An integrated catalog of reference genes in the human gut microbiome
Junhua Li
(1, 2)
,
Huijue Jia
(1)
,
Xianghang Cai
(1)
,
Huanzi Zhong
(1)
,
Qiang Feng
(1, 3)
,
Shinichi Sunagawa
(4)
,
Manimozhiyan Arumugam
(1, 4, 5)
,
Jens Roat Kultima
(4)
,
Edi Prifti
(6)
,
Trine Nielsen
(5)
,
Agnieszka Sierakowska Juncker
(7)
,
Chaysavanh Manichanh
(8)
,
Bing Chen
(1)
,
Wenwei Zhang
(1)
,
Florence Levenez
(6)
,
Juan Wang
(1)
,
Xun Xu
(1)
,
Liang Xiao
(1)
,
Suisha Liang
(1)
,
Dongya Zhang
(1)
,
Zhaoxi Zhang
(1)
,
Weineng Chen
(1)
,
Hailong Zhao
(1)
,
Jumana Yousuf Al-Aama
(9, 10)
,
Sherif Edris
(10, 11)
,
Huanming Yang
(1, 12, 13)
,
Jian Wang
(1, 13)
,
Torben Hansen
(5)
,
Henrik Bjørn Nielsen
(7)
,
Søren Brunak
(7)
,
Karsten Kristiansen
(3)
,
Francisco Guarner
(8)
,
Oluf Pedersen
(5)
,
Joel Dore
(14, 6)
,
Stanislav Ehrlich
(6, 15)
,
Peer Bork
(4, 16)
,
Jun Wang
(1, 3, 5, 10, 17)
,
Nicolas Pons
(6)
,
Emmanuelle Le Chatelier
(6)
,
Jean-Michel Batto
(14)
,
Sean Kennedy
(14)
,
Florence Haimet
(6)
,
Yohanan Winogradsky
(14)
,
Antonietta Cultrone
(14)
,
Marion Leclerc
(14)
,
Catherine Juste
(14)
,
Eric Guédon
(14)
,
Christine Delorme
(14)
,
Séverine Layec
(14)
,
Ghalia Kaci
(14)
,
Maarten van de Guchte
(14)
,
Gaetana Vandemeulebrouck
(14)
,
Alexandre Jamet
(14)
,
Rozenn Dervyn
(14)
,
Nicolas Sanchez
(14)
,
Herve Blottiere
(14)
,
Emmanuelle Maguin
(18)
,
Pierre Renault
(14)
,
Julien Tap
(14)
1
BGI -
Beijing Genomics Institute [Shenzhen]
2 School of Bioscience and Biotechnology
3 Department of Biology [Copenhagen]
4 European Molecular Biology Laboratory
5 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
6 MetaGenoPolis
7 Center for Biological Sequence Analysis
8 Digestive System Research Unit
9 Department of Genetic Medicine, Faculty of Medicine
10 Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine
11 Department of Biological Sciences, Faculty of Science
12 Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD)
13 James D. Watson Institute of Genome Science
14 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
15 Centre for Host-Microbiome Interactions, Dental Institute Central Office
16 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
17 MUST - Macau University of Science and Technology
18 MICA - Département Microbiologie et Chaîne Alimentaire
2 School of Bioscience and Biotechnology
3 Department of Biology [Copenhagen]
4 European Molecular Biology Laboratory
5 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
6 MetaGenoPolis
7 Center for Biological Sequence Analysis
8 Digestive System Research Unit
9 Department of Genetic Medicine, Faculty of Medicine
10 Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine
11 Department of Biological Sciences, Faculty of Science
12 Princess Al-Jawhara AlBrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD)
13 James D. Watson Institute of Genome Science
14 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
15 Centre for Host-Microbiome Interactions, Dental Institute Central Office
16 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
17 MUST - Macau University of Science and Technology
18 MICA - Département Microbiologie et Chaîne Alimentaire
Junhua Li
- Fonction : Auteur
- PersonId : 770145
- ORCID : 0000-0001-6784-1873
Huijue Jia
- Fonction : Auteur
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- ORCID : 0000-0002-3592-126X
Manimozhiyan Arumugam
- Fonction : Auteur
- PersonId : 770023
- ORCID : 0000-0002-0886-9101
Edi Prifti
- Fonction : Auteur
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- IdHAL : edi-prifti
- ORCID : 0000-0001-8861-1305
- IdRef : 155572822
Trine Nielsen
- Fonction : Auteur
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- ORCID : 0000-0002-2066-7895
Torben Hansen
- Fonction : Auteur
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- ORCID : 0000-0001-8748-3831
Karsten Kristiansen
- Fonction : Auteur
- PersonId : 757952
- ORCID : 0000-0002-6024-0917
Oluf Pedersen
- Fonction : Auteur
- PersonId : 1070332
Jun Wang
- Fonction : Auteur
- PersonId : 881572
Emmanuelle Le Chatelier
- Fonction : Auteur
- PersonId : 737756
- IdHAL : emmanuelle-le-chatelier
- ORCID : 0000-0002-2724-0536
Sean Kennedy
- Fonction : Auteur
- PersonId : 1203215
Marion Leclerc
- Fonction : Auteur
- PersonId : 748825
- IdHAL : marion-leclerc
- ORCID : 0000-0001-8684-2847
- IdRef : 142653721
Eric Guédon
- Fonction : Auteur
- PersonId : 743950
- IdHAL : eguedon35
- ORCID : 0000-0002-0901-4447
- IdRef : 140101888
Christine Delorme
- Fonction : Auteur
- PersonId : 736589
- IdHAL : christine-delorme
- ORCID : 0000-0002-5208-7238
- IdRef : 124303129
Séverine Layec
- Fonction : Auteur
- PersonId : 754110
- IdHAL : severine-layec
- ORCID : 0000-0001-5053-8712
Maarten van de Guchte
- Fonction : Auteur
- PersonId : 735862
- IdHAL : maarten-van-de-guchte
- ORCID : 0000-0002-5980-4631
Gaetana Vandemeulebrouck
- Fonction : Auteur
- PersonId : 969463
Alexandre Jamet
- Fonction : Auteur
- PersonId : 737690
- IdHAL : alexandre-jamet
- IdRef : 253129699
Herve Blottiere
- Fonction : Auteur
- PersonId : 747227
- IdHAL : herve-blottiere
- ORCID : 0000-0002-8390-0607
- IdRef : 076955648
Emmanuelle Maguin
- Fonction : Auteur
- PersonId : 751613
- IdHAL : e-maguin
- ORCID : 0000-0001-5452-3382
- IdRef : 032881487
Julien Tap
- Fonction : Auteur
- PersonId : 1172956
- IdHAL : julien-tap
- ORCID : 0000-0001-8998-5413
Résumé
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.