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.
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] BGI Hong Kong Research Institute, Hong Kong, China. [3] School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. [4].
authors.forename: Junhua
authors.initials: J
authors.lastname: Li
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2].
authors.forename: Huijue
authors.identifier: 000000023592126X
authors.initials: H
authors.lastname: Jia
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2].
authors.forename: Xianghang
authors.initials: X
authors.lastname: Cai
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2].
authors.forename: Huanzi
authors.initials: H
authors.lastname: Zhong
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3].
authors.forename: Qiang
authors.initials: Q
authors.lastname: Feng
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] European Molecular Biology Laboratory, Heidelberg, Germany. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Manimozhiyan
authors.identifier: 0000000208869101
authors.initials: M
authors.lastname: Arumugam
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Jens Roat
authors.initials: JR
authors.lastname: Kultima
authors.affiliation: INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
authors.forename: Edi
authors.identifier: 0000000188611305
authors.initials: E
authors.lastname: Prifti
authors.affiliation: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Trine
authors.initials: T
authors.lastname: Nielsen
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Agnieszka Sierakowska
authors.initials: AS
authors.lastname: Juncker
authors.affiliation: Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain.
authors.forename: Chaysavanh
authors.initials: C
authors.lastname: Manichanh
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Wenwei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Xiao
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Suisha
authors.initials: S
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Dongya
authors.initials: D
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhaoxi
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Weineng
authors.initials: W
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Hailong
authors.initials: H
authors.lastname: Zhao
authors.affiliation: 1] Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University (KAU), Jeddah, Saudi Arabia. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia.
authors.forename: Jumana Yousuf
authors.initials: JY
authors.lastname: Al-Aama
authors.affiliation: 1] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [2] Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah, Saudi Arabia.
authors.forename: Sherif
authors.initials: S
authors.lastname: Edris
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [3] James D. Watson Institute of Genome Science, Hangzhou, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Science, Hangzhou, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Torben
authors.initials: T
authors.lastname: Hansen
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Henrik Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.affiliation: Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Guarner
authors.affiliation: The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Oluf
authors.initials: O
authors.lastname: Pedersen
authors.affiliation: 1] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. [2] INRA, Institut National de la Recherche Agronomique, Unité mixte de Recherche 14121 Microbiologie de l'Alimentation au Service de la Santé, Jouy en Josas, France.
authors.forename: Joel
authors.initials: J
authors.lastname: Doré
authors.affiliation: 1] INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France. [2] Centre for Host-Microbiome Interactions, Dental Institute Central Office, King's College London, Guy's Hospital, London Bridge, UK.
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.affiliation: 1] European Molecular Biology Laboratory, Heidelberg, Germany. [2] Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: 1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [4] Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, KAU, Jeddah, Saudi Arabia. [5] Macau University of Science and Technology, Macau, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D002377:Catalogs as Topic; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D056186:Metagenomics; D064307:Microbiota