An integrated catalog of reference genes in the human gut microbiome

被引：1507

作者：

Li, Junhua ^{[1
,2
,3
]}

Jia, Huijue ^{[1
]}

Cai, Xianghang ^{[1
]}

Zhong, Huanzi ^{[1
]}

Feng, Qiang ^{[1
,4
]}

Sunagawa, Shinichi ^{[5
]}

Arumugam, Manimozhiyan ^{[1
,5
,6
]}

Kultima, Jens Roat ^{[5
]}

Prifti, Edi ^{[7
]}

Nielsen, Trine ^{[6
]}

Juncker, Agnieszka Sierakowska ^{[8
]}

Manichanh, Chaysavanh ^{[9
]}

Chen, Bing ^{[1
]}

Zhang, Wenwei ^{[1
]}

Levenez, Florence ^{[7
]}

Wang, Juan ^{[1
]}

Xu, Xun ^{[1
]}

Xiao, Liang ^{[1
]}

Liang, Suisha ^{[1
]}

Zhang, Dongya ^{[1
]}

Zhang, Zhaoxi ^{[1
]}

Chen, Weineng ^{[1
]}

Zhao, Hailong ^{[1
]}

Al-Aama, Jumana Yousuf ^{[10
,11
]}

Edris, Sherif ^{[11
,12
]}

Yang, Huanming ^{[1
,11
,13
]}

Wang, Jian ^{[1
,13
]}

Hansen, Torben ^{[6
]}

Nielsen, Henrik Bjorn ^{[8
]}

Brunak, Soren ^{[8
]}

Kristiansen, Karsten ^{[4
]}

Guarner, Francisco

Pedersen, Oluf ^{[6
]}

Dore, Joel ^{[7
,14
]}

Ehrlich, S. Dusko ^{[7
,15
]}

Bork, Peer ^{[5
,16
]}

Wang, Jun ^{[1
,4
,6
,11
,17
]}

机构：

[1] BGI Shenzhen, Shenzhen, Peoples R China

[2] BGI Hong Kong Res Inst, Hong Kong, Hong Kong, Peoples R China

[3] S China Univ Technol, Sch Biosci & Biotechnol, Guangzhou, Guangdong, Peoples R China

[4] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

[5] European Mol Biol Lab, D-69012 Heidelberg, Germany

[6] Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Basic Metab Res, Copenhagen, Denmark

[7] INRA, Metagenopolis, Jouy En Josas, France

[8] Tech Univ Denmark, Ctr Biol Sequence Anal, DK-2800 Lyngby, Denmark

[9] Univ Hosp Vall dHebron, Digest Syst Res Unit, Barcelona, Spain

[10] King Abdulaziz Univ, Fac Med, Dept Med Genet, Jeddah 21413, Saudi Arabia

[11] KAU, Fac Med, Princess Al Jawhara AlBrahim Ctr Excellence Res H, Jeddah, Saudi Arabia

[12] King Abdulaziz Univ, Fac Sci, Dept Biol Sci, Jeddah, Saudi Arabia

[13] James D Watson Inst Genome Sci, Hangzhou, Zhejiang, Peoples R China

[14] INRA, Unite Mixte Rech 14121, Microbiol Alimentat Serv Sante, Jouy En Josas, France

[15] Kings Coll London, Guys Hosp, Inst Dent, Cent Off,Ctr Host Microbiome Interact, London, England

[16] Max Delbruck Ctr Mol Med, Berlin, Germany

[17] Macau Univ Sci & Technol, Macau, Peoples R China

来源：

NATURE BIOTECHNOLOGY | 2014年 / 32卷 / 08期

基金：

欧洲研究理事会;

关键词：

EUKARYOTIC DIVERSITY; FECAL MICROBIOTA; POPULATION-SIZE; METAGENOME; GENOMES; IMPACT; SETS;

D O I：

10.1038/nbt.2942

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：834 / 841

页数：8

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