Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome

Recent work has demonstrated the existence of large inter-individual and inter-population variability in the microbiota of human milk from healthy women living across variable geographical and socio-cultural settings. However, no studies have evaluated the impact that variable sequencing approaches...

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Authors: Ruíz García, Lorena, Alba, Claudio, García-Carral, Cristina, Jiménez, Esther, Lackey, Kimberly A., McGuire, Michelle K., Meehan, Courtney L., Foster, James A., Sellen, Daniel W., Kamau‐Mbuthia, Elizabeth W., Kamundia, Egidioh W., Mbugua, Samwel, Moore, Sophie E., Prentice, Andrew M., Gindola, Debela, Otto, Gloria E., Pareja, Rossina G., Bode, Lars, McGuire, Mark A., Williams, Janet E., Rodríguez, Juan M.
Format: article
Status:Published version
Publication Date:2021
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/263465
Online Access:http://hdl.handle.net/10261/263465
Access Level:Open access
Keyword:Human milk
Microbiota
16S rRNA
Bacteria
Sequencing reproducibility
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spelling Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk MicrobiomeRuíz García, LorenaAlba, ClaudioGarcía-Carral, CristinaJiménez, EstherLackey, Kimberly A.McGuire, Michelle K.Meehan, Courtney L.Foster, James A.Sellen, Daniel W.Kamau‐Mbuthia, Elizabeth W.Kamundia, Egidioh W.Mbugua, SamwelMoore, Sophie E.Prentice, Andrew M.Gindola, DebelaOtto, Gloria E.Pareja, Rossina G.Bode, LarsMcGuire, Mark A.Williams, Janet E.Rodríguez, Juan M.Human milkMicrobiota16S rRNABacteriaSequencing reproducibilityRecent work has demonstrated the existence of large inter-individual and inter-population variability in the microbiota of human milk from healthy women living across variable geographical and socio-cultural settings. However, no studies have evaluated the impact that variable sequencing approaches targeting different 16S rRNA variable regions may have on the human milk microbiota profiling results. This hampers our ability to make meaningful comparisons across studies. In this context, the main purpose of the present study was to re-process and re-sequence the microbiome in a large set of human milk samples (n = 412) collected from healthy women living at diverse international sites (Spain, Sweden, Peru, United States, Ethiopia, Gambia, Ghana and Kenya), by targeting a different 16S rRNA variable region and reaching a larger sequencing depth. Despite some differences between the results obtained from both sequencing approaches were notable (especially regarding alpha and beta diversities and Proteobacteria representation), results indicate that both sequencing approaches revealed a relatively consistent microbiota configurations in the studied cohorts. Our data expand upon the milk microbiota results we previously reported from the INSPIRE cohort and provide, for the first time across globally diverse populations, evidence of the impact that different DNA processing and sequencing approaches have on the microbiota profiles obtained for human milk samples. Overall, our results corroborate some similarities regarding the microbial communities previously reported for the INSPIRE cohort, but some differences were also detected. Understanding the impact of different sequencing approaches on human milk microbiota profiles is essential to enable meaningful comparisons across studies. Clinical Trial Registration: www.clinicaltrials.gov, identifier NCT02670278.This project was primarily funded by the National Science Foundation (award 36 #1344288). LR (Spain) was funded by grant 624773 (FP-7-PEOPLE-2013-IEF, European Commission), project AGL2013-4190-P (Ministry of Economy and Competitiveness, Spain), and has received funding from RTI2018-095021-J-I00 (Ministry of Science Innovation and Universities CIU/AEI/FEDER, UE).Frontiers MediaNational Science Foundation (US)European CommissionMinisterio de Economía y Competitividad (España)Agencia Estatal de Investigación (España)Ministerio de Ciencia, Innovación y Universidades (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2022202220212022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/263465reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/FP7/624773info:eu-repo/grantAgreement/MINECO//AGL2013-4190-Pinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-095021-J-I00http://dx.doi.org/10.3389/fcimb.2021.622550Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2634652026-05-22T06:33:51Z
dc.title.none.fl_str_mv Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
title Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
spellingShingle Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
Ruíz García, Lorena
Human milk
Microbiota
16S rRNA
Bacteria
Sequencing reproducibility
title_short Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
title_full Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
title_fullStr Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
title_full_unstemmed Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
title_sort Comparison of Two Approaches for the Metataxonomic Analysis of the Human Milk Microbiome
dc.creator.none.fl_str_mv Ruíz García, Lorena
Alba, Claudio
García-Carral, Cristina
Jiménez, Esther
Lackey, Kimberly A.
