An integrated catalog of reference genes in the human gut microbiome
2014
Li, Junhua | Jia, Huijue | Cai, Xianghang | Zhong, Huanzi | Feng, Qiang | Sunagawa, Shinichi | Arumugam, Manimozhiyan | Kultima, Jens Roat | Prifti, Edi | Nielsen, Trine | Juncker, Agnieszka Sierakowska | 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 | Dore, Joel | Ehrlich, Stanislav | Bork, Peer | Wang, Jun | Pons, Nicolas | Le Chatelier, Emmanuelle | Batto, Jean-Michel | Kennedy, Sean | Haimet, Florence | Winogradsky, Yohanan | Cultrone, Antonietta | Leclerc, Marion | Juste, Catherine | Guédon, Eric | Delorme, Christine | Layec, Séverine | Kaci, Ghalia | van de Guchte, Maarten | Vandemeulebrouck, Gaetana | Jamet, Alexandre | Dervyn, Rozenn | Sanchez, Nicolas | Blottiere, Herve | Maguin, Emmanuelle | Renault, Pierre | Tap, Julien | Beijing Genomics Institute [Shenzhen] (BGI) | School of Bioscience and Biotechnology ; Southern University of Science and Technology (SUSTech) | Department of Biology [Copenhagen] ; Faculty of Science [Copenhagen] ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH) | European Molecular Biology Laboratory | Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) ; Faculty of Health and Medical Sciences ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH) | MetaGenoPolis ; Institut National de la Recherche Agronomique (INRA) | Center for Biological Sequence Analysis ; Danmarks Tekniske Universitet = Technical University of Denmark (DTU) | Digestive System Research Unit ; Vall d'Hebron University Hospital [Barcelona] | Department of Genetic Medicine, Faculty of Medicine ; King Abdulaziz University | Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine ; King Abdulaziz University | Department of Biological Sciences, Faculty of Science ; King Abdulaziz University | Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD) ; King Abdulaziz University | James D. Watson Institute of Genome Science ; Zhejiang University [Hangzhou, China] | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Centre for Host-Microbiome Interactions, Dental Institute Central Office ; King‘s College London | Max Delbrück Center for Molecular Medicine [Berlin] (MDC) ; Helmholtz-Gemeinschaft = Helmholtz Association | Macau University of Science and Technology (MUST) | Département Microbiologie et Chaîne Alimentaire (MICA) ; Institut National de la Recherche Agronomique (INRA) | ANR-11-DPBS-0001,MGP,MetaGenoPolis(2011)
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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