A community resource for paired genomic and metabolomic data mining

Michelle A Schorn; Stefan Verhoeven; Lars Ridder; Florian Huber; Deepa D Acharya; Alexander A Aksenov; Gajender Aleti; Jamshid Amiri Moghaddam; Allegra T Aron; Saefuddin Aziz; Anelize Bauermeister; Katherine D Bauman; Martin Baunach; Christine Beemelmanns; J Michael Beman; María Victoria Berlanga-Clavero; Alex A Blacutt; Helge B Bode; Anne Boullie; Asker Brejnrod; Tim S Bugni; Alexandra Calteau; Liu Cao; Víctor J Carrión; Raquel Castelo-Branco; Shaurya Chanana; Alexander B Chase; Marc G Chevrette; Leticia V Costa-Lotufo; Jason M Crawford; Cameron R Currie; Bart Cuypers; Tam Dang; Tristan de Rond; Alyssa M Demko; Elke Dittmann; Chao Du; Christopher Drozd; Jean-Claude Dujardin; Rachel J Dutton; Anna Edlund; David P Fewer; Neha Garg; Julia M Gauglitz; Emily C Gentry; Lena Gerwick; Evgenia Glukhov; Harald Gross; Muriel Gugger; Dulce G Guillén Matus; Eric J N Helfrich; Benjamin-Florian Hempel; Jae-Seoun Hur; Marianna Iorio; Paul R Jensen; Kyo Bin Kang; Leonard Kaysser; Neil L Kelleher; Chung Sub Kim; Ki Hyun Kim; Irina Koester; Gabriele M König; Tiago Leao; Seoung Rak Lee; Yi-Yuan Lee; Xuanji Li; Jessica C Little; Katherine N Maloney; Daniel Männle; Christian Martin H; Andrew C McAvoy; Willam W Metcalf; Hosein Mohimani; Carlos Molina-Santiago; Bradley S Moore; Michael W Mullowney; Mitchell Muskat; Louis-Félix Nothias; Ellis C O'Neill; Elizabeth I Parkinson; Daniel Petras; Jörn Piel; Emily C Pierce; Karine Pires; Raphael Reher; Diego Romero; M Caroline Roper; Michael Rust; Hamada Saad; Carmen Saenz; Laura M Sanchez; Søren Johannes Sørensen; Margherita Sosio; Roderich D Süssmuth; Douglas Sweeney; Kapil Tahlan; Regan J Thomson; Nicholas J Tobias; Amaro E Trindade-Silva; Gilles P van Wezel; Mingxun Wang; Kelly C Weldon; Fan Zhang; Nadine Ziemert; Katherine R Duncan; Max Crüsemann; Simon Rogers; Pieter C Dorrestein; Marnix H Medema; Justin J J van der Hooft

doi:10.1038/s41589-020-00724-z

A community resource for paired genomic and metabolomic data mining

Nat Chem Biol. 2021 Apr;17(4):363-368. doi: 10.1038/s41589-020-00724-z.

Authors

Michelle A Schorn^#^{1

2}, Stefan Verhoeven^#³, Lars Ridder³, Florian Huber³, Deepa D Acharya⁴, Alexander A Aksenov⁵, Gajender Aleti⁶, Jamshid Amiri Moghaddam⁷, Allegra T Aron⁵, Saefuddin Aziz^{8

9}, Anelize Bauermeister^{5

10}, Katherine D Bauman¹¹, Martin Baunach¹², Christine Beemelmanns⁷, J Michael Beman^{13

14}, María Victoria Berlanga-Clavero¹⁵, Alex A Blacutt¹⁶, Helge B Bode^{17

18

19

20}, Anne Boullie²¹, Asker Brejnrod⁵, Tim S Bugni²², Alexandra Calteau²³, Liu Cao²⁴, Víctor J Carrión^{25

26}, Raquel Castelo-Branco^{27

28

29}, Shaurya Chanana⁴, Alexander B Chase¹¹, Marc G Chevrette⁴, Leticia V Costa-Lotufo¹⁰, Jason M Crawford^{30

31

32}, Cameron R Currie^{33

34}, Bart Cuypers^{35

36}, Tam Dang³⁷, Tristan de Rond¹¹, Alyssa M Demko¹¹, Elke Dittmann¹², Chao Du²⁵, Christopher Drozd¹⁶, Jean-Claude Dujardin³⁶, Rachel J Dutton^{38

39}, Anna Edlund^{40

41}, David P Fewer²⁹, Neha Garg⁴², Julia M Gauglitz⁵, Emily C Gentry⁵, Lena Gerwick¹¹, Evgenia Glukhov¹¹, Harald Gross⁸, Muriel Gugger²¹, Dulce G Guillén Matus¹¹, Eric J N Helfrich^{17

