Towards Quantitative Microbiome Community Profiling Using Internal Standards
WOS:000459327600015 International audience An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates ch...
Published in: | Applied and Environmental Microbiology |
---|---|
Main Authors: | , , , , |
Other Authors: | , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2019
|
Subjects: | |
Online Access: | https://hal.science/hal-02871388 https://doi.org/10.1128/AEM.02634-18 |
id |
ftanrparis:oai:HAL:hal-02871388v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
Portail HAL-ANR (Agence Nationale de la Recherche) |
op_collection_id |
ftanrparis |
language |
English |
topic |
ACL ocean phytoplankton variability marine quantification bacteria abundances amplicon sequencing community profiling genome sequence internal standard marine microbiome metagenomics phaeocystis-antarctica [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
ACL ocean phytoplankton variability marine quantification bacteria abundances amplicon sequencing community profiling genome sequence internal standard marine microbiome metagenomics phaeocystis-antarctica [SDE.BE]Environmental Sciences/Biodiversity and Ecology Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas Towards Quantitative Microbiome Community Profiling Using Internal Standards |
topic_facet |
ACL ocean phytoplankton variability marine quantification bacteria abundances amplicon sequencing community profiling genome sequence internal standard marine microbiome metagenomics phaeocystis-antarctica [SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
WOS:000459327600015 International audience An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems. IMPORTANCE High-throughput-sequencing-based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative; it provides taxon counts only in relative abundances. In order to address this issue, we present a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking known amounts of internal DNA standards into each sample. We validated this method by comparing the calculated abundances to other independent estimates, including chemical markers (pigments) and total bacterial cell ... |
author2 |
Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Nicholas School of the Environment Duke University Durham University of North Carolina Chapel Hill (UNC) University of North Carolina System (UNC) Lamont-Doherty Earth Observatory (LDEO) Columbia University New York School of Environmental and Biological Sciences New Brunswick Rutgers, The State University of New Jersey New Brunswick (RU) Rutgers University System (Rutgers)-Rutgers University System (Rutgers) ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) |
format |
Article in Journal/Newspaper |
author |
Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas |
author_facet |
Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas |
author_sort |
Lin, Yajuan |
title |
Towards Quantitative Microbiome Community Profiling Using Internal Standards |
title_short |
Towards Quantitative Microbiome Community Profiling Using Internal Standards |
title_full |
Towards Quantitative Microbiome Community Profiling Using Internal Standards |
title_fullStr |
Towards Quantitative Microbiome Community Profiling Using Internal Standards |
title_full_unstemmed |
Towards Quantitative Microbiome Community Profiling Using Internal Standards |
title_sort |
towards quantitative microbiome community profiling using internal standards |
publisher |
HAL CCSD |
publishDate |
2019 |
url |
https://hal.science/hal-02871388 https://doi.org/10.1128/AEM.02634-18 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
ISSN: 0099-2240 EISSN: 1098-5336 Applied and Environmental Microbiology https://hal.science/hal-02871388 Applied and Environmental Microbiology, 2019, 85 (5), pp.UNSP e02634-18. ⟨10.1128/AEM.02634-18⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1128/AEM.02634-18 hal-02871388 https://hal.science/hal-02871388 doi:10.1128/AEM.02634-18 PUBMEDCENTRAL: PMC6384117 |
op_doi |
https://doi.org/10.1128/AEM.02634-18 |
container_title |
Applied and Environmental Microbiology |
container_volume |
85 |
container_issue |
5 |
_version_ |
1785528504882823168 |
spelling |
ftanrparis:oai:HAL:hal-02871388v1 2023-12-17T10:21:00+01:00 Towards Quantitative Microbiome Community Profiling Using Internal Standards Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM) Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) Nicholas School of the Environment Duke University Durham University of North Carolina Chapel Hill (UNC) University of North Carolina System (UNC) Lamont-Doherty Earth Observatory (LDEO) Columbia University New York School of Environmental and Biological Sciences New Brunswick Rutgers, The State University of New Jersey New Brunswick (RU) Rutgers University System (Rutgers)-Rutgers University System (Rutgers) ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010) 2019 https://hal.science/hal-02871388 https://doi.org/10.1128/AEM.02634-18 en eng HAL CCSD American Society for Microbiology info:eu-repo/semantics/altIdentifier/doi/10.1128/AEM.02634-18 hal-02871388 https://hal.science/hal-02871388 doi:10.1128/AEM.02634-18 PUBMEDCENTRAL: PMC6384117 ISSN: 0099-2240 EISSN: 1098-5336 Applied and Environmental Microbiology https://hal.science/hal-02871388 Applied and Environmental Microbiology, 2019, 85 (5), pp.UNSP e02634-18. ⟨10.1128/AEM.02634-18⟩ ACL ocean phytoplankton variability marine quantification bacteria abundances amplicon sequencing community profiling genome sequence internal standard marine microbiome metagenomics phaeocystis-antarctica [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2019 ftanrparis https://doi.org/10.1128/AEM.02634-18 2023-11-18T22:35:02Z WOS:000459327600015 International audience An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems. IMPORTANCE High-throughput-sequencing-based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative; it provides taxon counts only in relative abundances. In order to address this issue, we present a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking known amounts of internal DNA standards into each sample. We validated this method by comparing the calculated abundances to other independent estimates, including chemical markers (pigments) and total bacterial cell ... Article in Journal/Newspaper Antarc* Antarctica Portail HAL-ANR (Agence Nationale de la Recherche) Applied and Environmental Microbiology 85 5 |