Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries,...

Descripción completa

Detalles Bibliográficos
Autores: Pasolli, E., Asnicar, Francesco, Manara, S., Zolfo, M., Karcher, N., Armanini, Federica, Beghini, F., Manghi, P., Tett, A., Ghensi, P., Collado, María Carmen, Rice, B.L., DuLong, C., Morgan, X.C., Golden, Christopher D., Quince, C., Huttenhower, C., Segata, Nicola
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/196155
Acceso en línea:http://hdl.handle.net/10261/196155
Access Level:acceso abierto
Palabra clave:Metagenomic assembly
Human microbiome
Metagenomics
Metagenomic meta-analysis
Non-Westernized microbiomes
Uunexplored microbial diversity
Metagenomic mappability
id ES_cbdb2e1f2c6fc087913ffe0a458034a1
oai_identifier_str oai:digital.csic.es:10261/196155
network_acronym_str ES
network_name_str España
repository_id_str
spelling Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and LifestylePasolli, E.Asnicar, FrancescoManara, S.Zolfo, M.Karcher, N.Armanini, FedericaBeghini, F.Manghi, P.Tett, A.Ghensi, P.Collado, María CarmenRice, B.L.DuLong, C.Morgan, X.C.Golden, Christopher D.Quince, C.Huttenhower, C.Segata, NicolaMetagenomic assemblyHuman microbiomeMetagenomicsMetagenomic meta-analysisNon-Westernized microbiomesUunexplored microbial diversityMetagenomic mappabilityThe body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.The human microbiome harbors many unidentified species. By large-scale metagenomic assembly of samples from diverse populations, we uncovered >150,000 microbial genomes that are recapitulated in 4,930 species. Many species (77%) were never described before, increase the mappability of metagenomes, and expand our understanding of global body-wide human microbiomes.This work was supported by EU-H2020 (DiMeTrack-707345) to E.P.; by NIH NHGRI (R01HG005220), NIDDK (R24DK110499), NIDDK (U54DE023798), CMIT (6935956) to C.H.; and by ERC (MetaPG-716575), MIUR (RBFR13EWWI), EU-FP7 (PCIG13-GA-2013-618833), CARITRO (2013.0239), and LEO Pharma Foundation to N.S. Madagascar data and sample collection was supported by the Rockefeller Foundation to C.D.G.Peer ReviewedCell PressEuropean Research CouncilRockefeller FoundationLEO Pharma FoundationEuropean CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2019201920192019info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/196155reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/707345Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1961552026-05-22T06:33:51Z
dc.title.none.fl_str_mv Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
title Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
spellingShingle Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Pasolli, E.
Metagenomic assembly
Human microbiome
Metagenomics
Metagenomic meta-analysis
Non-Westernized microbiomes
Uunexplored microbial diversity
Metagenomic mappability
title_short Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
title_full Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
title_fullStr Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
title_full_unstemmed Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
title_sort Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
dc.creator.none.fl_str_mv Pasolli, E.
Asnicar, Francesco
Manara, S.
Zolfo, M.
Karcher, N.
Armanini, Federica
Beghini, F.
Manghi, P.
Tett, A.
Ghensi, P.
Collado, María Carmen
Rice, B.L.
DuLong, C.
Morgan, X.C.
Golden, Christopher D.
Quince, C.
Huttenhower, C.
Segata, Nicola
author Pasolli, E.
author_facet Pasolli, E.
Asnicar, Francesco
Manara, S.
Zolfo, M.
Karcher, N.
Armanini, Federica
Beghini, F.
Manghi, P.
Tett, A.
Ghensi, P.
Collado, María Carmen
Rice, B.L.
DuLong, C.
Morgan, X.C.
Golden, Christopher D.
Quince, C.
Huttenhower, C.
Segata, Nicola
author_role author
author2 Asnicar, Francesco
Manara, S.
Zolfo, M.
Karcher, N.
Armanini, Federica
Beghini, F.
Manghi, P.
Tett, A.
Ghensi, P.
Collado, María Carmen
Rice, B.L.
DuLong, C.
Morgan, X.C.
Golden, Christopher D.
Quince, C.
Huttenhower, C.
Segata, Nicola
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Research Council
Rockefeller Foundation
LEO Pharma Foundation
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Metagenomic assembly
Human microbiome
Metagenomics
Metagenomic meta-analysis
Non-Westernized microbiomes
Uunexplored microbial diversity
Metagenomic mappability
topic Metagenomic assembly
Human microbiome
Metagenomics
Metagenomic meta-analysis
Non-Westernized microbiomes
Uunexplored microbial diversity
Metagenomic mappability
description The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.The human microbiome harbors many unidentified species. By large-scale metagenomic assembly of samples from diverse populations, we uncovered >150,000 microbial genomes that are recapitulated in 4,930 species. Many species (77%) were never described before, increase the mappability of metagenomes, and expand our understanding of global body-wide human microbiomes.
publishDate 2019
dc.date.none.fl_str_mv 2019
2019
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/196155
url http://hdl.handle.net/10261/196155
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/707345
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Cell Press
publisher.none.fl_str_mv Cell Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869419625140191232
score 15,81155

Similares en LA Referencia