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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2018
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ftcarolinadr:cdr.lib.unc.edu:mc87q1841 2023-06-11T04:06:16+02:00 Towards quantitative microbiome community profiling using internal standards Lin, Y. Gifford, S. Ducklow, H. Schofield, O. Cassara, N. College of Arts and Sciences, Department of Marine Sciences 2018 https://doi.org/10.17615/hhfw-ey69 https://cdr.lib.unc.edu/downloads/8623j7243?file=thumbnail https://cdr.lib.unc.edu/downloads/8623j7243 English eng American Society for Microbiology https://doi.org/10.17615/hhfw-ey69 https://cdr.lib.unc.edu/downloads/8623j7243?file=thumbnail https://cdr.lib.unc.edu/downloads/8623j7243 http://rightsstatements.org/vocab/InC/1.0/ Applied and Environmental Microbiology, 85(5) Community profiling Internal standard Amplicon sequencing Marine microbiome Article 2018 ftcarolinadr https://doi.org/10.17615/hhfw-ey69 2023-05-28T21:02:58Z 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. Article in Journal/Newspaper Antarc* Antarctica Carolina Digital Repository (UNC - University of North Carolina) |
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Open Polar |
collection |
Carolina Digital Repository (UNC - University of North Carolina) |
op_collection_id |
ftcarolinadr |
language |
English |
topic |
Community profiling Internal standard Amplicon sequencing Marine microbiome |
spellingShingle |
Community profiling Internal standard Amplicon sequencing Marine microbiome Lin, Y. Gifford, S. Ducklow, H. Schofield, O. Cassara, N. Towards quantitative microbiome community profiling using internal standards |
topic_facet |
Community profiling Internal standard Amplicon sequencing Marine microbiome |
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. |
author2 |
College of Arts and Sciences, Department of Marine Sciences |
format |
Article in Journal/Newspaper |
author |
Lin, Y. Gifford, S. Ducklow, H. Schofield, O. Cassara, N. |
author_facet |
Lin, Y. Gifford, S. Ducklow, H. Schofield, O. Cassara, N. |
author_sort |
Lin, Y. |
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 |
2018 |
url |
https://doi.org/10.17615/hhfw-ey69 https://cdr.lib.unc.edu/downloads/8623j7243?file=thumbnail https://cdr.lib.unc.edu/downloads/8623j7243 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
Applied and Environmental Microbiology, 85(5) |
op_relation |
https://doi.org/10.17615/hhfw-ey69 https://cdr.lib.unc.edu/downloads/8623j7243?file=thumbnail https://cdr.lib.unc.edu/downloads/8623j7243 |
op_rights |
http://rightsstatements.org/vocab/InC/1.0/ |
op_doi |
https://doi.org/10.17615/hhfw-ey69 |
_version_ |
1768378116032430080 |