An integrated catalog of reference genes in the human gut microbiome

Junhua Li; Huijue Jia; Xianghang Cai; Huanzi Zhong; Qiang Feng; Shinichi Sunagawa; Manimozhiyan Arumugam; Jens Roat Kultima; Edi Prifti; Trine Nielsen; Agnieszka Sierakowska Juncker; Chaysavanh Manichanh; Bing Chen; Wenwei Zhang; Florence Levenez; Juan Wang; Xun Xu; Liang Xiao; Suisha Liang; Dongya Zhang; Zhaoxi Zhang; Weineng Chen; Hailong Zhao; Jumana Yousuf Al-Aama; Sherif Edris; Huanming Yang; Jian Wang; Torben Hansen; Henrik Bjørn Nielsen; Søren Brunak; Karsten Kristiansen; Francisco Guarner; Oluf Pedersen; Joel Doré; S. Dusko Ehrlich; Peer Bork; Jun Wang; Nicolas Pons; Emmanuelle Le Chatelier; Jean Michel Batto; Sean Kennedy; Florence Haimet; Yohanan Winogradski; Eric Pelletier; Denis Lepaslier; François Artiguenave; Thomas Bruls; Jean Weissenbach; Keith Turner; Julian Parkhill; Maria Antolin; Francesc Casellas; Natalia Borruel; Encarna Varela; Antonio Torrejon; Gérard Denariaz; Muriel Derrien; Johan E.T. van Hylckama Vlieg; Patrick Viega; Raish Oozeer; Jan Knoll; Maria Rescigno; Christian Brechot; Christine M’rini; Alexandre Mérieux; Takuji Yamada; Sebastian Tims; Erwin G. Zoetendal; Michiel Kleerebezem; Willem M. de Vos; Antonella Cultrone; Marion Leclerc; Catherine Juste; Eric Guedon; Christine Delorme; Séverine Layec; Ghalia Khaci; Maarten van de Guchte; Gaetana Vandemeulebrouck; Alexandre Jamet; Rozenn Dervyn; Nicolas Sanchez; Hervé Blottière; Emmanuelle Maguin; Pierre Renault; Julien Tap; Daniel R. Mende

doi:10.1038/nbt.2942

An integrated catalog of reference genes in the human gut microbiome

Junhua Li
, Huijue Jia
, Xianghang Cai
, Huanzi Zhong
, Qiang Feng
, Shinichi Sunagawa
, Manimozhiyan Arumugam
, Jens Roat Kultima
, Edi Prifti
, Trine Nielsen
, Agnieszka Sierakowska Juncker
, Chaysavanh Manichanh
, Bing Chen
, Wenwei Zhang
, Florence Levenez
, Juan Wang
, Xun Xu
, Liang Xiao
, Suisha Liang
, Dongya Zhang

Zhaoxi Zhang, Weineng Chen, Hailong Zhao, Jumana Yousuf Al-Aama, Sherif Edris, Huanming Yang, Jian Wang, Torben Hansen, Henrik Bjørn Nielsen, Søren Brunak, Karsten Kristiansen, Francisco Guarner, Oluf Pedersen, Joel Doré, S. Dusko Ehrlich, Peer Bork, Jun Wang, Nicolas Pons, Emmanuelle Le Chatelier, Jean Michel Batto, Sean Kennedy, Florence Haimet, Yohanan Winogradski, Eric Pelletier, Denis Lepaslier, François Artiguenave, Thomas Bruls, Jean Weissenbach, Keith Turner, Julian Parkhill, Maria Antolin, Francesc Casellas, Natalia Borruel, Encarna Varela, Antonio Torrejon, Gérard Denariaz, Muriel Derrien, Johan E.T. van Hylckama Vlieg, Patrick Viega, Raish Oozeer, Jan Knoll, Maria Rescigno, Christian Brechot, Christine M’rini, Alexandre Mérieux, Takuji Yamada, Sebastian Tims, Erwin G. Zoetendal, Michiel Kleerebezem, Willem M. de Vos, Antonella Cultrone, Marion Leclerc, Catherine Juste, Eric Guedon, Christine Delorme, Séverine Layec, Ghalia Khaci, Maarten van de Guchte, Gaetana Vandemeulebrouck, Alexandre Jamet, Rozenn Dervyn, Nicolas Sanchez, Hervé Blottière, Emmanuelle Maguin, Pierre Renault, Julien Tap, Daniel R. Mende

