Academic Journal
Προβολή σε EDS

Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies
Συγγραφείς: Plauzolles, Anne, Toumi, Eya, Bonnet, Marion, Pénaranda, Guillaume, Bidaut, Ghislain, Chiche, Laurent, Allardet-Servent, Jérôme, Retornaz, Frédérique, Goutorbe, Benoit, Halfon, Philippe
Συνεισφορές: ALPHABIO - Laboratoire de biologie médicale, Microbes Evolution Phylogénie et Infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes (IPC), Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Européen Fondation Ambroise Paré - Marseille, Mathématiques et Informatique Appliquées du Génome à l'Environnement Jouy-En-Josas (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Alphabio laboratory
Πηγή: ISSN: 2235-2988 ; Frontiers in Cellular and Infection Microbiology ; https://amu.hal.science/hal-03663784 ; Frontiers in Cellular and Infection Microbiology, 2022, 12, ⟨10.3389/fcimb.2022.722886⟩.
Στοιχεία εκδότη: CCSD
Frontiers
Έτος έκδοσης: 2022
Συλλογή: Inserm: HAL (Institut national de la santé et de la recherche médicale)
Θεματικοί όροι: 16S metagenomics, human gut, microbiota, preservation, stabilizing solution, standardization, stool, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Περιγραφή: International audience ; Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.
Τύπος εγγράφου: article in journal/newspaper
Γλώσσα: English
Relation: info:eu-repo/semantics/altIdentifier/pmid/35211421; PUBMED: 35211421; PUBMEDCENTRAL: PMC8860989; WOS: 000760495200001
DOI: 10.3389/fcimb.2022.722886
Διαθεσιμότητα: https://amu.hal.science/hal-03663784
https://amu.hal.science/hal-03663784v1/document
https://amu.hal.science/hal-03663784v1/file/fcimb-12-722886.pdf
https://doi.org/10.3389/fcimb.2022.722886
Rights: https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess
Αριθμός Καταχώρησης: edsbas.477D7E93
Βάση Δεδομένων: BASE
FullText Text:
  Availability: 0
CustomLinks:
  – Url: https://amu.hal.science/hal-03663784#
    Name: EDS - BASE (ns324271)
    Category: fullText
    Text: View record from BASE
Header DbId: edsbas
DbLabel: BASE
An: edsbas.477D7E93
RelevancyScore: 920
AccessLevel: 3
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 920.2763671875
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Plauzolles%2C+Anne%22">Plauzolles, Anne</searchLink><br /><searchLink fieldCode="AR" term="%22Toumi%2C+Eya%22">Toumi, Eya</searchLink><br /><searchLink fieldCode="AR" term="%22Bonnet%2C+Marion%22">Bonnet, Marion</searchLink><br /><searchLink fieldCode="AR" term="%22Pénaranda%2C+Guillaume%22">Pénaranda, Guillaume</searchLink><br /><searchLink fieldCode="AR" term="%22Bidaut%2C+Ghislain%22">Bidaut, Ghislain</searchLink><br /><searchLink fieldCode="AR" term="%22Chiche%2C+Laurent%22">Chiche, Laurent</searchLink><br /><searchLink fieldCode="AR" term="%22Allardet-Servent%2C+Jérôme%22">Allardet-Servent, Jérôme</searchLink><br /><searchLink fieldCode="AR" term="%22Retornaz%2C+Frédérique%22">Retornaz, Frédérique</searchLink><br /><searchLink fieldCode="AR" term="%22Goutorbe%2C+Benoit%22">Goutorbe, Benoit</searchLink><br /><searchLink fieldCode="AR" term="%22Halfon%2C+Philippe%22">Halfon, Philippe</searchLink>
– Name: Author
  Label: Contributors
  Group: Au
  Data: ALPHABIO - Laboratoire de biologie médicale<br />Microbes Evolution Phylogénie et Infections (MEPHI)<br />Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)<br />Centre de Recherche en Cancérologie de Marseille (CRCM)<br />Aix Marseille Université (AMU)-Institut Paoli-Calmettes (IPC)<br />Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)<br />Hôpital Européen Fondation Ambroise Paré - Marseille<br />Mathématiques et Informatique Appliquées du Génome à l'Environnement Jouy-En-Josas (MaIAGE)<br />Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)<br />Alphabio laboratory
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <i>ISSN: 2235-2988 ; Frontiers in Cellular and Infection Microbiology ; https://amu.hal.science/hal-03663784 ; Frontiers in Cellular and Infection Microbiology, 2022, 12, ⟨10.3389/fcimb.2022.722886⟩</i>.
