title: Ocean plankton. Structure and function of the global ocean microbiome.
abstract: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Luis Pedro
authors.initials: LP
authors.lastname: Coelho
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Samuel
authors.initials: S
authors.lastname: Chaffron
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Jens Roat
authors.initials: JR
authors.lastname: Kultima
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
authors.forename: Guillem
authors.initials: G
authors.lastname: Salazar
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Bardya
authors.initials: B
authors.lastname: Djahanschiri
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Cornejo-Castillo
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Paul I
authors.initials: PI
authors.lastname: Costea
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.affiliation: Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France.
authors.forename: Francesco
authors.initials: F
authors.lastname: d'Ovidio
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Engelen
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Ferrera
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
authors.forename: Josep M
authors.initials: JM
authors.lastname: Gasol
authors.affiliation: CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Lionel
authors.initials: L
authors.lastname: Guidi
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Kokoszka
authors.affiliation: Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France.
authors.forename: Cyrille
authors.initials: C
authors.lastname: Lepoivre
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Gipsi
authors.initials: G
authors.lastname: Lima-Mendez
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA.
authors.forename: Bonnie T
authors.initials: BT
authors.lastname: Poulos
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Royo-Llonch
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil.
authors.forename: Hugo
authors.initials: H
authors.lastname: Sarmento
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Sara
authors.initials: S
authors.lastname: Vieira-Silva
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Dimier
authors.affiliation: CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Picheral
authors.affiliation: CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Searson
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Kandels-Lewis
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France.
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.affiliation: CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.affiliation: CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Gorsky
authors.affiliation: CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France.
authors.forename: Nigel
authors.initials: N
authors.lastname: Grimsley
authors.affiliation: Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Hingamp
authors.affiliation: Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Iudicone
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Not
authors.affiliation: Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ogata
authors.affiliation: PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
authors.forename: Stephane
authors.initials: S
authors.lastname: Pesant
authors.affiliation: Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Speich
authors.affiliation: CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France.
authors.forename: Lars
authors.initials: L
authors.lastname: Stemmann
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.affiliation: CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.
authors.forename: Eric
authors.initials: E
authors.lastname: Karsenti
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.affiliation: Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.
authors.forename: Silvia G
authors.initials: SG
authors.lastname: Acinas
authors.affiliation: Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany. sunagawa@embl.de karsenti@embl.de jeroen.raes@vib-kuleuven.be sacinas@icm.csic.es bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D030541:Databases, Genetic; D017753:Ecosystem; D041981:Gastrointestinal Tract / Q000382:microbiology; D014644:Genetic Variation; D006801:Humans; D054892:Metagenome; D064307:Microbiota / Q000235:genetics*; D009792:Oceans and Seas; D010933:Plankton / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D012623:Seawater / Q000382:microbiology*