Exploring the universal healthy human gut microbiota around the world

The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, availa...

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Detalles Bibliográficos
Autores: Piquer-Esteban, Samuel, Ruiz-Ruiz, Susana, Arnau, Vicente, Díaz-Villanueva, Wladimiro, Moya, Andrés
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/285829
Acceso en línea:http://hdl.handle.net/10261/285829
Access Level:acceso abierto
Palabra clave:Human gut microbiota
Western bias
Core microbiota
Genome databases
Enrichment strategies
Metagenomics
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spelling Exploring the universal healthy human gut microbiota around the worldPiquer-Esteban, SamuelRuiz-Ruiz, SusanaArnau, VicenteDíaz-Villanueva, WladimiroMoya, AndrésHuman gut microbiotaWestern biasCore microbiotaGenome databasesEnrichment strategiesMetagenomicsThe human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.This work was supported by grant to AM from the Spanish Ministry of Science and Innovation (PID2019-105969 GB-I00), Generalitat Valenciana (project Prometeo/2018/A/133), Asociación Española contra el Cancer (project AECC 2017-1485) and co-financed by the European Regional Development Fund (ERDF). SP-E was funded by an ACIF fellowship from the Generalitat Valenciana during October 2021 (Reference: ACIF/2021/341), and later on since December 2021 by an FPU fellowship from the Spanish Ministry of Universities (Reference: FPU20/05756).Peer reviewedElsevierMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Asociación Española Contra el CáncerGeneralitat ValencianaEuropean CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/285829reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-105969GB-I00https://doi.org/10.1016/j.csbj.2021.12.035Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2858292026-05-22T06:33:51Z
dc.title.none.fl_str_mv Exploring the universal healthy human gut microbiota around the world
title Exploring the universal healthy human gut microbiota around the world
spellingShingle Exploring the universal healthy human gut microbiota around the world
Piquer-Esteban, Samuel
Human gut microbiota
Western bias
Core microbiota
Genome databases
Enrichment strategies
Metagenomics
title_short Exploring the universal healthy human gut microbiota around the world
title_full Exploring the universal healthy human gut microbiota around the world
title_fullStr Exploring the universal healthy human gut microbiota around the world
title_full_unstemmed Exploring the universal healthy human gut microbiota around the world
title_sort Exploring the universal healthy human gut microbiota around the world
dc.creator.none.fl_str_mv Piquer-Esteban, Samuel
Ruiz-Ruiz, Susana
Arnau, Vicente
Díaz-Villanueva, Wladimiro
Moya, Andrés
author Piquer-Esteban, Samuel
author_facet Piquer-Esteban, Samuel
Ruiz-Ruiz, Susana
Arnau, Vicente
Díaz-Villanueva, Wladimiro
Moya, Andrés
author_role author
author2 Ruiz-Ruiz, Susana
Arnau, Vicente
Díaz-Villanueva, Wladimiro
Moya, Andrés
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
Asociación Española Contra el Cáncer
Generalitat Valenciana
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Human gut microbiota
Western bias
Core microbiota
Genome databases
Enrichment strategies
Metagenomics
topic Human gut microbiota
Western bias
Core microbiota
Genome databases
Enrichment strategies
Metagenomics
description The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
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/10261/285829
url http://hdl.handle.net/10261/285829
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/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-105969GB-I00
https://doi.org/10.1016/j.csbj.2021.12.035
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
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
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