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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fttriple:oai:gotriple.eu:10670/1.p4fcbh 2023-05-15T14:02:48+02:00 Towards Quantitative Microbiome Community Profiling Using Internal Standards Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas https://doi.org/10.1128/AEM.02634-18 https://archimer.ifremer.fr/doc/00484/59562/62553.pdf https://archimer.ifremer.fr/doc/00484/59562/62554.pdf https://archimer.ifremer.fr/doc/00484/59562/62555.xlsx en eng Amer Soc Microbiology doi:10.1128/AEM.02634-18 10670/1.p4fcbh https://archimer.ifremer.fr/doc/00484/59562/62553.pdf https://archimer.ifremer.fr/doc/00484/59562/62554.pdf https://archimer.ifremer.fr/doc/00484/59562/62555.xlsx other Archimer, archive institutionnelle de l'Ifremer Applied And Environmental Microbiology (0099-2240) (Amer Soc Microbiology), 2019-03 , Vol. 85 , N. 5 , P. e02634-18 (14p.) envir geo Text https://vocabularies.coar-repositories.org/resource_types/c_18cf/ fttriple https://doi.org/10.1128/AEM.02634-18 2023-01-22T16:47:24Z 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 Unknown Applied and Environmental Microbiology 85 5 |
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envir geo Lin, Yajuan Gifford, Scott Ducklow, Hugh Schofield, Oscar Cassar, Nicolas Towards Quantitative Microbiome Community Profiling Using Internal Standards |
topic_facet |
envir geo |
description |
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 |
Amer Soc Microbiology |
url |
https://doi.org/10.1128/AEM.02634-18 https://archimer.ifremer.fr/doc/00484/59562/62553.pdf https://archimer.ifremer.fr/doc/00484/59562/62554.pdf https://archimer.ifremer.fr/doc/00484/59562/62555.xlsx |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Archimer, archive institutionnelle de l'Ifremer Applied And Environmental Microbiology (0099-2240) (Amer Soc Microbiology), 2019-03 , Vol. 85 , N. 5 , P. e02634-18 (14p.) |
op_relation |
doi:10.1128/AEM.02634-18 10670/1.p4fcbh https://archimer.ifremer.fr/doc/00484/59562/62553.pdf https://archimer.ifremer.fr/doc/00484/59562/62554.pdf https://archimer.ifremer.fr/doc/00484/59562/62555.xlsx |
op_rights |
other |
op_doi |
https://doi.org/10.1128/AEM.02634-18 |
container_title |
Applied and Environmental Microbiology |
container_volume |
85 |
container_issue |
5 |
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1766273215407063040 |