– Name: Publisher
  Label: Publisher Information
  Group: PubInfo
  Data: CCSD<br />Frontiers
– Name: DatePubCY
  Label: Publication Year
  Group: Date
  Data: 2022
– Name: Subset
  Label: Collection
  Group: HoldingsInfo
  Data: Inserm: HAL (Institut national de la santé et de la recherche médicale)
– Name: Subject
  Label: Subject Terms
  Group: Su
  Data: <searchLink fieldCode="DE" term="%2216S+metagenomics%22">16S metagenomics</searchLink><br /><searchLink fieldCode="DE" term="%22human+gut%22">human gut</searchLink><br /><searchLink fieldCode="DE" term="%22microbiota%22">microbiota</searchLink><br /><searchLink fieldCode="DE" term="%22preservation%22">preservation</searchLink><br /><searchLink fieldCode="DE" term="%22stabilizing+solution%22">stabilizing solution</searchLink><br /><searchLink fieldCode="DE" term="%22standardization%22">standardization</searchLink><br /><searchLink fieldCode="DE" term="%22stool%22">stool</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMP%2EBAC]Life+Sciences+[q-bio]%2FMicrobiology+and+Parasitology%2FBacteriology%22">[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMP%2EVIR]Life+Sciences+[q-bio]%2FMicrobiology+and+Parasitology%2FVirology%22">[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMP%2EPAR]Life+Sciences+[q-bio]%2FMicrobiology+and+Parasitology%2FParasitology%22">[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMHEP%2ECSC]Life+Sciences+[q-bio]%2FHuman+health+and+pathology%2FCardiology+and+cardiovascular+system%22">[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMHEP%2EME]Life+Sciences+[q-bio]%2FHuman+health+and+pathology%2FEmerging+diseases%22">[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases</searchLink><br /><searchLink fieldCode="DE" term="%22[SDV%2EMHEP%2EMI]Life+Sciences+[q-bio]%2FHuman+health+and+pathology%2FInfectious+diseases%22">[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases</searchLink>
– Name: Abstract
  Label: Description
  Group: Ab
  Data: International audience ; Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.
– Name: TypeDocument
  Label: Document Type
  Group: TypDoc
  Data: article in journal/newspaper
– Name: Language
  Label: Language
  Group: Lang
  Data: English
– Name: NoteTitleSource
  Label: Relation
  Group: SrcInfo
  Data: info:eu-repo/semantics/altIdentifier/pmid/35211421; PUBMED: 35211421; PUBMEDCENTRAL: PMC8860989; WOS: 000760495200001
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.3389/fcimb.2022.722886
– Name: URL
  Label: Availability
  Group: URL
  Data: https://amu.hal.science/hal-03663784<br />https://amu.hal.science/hal-03663784v1/document<br />https://amu.hal.science/hal-03663784v1/file/fcimb-12-722886.pdf<br />https://doi.org/10.3389/fcimb.2022.722886
– Name: Copyright
  Label: Rights
  Group: Cpyrght
  Data: https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess
– Name: AN
  Label: Accession Number
  Group: ID
  Data: edsbas.477D7E93
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=edsbas&AN=edsbas.477D7E93
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.3389/fcimb.2022.722886
    Languages:
      – Text: English
    Subjects:
      – SubjectFull: 16S metagenomics
        Type: general
      – SubjectFull: human gut
        Type: general
      – SubjectFull: microbiota
        Type: general
      – SubjectFull: preservation
        Type: general
      – SubjectFull: stabilizing solution
        Type: general
      – SubjectFull: standardization
        Type: general
      – SubjectFull: stool
        Type: general
      – SubjectFull: [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
        Type: general
      – SubjectFull: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
        Type: general
      – SubjectFull: [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
        Type: general
      – SubjectFull: [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system
        Type: general
      – SubjectFull: [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases
        Type: general
      – SubjectFull: [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
        Type: general
    Titles:
      – TitleFull: Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Plauzolles, Anne
      – PersonEntity:
          Name:
            NameFull: Toumi, Eya
      – PersonEntity:
          Name:
            NameFull: Bonnet, Marion
      – PersonEntity:
          Name:
            NameFull: Pénaranda, Guillaume
      – PersonEntity:
          Name:
            NameFull: Bidaut, Ghislain
      – PersonEntity:
          Name:
            NameFull: Chiche, Laurent
      – PersonEntity:
          Name:
            NameFull: Allardet-Servent, Jérôme
      – PersonEntity:
          Name:
            NameFull: Retornaz, Frédérique
      – PersonEntity:
          Name:
            NameFull: Goutorbe, Benoit
      – PersonEntity:
          Name:
            NameFull: Halfon, Philippe
      – PersonEntity:
          Name:
            NameFull: ALPHABIO - Laboratoire de biologie médicale
      – PersonEntity:
          Name:
            NameFull: Microbes Evolution Phylogénie et Infections (MEPHI)
      – PersonEntity:
          Name:
            NameFull: Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)
      – PersonEntity:
          Name:
            NameFull: Centre de Recherche en Cancérologie de Marseille (CRCM)
      – PersonEntity:
          Name:
            NameFull: Aix Marseille Université (AMU)-Institut Paoli-Calmettes (IPC)
      – PersonEntity:
          Name:
            NameFull: Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
      – PersonEntity:
          Name:
            NameFull: Hôpital Européen Fondation Ambroise Paré - Marseille
      – PersonEntity:
          Name:
            NameFull: Mathématiques et Informatique Appliquées du Génome à l'Environnement Jouy-En-Josas (MaIAGE)
      – PersonEntity:
          Name:
            NameFull: Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
      – PersonEntity:
          Name:
            NameFull: Alphabio laboratory
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 01
              Type: published
              Y: 2022
          Identifiers:
            – Type: issn-locals
              Value: edsbas
            – Type: issn-locals
              Value: edsbas.oa
          Titles:
            – TitleFull: ISSN: 2235-2988 ; Frontiers in Cellular and Infection Microbiology ; https://amu.hal.science/hal-03663784 ; Frontiers in Cellular and Infection Microbiology, 2022, 12, ⟨10.3389/fcimb.2022.722886⟩
              Type: main
ResultId 1