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Nat Biotechnol. 2014 Aug;32(8):834-41. doi: 10.1038/nbt.2942. Epub 2014 Jul 6.

An integrated catalog of reference genes in the human gut microbiome.

Author information

1
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].
2
1] BGI-Shenzhen, Shenzhen, China. [2].
3
1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3].
4
European Molecular Biology Laboratory, Heidelberg, Germany.
5
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.
6
INRA, Institut National de la Recherche Agronomique, Metagenopolis, Jouy en Josas, France.
7
The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
8
Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.
9
Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, Barcelona, Spain.
10
BGI-Shenzhen, Shenzhen, China.
11
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.
12
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.
13
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.
14
1] BGI-Shenzhen, Shenzhen, China. [2] James D. Watson Institute of Genome Science, Hangzhou, China.
15
Department of Biology, University of Copenhagen, Copenhagen, Denmark.
16
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.
17
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.
18
1] European Molecular Biology Laboratory, Heidelberg, Germany. [2] Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
19
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.

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.

PMID:
24997786
DOI:
10.1038/nbt.2942
[Indexed for MEDLINE]

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