Towards Quantitative Microbiome Community Profiling Using Internal Standards
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 quant...
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ftpubmed:oai:pubmedcentral.nih.gov:6384117 2023-05-15T13:57:24+02:00 Towards Quantitative Microbiome Community Profiling Using Internal Standards Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas 2019-02-20 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384117/ http://www.ncbi.nlm.nih.gov/pubmed/30552195 https://doi.org/10.1128/AEM.02634-18 en eng American Society for Microbiology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384117/ http://www.ncbi.nlm.nih.gov/pubmed/30552195 http://dx.doi.org/10.1128/AEM.02634-18 Copyright © 2019 American Society for Microbiology. https://doi.org/10.1128/ASMCopyrightv2 All Rights Reserved (https://doi.org/10.1128/ASMCopyrightv2) . Methods Text 2019 ftpubmed https://doi.org/10.1128/AEM.02634-18 2019-08-25T00:09:29Z 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 counts by flow cytometry. The internal standard ... Text Antarc* Antarctica PubMed Central (PMC) Applied and Environmental Microbiology 85 5 |
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Methods Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas Towards Quantitative Microbiome Community Profiling Using Internal Standards |
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Methods |
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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 counts by flow cytometry. The internal standard ... |
format |
Text |
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 |
American Society for Microbiology |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384117/ http://www.ncbi.nlm.nih.gov/pubmed/30552195 https://doi.org/10.1128/AEM.02634-18 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384117/ http://www.ncbi.nlm.nih.gov/pubmed/30552195 http://dx.doi.org/10.1128/AEM.02634-18 |
op_rights |
Copyright © 2019 American Society for Microbiology. https://doi.org/10.1128/ASMCopyrightv2 All Rights Reserved (https://doi.org/10.1128/ASMCopyrightv2) . |
op_doi |
https://doi.org/10.1128/AEM.02634-18 |
container_title |
Applied and Environmental Microbiology |
container_volume |
85 |
container_issue |
5 |
_version_ |
1766265074325913600 |