Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
H Bjørn Nielsen
(1, 2)
,
Mathieu Almeida
(3, 4)
,
Agnieszka Sierakowska Juncker
(1, 2)
,
Simon Rasmussen
(1)
,
Junhua Li
(5, 6)
,
Shinichi Sunagawa
(7)
,
Damian R Plichta
(1)
,
Laurent Gautier
(1)
,
Anders G Pedersen
(1)
,
Emmanuelle Le Chatelier
(8, 3)
,
Eric Pelletier
(9, 10)
,
Ida Bonde
(1, 2)
,
Trine Nielsen
(11)
,
Chaysavanh Manichanh
(12)
,
Manimozhiyan Arumugam
(13, 7, 11)
,
Jean-Michel Batto
(3, 8)
,
Marcelo B Quintanilha dos Santos
(1)
,
Nikolaj Blom
(2)
,
Natalia Borruel
(12)
,
Kristoffer S Burgdorf
(11)
,
Fouad Boumezbeur
(3, 8)
,
Francesc Casellas
(12)
,
Joel Dore
(3, 8)
,
Piotr Dworzynski
(1)
,
Francisco Guarner
(12)
,
Torben Hansen
(11, 14)
,
Falk Hildebrand
(15, 16)
,
Rolf S Kaas
(17)
,
Sean Kennedy
(8)
,
Karsten Kristiansen
(13, 18)
,
Jens Roat Kultima
(7)
,
Pierre Léonard
(8, 3)
,
Florence Levenez
(8, 3)
,
Ole Lund
(1)
,
Bouziane Moumen
(3, 8)
,
Denis Le Paslier
(9, 10)
,
Nicolas Pons
(8, 3)
,
Oluf Pedersen
(11, 19, 20)
,
Edi Prifti
(8, 3)
,
Junjie Qin
(21, 13)
,
Jeroen Raes
(16, 22, 23)
,
Søren Sørensen
(24)
,
Julien Tap
(7)
,
Sebastian Tims
(25)
,
David W Ussery
(1)
,
Takuji Yamada
(7, 26)
,
Pierre Renault
(3)
,
Thomas Sicheritz-Ponten
(1, 2)
,
Peer Bork
(7, 27)
,
Jun Wang
(13, 11, 18, 28)
,
Søren Brunak
(1, 2)
,
Stanislav Ehrlich
(8, 3, 29)
,
Alexandre Jamet
(3)
,
Antonietta Cultrone
(3)
,
Christine Delorme
(3)
,
Emmanuelle Maguin
(30)
,
Eric Guédon
(3)
,
Gaetana Vandemeulebrouck
(3)
,
Ghalia Kaci
(3)
,
Herve Blottiere
(3)
,
Maarten van de Guchte
(3)
,
Nicolas Sanchez
(3)
,
Rozenn Dervyn
(3)
,
Séverine Layec
(3)
,
Yohanan Winogradsky
(3)
1
Center for Biological Sequence Analysis
2 Novo Nordisk Foundation Center for Biosustainability
3 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
4 Department of Computer Science [Baltimore]
5 BGI Hong Kong Researche Institute
6 School of Bioscience and Biotechnology
7 European Molecular Biology Laboratory
8 MetaGenoPolis
9 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
10 UEVE - Université d'Évry-Val-d'Essonne
11 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
12 Digestive System Research Unit
13 BGI - Beijing Genomics Institute [Shenzhen]
14 Faculty of Health Sciences
15 Department of Structural Biology
16 Department of Bioscience Engineering
17 8National Food Institute - Division for Epidemiology and Microbial Genomics
18 Department of Biology [Copenhagen]
19 Hagedorn Research Institute
20 Faculty of Health
21 BGI Hong Kong research Institute
22 Rega Institute - Department of Microbiology and Immunology
23 VIB Center for the Biology of Disease
24 Section of Microbiology [Copenhagen]
25 Laboratory of Microbiology
26 Department of Biological Information
27 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
28 Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders
29 Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital
30 MICA - Département Microbiologie et Chaîne Alimentaire
2 Novo Nordisk Foundation Center for Biosustainability
3 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
4 Department of Computer Science [Baltimore]
5 BGI Hong Kong Researche Institute
6 School of Bioscience and Biotechnology
7 European Molecular Biology Laboratory
8 MetaGenoPolis
9 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