McGuire, Michelle K.
Meehan, Courtney L.
Foster, James A.
Sellen, Daniel W.
Kamau‐Mbuthia, Elizabeth W.
Kamundia, Egidioh W.
Mbugua, Samwel
Moore, Sophie E.
Prentice, Andrew M.
Gindola, Debela
Otto, Gloria E.
Pareja, Rossina G.
Bode, Lars
McGuire, Mark A.
Williams, Janet E.
Rodríguez, Juan M.
author Ruíz García, Lorena
author_facet Ruíz García, Lorena
Alba, Claudio
García-Carral, Cristina
Jiménez, Esther
Lackey, Kimberly A.
McGuire, Michelle K.
Meehan, Courtney L.
Foster, James A.
Sellen, Daniel W.
Kamau‐Mbuthia, Elizabeth W.
Kamundia, Egidioh W.
Mbugua, Samwel
Moore, Sophie E.
Prentice, Andrew M.
Gindola, Debela
Otto, Gloria E.
Pareja, Rossina G.
Bode, Lars
McGuire, Mark A.
Williams, Janet E.
Rodríguez, Juan M.
author_role author
author2 Alba, Claudio
García-Carral, Cristina
Jiménez, Esther
Lackey, Kimberly A.
McGuire, Michelle K.
Meehan, Courtney L.
Foster, James A.
Sellen, Daniel W.
Kamau‐Mbuthia, Elizabeth W.
Kamundia, Egidioh W.
Mbugua, Samwel
Moore, Sophie E.
Prentice, Andrew M.
Gindola, Debela
Otto, Gloria E.
Pareja, Rossina G.
Bode, Lars
McGuire, Mark A.
Williams, Janet E.
Rodríguez, Juan M.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv National Science Foundation (US)
European Commission
Ministerio de Economía y Competitividad (España)
Agencia Estatal de Investigación (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Human milk
Microbiota
16S rRNA
Bacteria
Sequencing reproducibility
topic Human milk
Microbiota
16S rRNA
Bacteria
Sequencing reproducibility
description Recent work has demonstrated the existence of large inter-individual and inter-population variability in the microbiota of human milk from healthy women living across variable geographical and socio-cultural settings. However, no studies have evaluated the impact that variable sequencing approaches targeting different 16S rRNA variable regions may have on the human milk microbiota profiling results. This hampers our ability to make meaningful comparisons across studies. In this context, the main purpose of the present study was to re-process and re-sequence the microbiome in a large set of human milk samples (n = 412) collected from healthy women living at diverse international sites (Spain, Sweden, Peru, United States, Ethiopia, Gambia, Ghana and Kenya), by targeting a different 16S rRNA variable region and reaching a larger sequencing depth. Despite some differences between the results obtained from both sequencing approaches were notable (especially regarding alpha and beta diversities and Proteobacteria representation), results indicate that both sequencing approaches revealed a relatively consistent microbiota configurations in the studied cohorts. Our data expand upon the milk microbiota results we previously reported from the INSPIRE cohort and provide, for the first time across globally diverse populations, evidence of the impact that different DNA processing and sequencing approaches have on the microbiota profiles obtained for human milk samples. Overall, our results corroborate some similarities regarding the microbial communities previously reported for the INSPIRE cohort, but some differences were also detected. Understanding the impact of different sequencing approaches on human milk microbiota profiles is essential to enable meaningful comparisons across studies. Clinical Trial Registration: www.clinicaltrials.gov, identifier NCT02670278.
publishDate 2021
dc.date.none.fl_str_mv 2021
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/10261/263465
url http://hdl.handle.net/10261/263465
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
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#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/FP7/624773
info:eu-repo/grantAgreement/MINECO//AGL2013-4190-P
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-095021-J-I00
http://dx.doi.org/10.3389/fcimb.2021.622550
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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
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