19

43

44}, Benjamin-Florian Hempel^{37

45}, Jae-Seoun Hur⁴⁶, Marianna Iorio⁴⁷, Paul R Jensen¹¹, Kyo Bin Kang⁴⁸, Leonard Kaysser^{8

49}, Neil L Kelleher⁵⁰, Chung Sub Kim^{30

31

51}, Ki Hyun Kim⁵¹, Irina Koester⁵², Gabriele M König⁵³, Tiago Leao^{5

11}, Seoung Rak Lee^{51

54}, Yi-Yuan Lee²⁴, Xuanji Li⁵⁵, Jessica C Little⁵⁶, Katherine N Maloney⁵⁷, Daniel Männle^{8

49

58}, Christian Martin H⁵⁹, Andrew C McAvoy⁴², Willam W Metcalf⁶⁰, Hosein Mohimani²⁴, Carlos Molina-Santiago¹⁵, Bradley S Moore^{11

39

61}, Michael W Mullowney⁵⁰, Mitchell Muskat¹¹, Louis-Félix Nothias⁵, Ellis C O'Neill⁶², Elizabeth I Parkinson⁶³, Daniel Petras^{5

52}, Jörn Piel⁴³, Emily C Pierce³⁸, Karine Pires⁶⁴, Raphael Reher¹¹, Diego Romero¹⁵, M Caroline Roper¹⁶, Michael Rust⁴³, Hamada Saad^{8

65}, Carmen Saenz⁶⁶, Laura M Sanchez⁵⁶, Søren Johannes Sørensen⁵⁵, Margherita Sosio⁴⁷, Roderich D Süssmuth³⁷, Douglas Sweeney¹¹, Kapil Tahlan⁶⁷, Regan J Thomson⁵⁰, Nicholas J Tobias^{19

68}, Amaro E Trindade-Silva⁶⁹, Gilles P van Wezel²⁵, Mingxun Wang⁵, Kelly C Weldon^{5

39}, Fan Zhang²², Nadine Ziemert^{49

58}, Katherine R Duncan⁷⁰, Max Crüsemann⁵³, Simon Rogers⁷¹, Pieter C Dorrestein^{72

73

74

75}, Marnix H Medema⁷⁶, Justin J J van der Hooft⁷⁷

Affiliations

¹ Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands.
² Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
³ Netherlands eScience Center, Amsterdam, the Netherlands.
⁴ Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
⁵ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁶ Department of Psychiatry, University of California San Diego, San Diego, CA, USA.
⁷ Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany.
⁸ Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
⁹ Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia.
¹⁰ Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
¹¹ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
¹² University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany.
¹³ Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA.
¹⁴ Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA.
¹⁵ Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain.
¹⁶ Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
¹⁷ Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
¹⁸ Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
¹⁹ Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.
²⁰ Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany.
²¹ Institut Pasteur, Collection of Cyanobacteria, Paris, France.
²² Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA.
²³ Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
²⁴ Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
²⁵ Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.
²⁶ Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands.
²⁷ Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal.
²⁸ Faculty of Sciences, University of Porto, Porto, Portugal.
²⁹ Department of Microbiology, University of Helsinki, Helsinki, Finland.
³⁰ Department of Chemistry, Yale University, New Haven, CT, USA.
³¹ Chemical Biology Institute, Yale University, West Haven, CT, USA.
³² Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
³³ Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
³⁴ Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA.
³⁵ Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium.
³⁶ Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
³⁷ Technische Universität Berlin, Institut für Chemie, Berlin, Germany.
³⁸ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
³⁹ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁴⁰ J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA.
⁴¹ Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
⁴² School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
⁴³ Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
⁴⁴ Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
⁴⁵ Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany.
⁴⁶ Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea.
⁴⁷ Naicons Srl, Milano, Italy.
⁴⁸ College of Pharmacy, Sookmyung Women's University, Seoul, Korea.
⁴⁹ German Centre for Infection Research (DZIF), Tübingen, Germany.
⁵⁰ Department of Chemistry, Northwestern University, Evanston, IL, USA.
⁵¹ School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
⁵² Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁵³ Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
⁵⁴ Department of Chemistry, Princeton University, Princeton, NJ, USA.
⁵⁵ Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
⁵⁶ Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
⁵⁷ Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA.
⁵⁸ Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany.
⁵⁹ Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama.
⁶⁰ Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
⁶¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁶² School of Chemistry, University of Nottingham, Nottingham, UK.
⁶³ Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
⁶⁴ Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.
⁶⁵ Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt.
⁶⁶ The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
⁶⁷ Department of Biology, Memorial University of Newfoundland, St. John's, Canada.
⁶⁸ LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
⁶⁹ Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.
⁷⁰ University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK.
⁷¹ School of Computing Science, University of Glasgow, Glasgow, UK.
⁷² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁷³ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁷⁴ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁷⁵ Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁷⁶ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands. marnix.medema@wur.nl.
⁷⁷ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands. justin.vanderhooft@wur.nl.

^# Contributed equally.

Abstract

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.

A community resource for paired genomic and metabolomic data mining

Authors

Affiliations

Abstract

Publication types

MeSH terms

Grants and funding