BGI-Shenzhen
BGI Hong Kong Research Institute
South China University of Technology
University of Copenhagen
European Molecular Biology Laboratory
Institut National de la Recherche Agronomique
Technical University of Denmark
Hosp Valle De Hebron
King Abdulaziz University
Zhejiang University
Unité mixte de Recherche 14121 Microbiologie de l’Alimentation au Service de la Santé
Guy's and St Thomas' NHS Foundation Trust
Max Delbrück Center for Molecular Medicine in the Helmholtz Association
Macau University of Science and Technology
Commissariat À L Energie Atomique
CNRS
CNRS-UMR8030 and Université Paris-Saclay
Wellcome Trust Genome Campus
Danone Research
Danone S.A.
IRCCS Istituto Europeo di Oncologia - Milano
BioMerieux
Wageningen University & Research
University of Helsinki

Research output: Contribution to journal › Article › peer-review

1754 Scopus citations

Abstract

Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

Original language	English
Pages (from-to)	834-841
Number of pages	8
Journal	Nature Biotechnology
Volume	32
Issue number	8
DOIs	https://doi.org/10.1038/nbt.2942
State	Published - 1 Aug 2014
Externally published	Yes

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/nbt.2942

Cite this

Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., Juncker, A. S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., ... Mende, D. R. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834-841. https://doi.org/10.1038/nbt.2942

@article{1fbaf383b5b24f3196169c235c0420dd,

title = "An integrated catalog of reference genes in the human gut microbiome",

abstract = "Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.",

author = "Junhua Li and Huijue Jia and Xianghang Cai and Huanzi Zhong and Qiang Feng and Shinichi Sunagawa and Manimozhiyan Arumugam and Kultima, \{Jens Roat\} and Edi Prifti and Trine Nielsen and Juncker, \{Agnieszka Sierakowska\} and Chaysavanh Manichanh and Bing Chen and Wenwei Zhang and Florence Levenez and Juan Wang and Xun Xu and Liang Xiao and Suisha Liang and Dongya Zhang and Zhaoxi Zhang and Weineng Chen and Hailong Zhao and Al-Aama, \{Jumana Yousuf\} and Sherif Edris and Huanming Yang and Jian Wang and Torben Hansen and Nielsen, \{Henrik Bj{\o}rn\} and S{\o}ren Brunak and Karsten Kristiansen and Francisco Guarner and Oluf Pedersen and Joel Dor{\'e} and Ehrlich, \{S. Dusko\} and Peer Bork and Jun Wang and Nicolas Pons and \{Le Chatelier\}, Emmanuelle and Batto, \{Jean Michel\} and Sean Kennedy and Florence Haimet and Yohanan Winogradski and Eric Pelletier and Denis Lepaslier and Fran{\c c}ois Artiguenave and Thomas Bruls and Jean Weissenbach and Keith Turner and Julian Parkhill and Maria Antolin and Francesc Casellas and Natalia Borruel and Encarna Varela and Antonio Torrejon and G{\'e}rard Denariaz and Muriel Derrien and \{van Hylckama Vlieg\}, \{Johan E.T.\} and Patrick Viega and Raish Oozeer and Jan Knoll and Maria Rescigno and Christian Brechot and Christine M{\textquoteright}rini and Alexandre M{\'e}rieux and Takuji Yamada and Sebastian Tims and Zoetendal, \{Erwin G.\} and Michiel Kleerebezem and \{de Vos\}, \{Willem M.\} and Antonella Cultrone and Marion Leclerc and Catherine Juste and Eric Guedon and Christine Delorme and S{\'e}verine Layec and Ghalia Khaci and \{van de Guchte\}, Maarten and Gaetana Vandemeulebrouck and Alexandre Jamet and Rozenn Dervyn and Nicolas Sanchez and Herv{\'e} Blotti{\`e}re and Emmanuelle Maguin and Pierre Renault and Julien Tap and Mende, \{Daniel R.\}",

