An integrated catalog of reference genes in the human gut microbiome

J. Li; H. Jia; X. Cai; H. Zhong; Q. Feng; S. Sunagawa; M. Arumugam; J.R. Kultima; E. Prifti; T. Nielsen; A.S. Juncker; C. Manichanh; B. Chen; W. Zhang; F. Levenez; X. Xu; L. Xiao; S. Liang; D. Zhang; Z. Zhang; W. Chen; H. Zhao; J.Y. Al-Aama; S. Edris; H. Yang; H. Hansen; H.B. Nielsen; S. Brunak; K. Kristiansen; F. Guarner; O. Pedersen; J. Doré; S.D. Ehrlich; P. Bork; J. Wang; W.M. de Vos; S. Tims; E.G. Zoetendal; M. Kleerebezem

doi:10.1038/nbt.2942

An integrated catalog of reference genes in the human gut microbiome

J. Li, H. Jia, X. Cai, H. Zhong, Q. Feng, S. Sunagawa, M. Arumugam, J.R. Kultima, E. Prifti, T. Nielsen, A.S. Juncker, C. Manichanh, B. Chen, W. Zhang, F. Levenez, X. Xu, L. Xiao, S. Liang, D. Zhang, Z. ZhangW. Chen, H. Zhao, J.Y. Al-Aama, S. Edris, H. Yang, H. Hansen, H.B. Nielsen, S. Brunak, K. Kristiansen, F. Guarner, O. Pedersen, J. Doré, S.D. Ehrlich, P. Bork, J. Wang, W.M. de Vos, S. Tims, E.G. Zoetendal, M. Kleerebezem

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

1552 Citations (Scopus)

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
Journal	Nature Biotechnology
Volume	32
Issue number	8
DOIs	https://doi.org/10.1038/nbt.2942
Publication status	Published - 2014

Keywords

eukaryotic diversity
fecal microbiota
population-size
metagenome
sequences
genomes
tool
alignment
impact
twins

UN SDGs

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

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10.1038/nbt.2942

METAHIT: Metagenomics of the Human Intestinal Tract
1/01/08 → 30/06/12
Project: EU research project

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., Xu, X., Xiao, L., Liang, S., Zhang, D., ... Kleerebezem, M. (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{c90a75e9cc2048088dfd4a1ed30355fb,

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.",

keywords = "eukaryotic diversity, fecal microbiota, population-size, metagenome, sequences, genomes, tool, alignment, impact, twins",

author = "J. Li and H. Jia and X. Cai and H. Zhong and Q. Feng and S. Sunagawa and M. Arumugam and J.R. Kultima and E. Prifti and T. Nielsen and A.S. Juncker and C. Manichanh and B. Chen and W. Zhang and F. Levenez and X. Xu and L. Xiao and S. Liang and D. Zhang and Z. Zhang and W. Chen and H. Zhao and J.Y. Al-Aama and S. Edris and H. Yang and H. Hansen and H.B. Nielsen and S. Brunak and K. Kristiansen and F. Guarner and O. Pedersen and J. Dor{\'e} and S.D. Ehrlich and P. Bork and J. Wang and {de Vos}, W.M. and S. Tims and E.G. Zoetendal and M. Kleerebezem",

year = "2014",

doi = "10.1038/nbt.2942",

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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, Xu, X, Xiao, L, Liang, S, Zhang, D, Zhang, Z, Chen, W, Zhao, H, Al-Aama, JY, Edris, S, Yang, H, Hansen, H, Nielsen, HB, Brunak, S, Kristiansen, K, Guarner, F, Pedersen, O, Doré, J, Ehrlich, SD, Bork, P, Wang, J, de Vos, WM, Tims, S, Zoetendal, EG & Kleerebezem, M 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, J.

AU - Jia, H.

AU - Cai, X.

AU - Zhong, H.

AU - Feng, Q.

AU - Sunagawa, S.

AU - Arumugam, M.

AU - Kultima, J.R.

AU - Prifti, E.

AU - Nielsen, T.

AU - Juncker, A.S.

AU - Manichanh, C.

AU - Chen, B.

AU - Zhang, W.

AU - Levenez, F.

AU - Xu, X.

AU - Xiao, L.

AU - Liang, S.

AU - Zhang, D.

AU - Zhang, Z.

AU - Chen, W.

AU - Zhao, H.

AU - Al-Aama, J.Y.

AU - Edris, S.

AU - Yang, H.

AU - Hansen, H.

AU - Nielsen, H.B.

AU - Brunak, S.

AU - Kristiansen, K.

AU - Guarner, F.

AU - Pedersen, O.

AU - Doré, J.

AU - Ehrlich, S.D.

AU - Bork, P.

AU - Wang, J.

AU - de Vos, W.M.

AU - Tims, S.

AU - Zoetendal, E.G.

AU - Kleerebezem, M.

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.

KW - eukaryotic diversity

KW - fecal microbiota

KW - population-size

KW - metagenome

KW - sequences

KW - genomes

KW - tool

KW - alignment

KW - impact

KW - twins

U2 - 10.1038/nbt.2942

DO - 10.1038/nbt.2942

M3 - Article

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

Keywords

UN SDGs

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Projects

METAHIT: Metagenomics of the Human Intestinal Tract

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