10 UEVE - Université d'Évry-Val-d'Essonne
11 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
12 Digestive System Research Unit
13 BGI - Beijing Genomics Institute [Shenzhen]
14 Faculty of Health Sciences
15 Department of Structural Biology
16 Department of Bioscience Engineering
17 8National Food Institute - Division for Epidemiology and Microbial Genomics
18 Department of Biology [Copenhagen]
19 Hagedorn Research Institute
20 Faculty of Health
21 BGI Hong Kong research Institute
22 Rega Institute - Department of Microbiology and Immunology
23 VIB Center for the Biology of Disease
24 Section of Microbiology [Copenhagen]
25 Laboratory of Microbiology
26 Department of Biological Information
27 MDC - Max Delbrück Center for Molecular Medicine [Berlin]
28 Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders
29 Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital
30 MICA - Département Microbiologie et Chaîne Alimentaire
Junhua Li
- Fonction : Auteur
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- ORCID : 0000-0001-6784-1873
Emmanuelle Le Chatelier
- Fonction : Auteur
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Eric Pelletier
- Fonction : Auteur
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- ORCID : 0000-0003-4228-1712
- IdRef : 250792974
Trine Nielsen
- Fonction : Auteur
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- ORCID : 0000-0002-2066-7895
Manimozhiyan Arumugam
- Fonction : Auteur
- PersonId : 770023
- ORCID : 0000-0002-0886-9101
Fouad Boumezbeur
- Fonction : Auteur
- PersonId : 969895
Torben Hansen
- Fonction : Auteur
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- ORCID : 0000-0001-8748-3831
Karsten Kristiansen
- Fonction : Auteur
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- ORCID : 0000-0002-6024-0917
Bouziane Moumen
- Fonction : Auteur
- PersonId : 743282
- IdHAL : bmoumen
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- IdRef : 143445324
Denis Le Paslier
- Fonction : Auteur
- PersonId : 742161
- IdHAL : denis-le-paslier
- ORCID : 0000-0003-4335-9956
- IdRef : 080524486
Oluf Pedersen
- Fonction : Auteur
- PersonId : 1070332
Edi Prifti
- Fonction : Auteur
- PersonId : 1151183
- IdHAL : edi-prifti
- ORCID : 0000-0001-8861-1305
- IdRef : 155572822
Julien Tap
- Fonction : Auteur
- PersonId : 1172956
- IdHAL : julien-tap
- ORCID : 0000-0001-8998-5413
Alexandre Jamet
- Fonction : Auteur
- PersonId : 737690
- IdHAL : alexandre-jamet
- IdRef : 253129699
Christine Delorme
- Fonction : Auteur
- PersonId : 736589
- IdHAL : christine-delorme
- ORCID : 0000-0002-5208-7238
- IdRef : 124303129
Emmanuelle Maguin
- Fonction : Auteur
- PersonId : 751613
- IdHAL : e-maguin
- ORCID : 0000-0001-5452-3382
- IdRef : 032881487
Eric Guédon
- Fonction : Auteur
- PersonId : 743950
- IdHAL : eguedon35
- ORCID : 0000-0002-0901-4447
- IdRef : 140101888
Gaetana Vandemeulebrouck
- Fonction : Auteur
- PersonId : 969463
Herve Blottiere
- Fonction : Auteur
- PersonId : 747227
- IdHAL : herve-blottiere
- ORCID : 0000-0002-8390-0607
- IdRef : 076955648
Maarten van de Guchte
- Fonction : Auteur
- PersonId : 735862
- IdHAL : maarten-van-de-guchte
- ORCID : 0000-0002-5980-4631
Séverine Layec
- Fonction : Auteur
- PersonId : 754110
- IdHAL : severine-layec
- ORCID : 0000-0001-5053-8712
Résumé
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.