Structure and function of the global ocean microbiome

Shinichi Sunagawa, Luis Pedro Coelho, Samuel Chaffron, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri, Georg Zeller, Daniel R. Mende, Adriana Alberti, Francisco M. Cornejo-Castillo, Paul I. Costea, Corinne Cruaud, Francesco D'Ovidio, Stefan Engelen, Isabel Ferrera, Josep M. Gasol, Lionel Guidi, Falk Hildebrand, Florian KokoszkaCyrille Lepoivre, Gipsi Lima-Mendez, Julie Poulain, Bonnie T. Poulos, Marta Royo-Llonch, Hugo Sarmento, Sara Vieira-Silva, Céline Dimier, Marc Picheral, Sarah Searson, Stefanie Kandels-Lewis, Emmanuel Boss, Michael Follows, Lee Karp-Boss, Uros Krzic, Emmanuel G. Reynaud, Christian Sardet, Mike Sieracki, Didier Velayoudon, Chris Bowler, Colomban De Vargas, Gabriel Gorsky, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Lars Stemmann, Matthew Sullivan, Jean Weissenbach, Patrick Wincker, Eric Karsenti, Jeroen Raes, Silvia G. Acinas, Peer Bork

Research output: Contribution to journalArticle

563 Citations (Scopus)

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.

Original languageEnglish (US)
Article number1261359
JournalScience
Volume348
Issue number6237
DOIs
StatePublished - May 22 2015

Fingerprint

Microbiota
Oceans and Seas
Microbial Genes
Metagenomics
Biota
Geography
Ecosystem
Viruses
Temperature
Water

ASJC Scopus subject areas

  • General

Cite this

Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., ... Bork, P. (2015). Structure and function of the global ocean microbiome. Science, 348(6237), [1261359]. https://doi.org/10.1126/science.1261359

Structure and function of the global ocean microbiome. / Sunagawa, Shinichi; Coelho, Luis Pedro; Chaffron, Samuel; Kultima, Jens Roat; Labadie, Karine; Salazar, Guillem; Djahanschiri, Bardya; Zeller, Georg; Mende, Daniel R.; Alberti, Adriana; Cornejo-Castillo, Francisco M.; Costea, Paul I.; Cruaud, Corinne; D'Ovidio, Francesco; Engelen, Stefan; Ferrera, Isabel; Gasol, Josep M.; Guidi, Lionel; Hildebrand, Falk; Kokoszka, Florian; Lepoivre, Cyrille; Lima-Mendez, Gipsi; Poulain, Julie; Poulos, Bonnie T.; Royo-Llonch, Marta; Sarmento, Hugo; Vieira-Silva, Sara; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Boss, Emmanuel; Follows, Michael; Karp-Boss, Lee; Krzic, Uros; Reynaud, Emmanuel G.; Sardet, Christian; Sieracki, Mike; Velayoudon, Didier; Bowler, Chris; De Vargas, Colomban; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew; Weissenbach, Jean; Wincker, Patrick; Karsenti, Eric; Raes, Jeroen; Acinas, Silvia G.; Bork, Peer.

In: Science, Vol. 348, No. 6237, 1261359, 22.05.2015.

