Sep 20. Date of Electronic Publication: 2024 Sep 20.

Pruning Wound Protection Products Induce Alterations in the Wood Mycobiome Profile of Grapevines.

Autor: Del Frari G; LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal., Aggerbeck MR; Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark., Gobbi A; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark., Ingrà C; Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy., Volpi L; LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal., Nascimento T; LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal., Ferrandino A; Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy., Hansen LH; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark., Ferreira RB; LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal.

Publikováno v: Journal of fungi (Basel, Switzerland) [J Fungi (Basel)] 2023 Apr 19; Vol. 9 (4). Date of Electronic Publication: 2023 Apr 19.

Muskoxen homogenise soil microbial communities and affect the abundance of methanogens and methanotrophs.

Autor: Aggerbeck MR; Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark., Nielsen TK; Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark., Mosbacher JB; Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark., Schmidt NM; Department of Ecoscience, Aarhus University, 4000 Roskilde, Denmark; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark., Hansen LH; Department of Plant and Environmental Science, University of Copenhagen, 1871 Copenhagen, Denmark. Electronic address: lhha@plen.ku.dk.

Publikováno v: The Science of the total environment [Sci Total Environ] 2022 Jun 25; Vol. 827, pp. 153877. Date of Electronic Publication: 2022 Feb 23.

Identification and Characterization of 33 Bacillus cereus sensu lato Isolates from Agricultural Fields from Eleven Widely Distributed Countries by Whole Genome Sequencing.

Autor: Zervas A; Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark., Aggerbeck MR; Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark., Allaga H; Department of Microbiology, University of Szeged, 6726 Szeged, Hungary., Güzel M; Department of Food Engineering, Hitit University, 19030 Çorum, Turkey., Hendriks M; Wageningen Plant Research, Wageningen University, 6708PB Wageningen, The Netherlands., Jonuškienė I; Department of Organic Chemistry, Kaunas University of Technology, 50254 Kaunas, Lithuania., Kedves O; Department of Microbiology, University of Szeged, 6726 Szeged, Hungary., Kupeli A; Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkey., Lamovšek J; Plant Protection Department, Agricultural Institute of Slovenia, 1000 Ljubljana, Slovenia., Mülner P; Graz University of Technology, 8010 Graz, Austria., Munday D; Sumitomo Chemical Agro Europe, 1260 Nyon, Switzerland., Namli Ş; Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkey., Samut H; Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkey., Tomičić R; Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia., Tomičić Z; Institute of Food Technology, University of Novi Sad, 21000 Novi Sad, Serbia., Yeni F; Department of Food Engineering, Middle East Technical University, 06800 Ankara, Turkey., Zghal RZ; Sfax Preparatory Engineering Institute, Sfax University, P.O. Box 1172, 3000 Sfax, Tunisia.; Centre of Biotechnology of Sfax, Biopesticides Laboratory, P.O. Box 1177, 3018 Sfax, Tunisia., Zhao X; Laboratory of Food Microbiology and Food Preservation, Ghent University, 9000 Ghent, Belgium., Sanchis-Borja V; Micalis Institute, INRA, Université Paris-Saclay, 78 350 Jouy-en-Josas, France., Hendriksen NB; Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark.

Publikováno v: Microorganisms [Microorganisms] 2020 Dec 18; Vol. 8 (12). Date of Electronic Publication: 2020 Dec 18.

Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms.

Autor: Del Frari G; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal., Gobbi A; Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark., Aggerbeck MR; Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark., Oliveira H; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal., Hansen LH; Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark., Ferreira RB; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal.

Publikováno v: Frontiers in plant science [Front Plant Sci] 2019 Jul 12; Vol. 10, pp. 910. Date of Electronic Publication: 2019 Jul 12 (Print Publication: 2019).