Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota

This research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial...

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Detalles Bibliográficos
Autores: Biada, Iliyass, Santacreu, María Antonia, González Recio, Oscar, Ibáñez-Escriche, Noelia
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/399983
Acceso en línea:http://hdl.handle.net/10261/399983
https://api.elsevier.com/content/abstract/scopus_id/105007041863
Access Level:acceso abierto
Palabra clave:16S rRNA
Illumina
Microbiota
Nanopore
PacBio
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spelling Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiotaBiada, IliyassSantacreu, María AntoniaGonzález Recio, OscarIbáñez-Escriche, Noelia16S rRNAIlluminaMicrobiotaNanoporePacBioThis research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial communities detected across the three platforms. The study employed DNA from four rabbit does’ soft feces, sequenced using Illumina MiSeq for specific 16S rRNA gene regions V3-V4, and for the complete gene sequencing using PacBio HiFi and ONT MinION. Results highlight different levels of taxonomic resolution. At the species level, PacBio and ONT exhibited the better resolutions with 63% and 76% respectively, while 48% for Illumina. However, across all three platforms, the classification output at species level was mainly labeled as “Uncultured_bacterium” for most of the classified sequences, which does not improve the understanding of the gut microbiota composition in rabbits. Moreover, although high correlations between relative abundances of taxa were observed, diversity analysis showed significant differences between the taxonomic compositions of the three platforms. These findings suggest that while PacBio and ONT offer improvements in species-level resolution compared to Illumina, due to references databases ambiguous annotation, all three platforms still fall short in providing a precise species level characterization of the gut microbiota composition in rabbits. Additionally, the disparities observed across the results from these platforms highlight the significant impact of sequencing platform, especially when different primers are used. This consideration is particularly important when comparing or analyzing sequences derived from different sequencing technologies.The author(s) declare that financial support was received for the research and/or publication of this article. This research was supported by MEC (PID2020-115558GB-C21) and Generalitat Valenciana (AICO/2020/349).Peer reviewedFrontiers MediaMinisterio de Educación y Ciencia (España)Generalitat ValencianaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/399983https://api.elsevier.com/content/abstract/scopus_id/105007041863reponame: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/PID2020-115558GB-C21The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3389/frmbi.2025.1587712https://doi.org/10.3389/frmbi.2025.1587712Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3999832026-05-22T06:33:51Z
dc.title.none.fl_str_mv Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
title Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
spellingShingle Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
Biada, Iliyass
16S rRNA
Illumina
Microbiota
Nanopore
PacBio
title_short Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
title_full Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
title_fullStr Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
title_full_unstemmed Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
title_sort Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota
dc.creator.none.fl_str_mv Biada, Iliyass
Santacreu, María Antonia
González Recio, Oscar
Ibáñez-Escriche, Noelia
author Biada, Iliyass
author_facet Biada, Iliyass
Santacreu, María Antonia
González Recio, Oscar
Ibáñez-Escriche, Noelia
author_role author
author2 Santacreu, María Antonia
González Recio, Oscar
Ibáñez-Escriche, Noelia
author2_role author
author
author
dc.contributor.none.fl_str_mv Ministerio de Educación y Ciencia (España)
Generalitat Valenciana
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv 16S rRNA
Illumina
Microbiota
Nanopore
PacBio
topic 16S rRNA
Illumina
Microbiota
Nanopore
PacBio
description This research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial communities detected across the three platforms. The study employed DNA from four rabbit does’ soft feces, sequenced using Illumina MiSeq for specific 16S rRNA gene regions V3-V4, and for the complete gene sequencing using PacBio HiFi and ONT MinION. Results highlight different levels of taxonomic resolution. At the species level, PacBio and ONT exhibited the better resolutions with 63% and 76% respectively, while 48% for Illumina. However, across all three platforms, the classification output at species level was mainly labeled as “Uncultured_bacterium” for most of the classified sequences, which does not improve the understanding of the gut microbiota composition in rabbits. Moreover, although high correlations between relative abundances of taxa were observed, diversity analysis showed significant differences between the taxonomic compositions of the three platforms. These findings suggest that while PacBio and ONT offer improvements in species-level resolution compared to Illumina, due to references databases ambiguous annotation, all three platforms still fall short in providing a precise species level characterization of the gut microbiota composition in rabbits. Additionally, the disparities observed across the results from these platforms highlight the significant impact of sequencing platform, especially when different primers are used. This consideration is particularly important when comparing or analyzing sequences derived from different sequencing technologies.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
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/10261/399983
https://api.elsevier.com/content/abstract/scopus_id/105007041863
url http://hdl.handle.net/10261/399983
https://api.elsevier.com/content/abstract/scopus_id/105007041863
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/PID2020-115558GB-C21
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3389/frmbi.2025.1587712
https://doi.org/10.3389/frmbi.2025.1587712
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 Frontiers Media
publisher.none.fl_str_mv Frontiers Media
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
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