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 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

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 Juncker, Chaysavanh Manichanh, Bing Chen, Wenwei Zhang, Florence Levenez, Juan Wang, Xun Xu, Liang Xiao, Suisha Liang, Dongya ZhangZhaoxi 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

Genome Research and Molecular Bio Medicine

823 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
Journal	Nature Biotechnology
Volume	32
Issue number	8
Pages (from-to)	834-845
Number of pages	12
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.2942
Publication status	Published - 1 Aug 2014

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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

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

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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.",

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AU - Sunagawa, Shinichi

AU - Arumugam, Manimozhiyan

AU - Kultima, Jens Roat

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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

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An integrated catalog of reference genes in the human gut microbiome

Abstract

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