Research output: Contribution to journalArticle

Sunagawa, S, Coelho, LP, Chaffron, S, Kultima, JR, Labadie, K, Salazar, G, Djahanschiri, B, Zeller, G, Mende, DR, Alberti, A, Cornejo-Castillo, FM, Costea, PI, Cruaud, C, D'Ovidio, F, Engelen, S, Ferrera, I, Gasol, JM, Guidi, L, Hildebrand, F, Kokoszka, F, Lepoivre, C, Lima-Mendez, G, Poulain, J, Poulos, BT, Royo-Llonch, M, Sarmento, H, Vieira-Silva, S, Dimier, C, Picheral, M, Searson, S, Kandels-Lewis, S, Boss, E, Follows, M, Karp-Boss, L, Krzic, U, Reynaud, EG, Sardet, C, Sieracki, M, Velayoudon, D, Bowler, C, De Vargas, C, Gorsky, G, Grimsley, N, Hingamp, P, Iudicone, D, Jaillon, O, Not, F, Ogata, H, Pesant, S, Speich, S, Stemmann, L, Sullivan, M, Weissenbach, J, Wincker, P, Karsenti, E, Raes, J, Acinas, SG & Bork, P 2015, 'Structure and function of the global ocean microbiome', Science, vol. 348, no. 6237, 1261359. https://doi.org/10.1126/science.1261359
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G et al. Structure and function of the global ocean microbiome. Science. 2015 May 22;348(6237). 1261359. https://doi.org/10.1126/science.1261359
Sunagawa, Shinichi ; Coelho, Luis Pedro ; Chaffron, Samuel ; Kultima, Jens Roat ; Labadie, Karine ; Salazar, Guillem ; Djahanschiri, Bardya ; Zeller, Georg ; Mende, Daniel R. ; Alberti, Adriana ; Cornejo-Castillo, Francisco M. ; Costea, Paul I. ; Cruaud, Corinne ; D'Ovidio, Francesco ; Engelen, Stefan ; Ferrera, Isabel ; Gasol, Josep M. ; Guidi, Lionel ; Hildebrand, Falk ; Kokoszka, Florian ; Lepoivre, Cyrille ; Lima-Mendez, Gipsi ; Poulain, Julie ; Poulos, Bonnie T. ; Royo-Llonch, Marta ; Sarmento, Hugo ; Vieira-Silva, Sara ; Dimier, Céline ; Picheral, Marc ; Searson, Sarah ; Kandels-Lewis, Stefanie ; Boss, Emmanuel ; Follows, Michael ; Karp-Boss, Lee ; Krzic, Uros ; Reynaud, Emmanuel G. ; Sardet, Christian ; Sieracki, Mike ; Velayoudon, Didier ; Bowler, Chris ; De Vargas, Colomban ; Gorsky, Gabriel ; Grimsley, Nigel ; Hingamp, Pascal ; Iudicone, Daniele ; Jaillon, Olivier ; Not, Fabrice ; Ogata, Hiroyuki ; Pesant, Stephane ; Speich, Sabrina ; Stemmann, Lars ; Sullivan, Matthew ; Weissenbach, Jean ; Wincker, Patrick ; Karsenti, Eric ; Raes, Jeroen ; Acinas, Silvia G. ; Bork, Peer. / Structure and function of the global ocean microbiome. In: Science. 2015 ; Vol. 348, No. 6237.
@article{f695ad8e7ac5444386cf68d8526ffc0b,
title = "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.",
author = "Shinichi Sunagawa and Coelho, {Luis Pedro} and Samuel Chaffron and Kultima, {Jens Roat} and Karine Labadie and Guillem Salazar and Bardya Djahanschiri and Georg Zeller and Mende, {Daniel R.} and Adriana Alberti and Cornejo-Castillo, {Francisco M.} and Costea, {Paul I.} and Corinne Cruaud and Francesco D'Ovidio and Stefan Engelen and Isabel Ferrera and Gasol, {Josep M.} and Lionel Guidi and Falk Hildebrand and Florian Kokoszka and Cyrille Lepoivre and Gipsi Lima-Mendez and Julie Poulain and Poulos, {Bonnie T.} and Marta Royo-Llonch and Hugo Sarmento and Sara Vieira-Silva and C{\'e}line Dimier and Marc Picheral and Sarah Searson and Stefanie Kandels-Lewis and Emmanuel Boss and Michael Follows and Lee Karp-Boss and Uros Krzic and Reynaud, {Emmanuel G.} and Christian Sardet and Mike Sieracki and Didier Velayoudon and Chris Bowler and {De Vargas}, Colomban and Gabriel Gorsky and Nigel Grimsley and Pascal Hingamp and Daniele Iudicone and Olivier Jaillon and Fabrice Not and Hiroyuki Ogata and Stephane Pesant and Sabrina Speich and Lars Stemmann and Matthew Sullivan and Jean Weissenbach and Patrick Wincker and Eric Karsenti and Jeroen Raes and Acinas, {Silvia G.} and Peer Bork",
year = "2015",
month = "5",
day = "22",
doi = "10.1126/science.1261359",
language = "English (US)",
volume = "348",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6237",

}

TY - JOUR

T1 - Structure and function of the global ocean microbiome

AU - Sunagawa, Shinichi

AU - Coelho, Luis Pedro

AU - Chaffron, Samuel

AU - Kultima, Jens Roat

AU - Labadie, Karine

AU - Salazar, Guillem

AU - Djahanschiri, Bardya

AU - Zeller, Georg

AU - Mende, Daniel R.

AU - Alberti, Adriana

AU - Cornejo-Castillo, Francisco M.

AU - Costea, Paul I.

AU - Cruaud, Corinne

AU - D'Ovidio, Francesco

AU - Engelen, Stefan

AU - Ferrera, Isabel

AU - Gasol, Josep M.

AU - Guidi, Lionel

AU - Hildebrand, Falk

AU - Kokoszka, Florian

AU - Lepoivre, Cyrille

AU - Lima-Mendez, Gipsi

AU - Poulain, Julie

AU - Poulos, Bonnie T.

AU - Royo-Llonch, Marta

AU - Sarmento, Hugo

AU - Vieira-Silva, Sara

AU - Dimier, Céline

AU - Picheral, Marc

AU - Searson, Sarah

AU - Kandels-Lewis, Stefanie

AU - Boss, Emmanuel

AU - Follows, Michael

AU - Karp-Boss, Lee

AU - Krzic, Uros

AU - Reynaud, Emmanuel G.

AU - Sardet, Christian

AU - Sieracki, Mike

AU - Velayoudon, Didier

AU - Bowler, Chris

AU - De Vargas, Colomban

AU - Gorsky, Gabriel

AU - Grimsley, Nigel

AU - Hingamp, Pascal

AU - Iudicone, Daniele

AU - Jaillon, Olivier

AU - Not, Fabrice

AU - Ogata, Hiroyuki

AU - Pesant, Stephane

AU - Speich, Sabrina

AU - Stemmann, Lars

AU - Sullivan, Matthew

AU - Weissenbach, Jean

AU - Wincker, Patrick

AU - Karsenti, Eric

AU - Raes, Jeroen

AU - Acinas, Silvia G.

AU - Bork, Peer

PY - 2015/5/22

Y1 - 2015/5/22

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84929992013&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84929992013&partnerID=8YFLogxK

U2 - 10.1126/science.1261359

DO - 10.1126/science.1261359

M3 - Article

C2 - 25999513

AN - SCOPUS:84929992013

VL - 348

JO - Science

JF - Science

SN - 0036-8075

IS - 6237

M1 - 1261359

ER -