An integrated catalog of reference genes in the human gut microbiome

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

An integrated catalog of reference genes in the human gut microbiome. / Li, Junhua; Jia, Huijue; Cai, Xianghang; Zhong, Huanzi; Feng, Qiang; Sunagawa, Shinichi; Arumugam, Manimozhiyan; Kultima, Jens Roat; Prifti, Edi; Nielsen, Trine; Juncker, Agnieszka; Manichanh, Chaysavanh; Chen, Bing; Zhang, Wenwei; Levenez, Florence; Wang, Juan; Xu, Xun; Xiao, Liang; Liang, Suisha; Zhang, Dongya; Zhang, Zhaoxi; Chen, Weineng; Zhao, Hailong; Al-Aama, Jumana Yousuf; Edris, Sherif; Yang, Huanming; Wang, Jian; Hansen, Torben; Nielsen, Henrik Bjørn; Brunak, Søren; Kristiansen, Karsten; Guarner, Francisco; Pedersen, Oluf; Doré, Joel; Ehrlich, S Dusko; Bork, Peer; Wang, Jun.

In: Nature Biotechnology, Vol. 32, No. 8, 2014, p. 834-845.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Li, J, Jia, H, Cai, X, Zhong, H, Feng, Q, Sunagawa, S, Arumugam, M, Kultima, JR, Prifti, E, Nielsen, T, Juncker, A, 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 2014, 'An integrated catalog of reference genes in the human gut microbiome', Nature Biotechnology, vol. 32, no. 8, pp. 834-845. https://doi.org/10.1038/nbt.2942

APA

Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., Juncker, A., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., ... Wang, J. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834-845. https://doi.org/10.1038/nbt.2942

Vancouver

Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S et al. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology. 2014;32(8):834-845. https://doi.org/10.1038/nbt.2942

Author

Li, Junhua ; Jia, Huijue ; Cai, Xianghang ; Zhong, Huanzi ; Feng, Qiang ; Sunagawa, Shinichi ; Arumugam, Manimozhiyan ; Kultima, Jens Roat ; Prifti, Edi ; Nielsen, Trine ; Juncker, Agnieszka ; Manichanh, Chaysavanh ; Chen, Bing ; Zhang, Wenwei ; Levenez, Florence ; Wang, Juan ; Xu, Xun ; Xiao, Liang ; Liang, Suisha ; Zhang, Dongya ; Zhang, Zhaoxi ; Chen, Weineng ; Zhao, Hailong ; Al-Aama, Jumana Yousuf ; Edris, Sherif ; Yang, Huanming ; Wang, Jian ; Hansen, Torben ; Nielsen, Henrik Bjørn ; Brunak, Søren ; Kristiansen, Karsten ; Guarner, Francisco ; Pedersen, Oluf ; Doré, Joel ; Ehrlich, S Dusko ; Bork, Peer ; Wang, Jun. / An integrated catalog of reference genes in the human gut microbiome. In: Nature Biotechnology. 2014 ; Vol. 32, No. 8. pp. 834-845.

Bibtex

@article{b39d4a15c465428e828b3915444cbb14,
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 Agnieszka Juncker 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",
year = "2014",
doi = "10.1038/nbt.2942",
language = "English",
volume = "32",
pages = "834--845",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "nature publishing group",
number = "8",

}

RIS

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

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

PY - 2014

Y1 - 2014

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.

U2 - 10.1038/nbt.2942

DO - 10.1038/nbt.2942

M3 - Journal article

C2 - 24997786

VL - 32

SP - 834

EP - 845

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 8

ER -

ID: 119293288