year = "2014",

month = aug,

day = "1",

doi = "10.1038/nbt.2942",

language = "英语",

volume = "32",

pages = "834--841",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "8",

}

Li, J, Jia, H, Cai, X, Zhong, H, Feng, Q, Sunagawa, S, Arumugam, M, Kultima, JR, Prifti, E, Nielsen, T, Juncker, AS, Manichanh, C, Chen, B, Zhang, W, Levenez, F, Wang, J, Xu, X, Xiao, L, Liang, S, Zhang, D, Zhang, Z, Chen, W, Zhao, H, Al-Aama, JY, Edris, S, Yang, H, Wang, J, Hansen, T, Nielsen, HB, Brunak, S, Kristiansen, K, Guarner, F, Pedersen, O, Doré, J, Ehrlich, SD, Bork, P, Wang, J, Pons, N, Le Chatelier, E, Batto, JM, Kennedy, S, Haimet, F, Winogradski, Y, Pelletier, E, Lepaslier, D, Artiguenave, F, Bruls, T, Weissenbach, J, Turner, K, Parkhill, J, Antolin, M, Casellas, F, Borruel, N, Varela, E, Torrejon, A, Denariaz, G, Derrien, M, van Hylckama Vlieg, JET, Viega, P, Oozeer, R, Knoll, J, Rescigno, M, Brechot, C, M’rini, C, Mérieux, A, Yamada, T, Tims, S, Zoetendal, EG, Kleerebezem, M, de Vos, WM, Cultrone, A, Leclerc, M, Juste, C, Guedon, E, Delorme, C, Layec, S, Khaci, G, van de Guchte, M, Vandemeulebrouck, G, Jamet, A, Dervyn, R, Sanchez, N, Blottière, H, Maguin, E, Renault, P, Tap, J & Mende, DR 2014, 'An integrated catalog of reference genes in the human gut microbiome', Nature Biotechnology, vol. 32, no. 8, pp. 834-841. https://doi.org/10.1038/nbt.2942

TY - JOUR

T1 - An integrated catalog of reference genes in the human gut microbiome

AU - Li, Junhua

AU - Jia, Huijue

AU - Cai, Xianghang

AU - Zhong, Huanzi

AU - Feng, Qiang

AU - Sunagawa, Shinichi

AU - Arumugam, Manimozhiyan

AU - Kultima, Jens Roat

AU - Prifti, Edi

AU - Nielsen, Trine

AU - Juncker, Agnieszka Sierakowska

AU - Manichanh, Chaysavanh

AU - Chen, Bing

AU - Zhang, Wenwei

AU - Levenez, Florence

AU - Wang, Juan

AU - Xu, Xun

AU - Xiao, Liang

AU - Liang, Suisha

AU - Zhang, Dongya

AU - Zhang, Zhaoxi

AU - Chen, Weineng

AU - Zhao, Hailong

AU - Al-Aama, Jumana Yousuf

AU - Edris, Sherif

AU - Yang, Huanming

AU - Wang, Jian

AU - Hansen, Torben

AU - Nielsen, Henrik Bjørn

AU - Brunak, Søren

AU - Kristiansen, Karsten

AU - Guarner, Francisco

AU - Pedersen, Oluf

AU - Doré, Joel

AU - Ehrlich, S. Dusko

AU - Bork, Peer

AU - Wang, Jun

AU - Pons, Nicolas

AU - Le Chatelier, Emmanuelle

AU - Batto, Jean Michel

AU - Kennedy, Sean

AU - Haimet, Florence

AU - Winogradski, Yohanan

AU - Pelletier, Eric

AU - Lepaslier, Denis

AU - Artiguenave, François

AU - Bruls, Thomas

AU - Weissenbach, Jean

AU - Turner, Keith

AU - Parkhill, Julian

AU - Antolin, Maria

AU - Casellas, Francesc

AU - Borruel, Natalia

AU - Varela, Encarna

AU - Torrejon, Antonio

AU - Denariaz, Gérard

AU - Derrien, Muriel

AU - van Hylckama Vlieg, Johan E.T.

AU - Viega, Patrick

AU - Oozeer, Raish

AU - Knoll, Jan

AU - Rescigno, Maria

AU - Brechot, Christian

AU - M’rini, Christine

AU - Mérieux, Alexandre

AU - Yamada, Takuji

AU - Tims, Sebastian

AU - Zoetendal, Erwin G.

AU - Kleerebezem, Michiel

AU - de Vos, Willem M.

AU - Cultrone, Antonella

AU - Leclerc, Marion

AU - Juste, Catherine

AU - Guedon, Eric

AU - Delorme, Christine

AU - Layec, Séverine

AU - Khaci, Ghalia

AU - van de Guchte, Maarten

AU - Vandemeulebrouck, Gaetana

AU - Jamet, Alexandre

AU - Dervyn, Rozenn

AU - Sanchez, Nicolas

AU - Blottière, Hervé

AU - Maguin, Emmanuelle

AU - Renault, Pierre

AU - Tap, Julien

AU - Mende, Daniel R.

PY - 2014/8/1

Y1 - 2014/8/1

N2 - Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

AB - Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

UR - https://www.scopus.com/pages/publications/84905730165

U2 - 10.1038/nbt.2942

DO - 10.1038/nbt.2942

M3 - 文章

C2 - 24997786

AN - SCOPUS:84905730165

SN - 1087-0156

VL - 32

SP - 834

EP - 841

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 8

ER -

An integrated catalog of reference genes in the human gut microbiome

Abstract

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