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Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting
With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulne...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756869/ https://www.ncbi.nlm.nih.gov/pubmed/33226702 http://dx.doi.org/10.1111/prd.12359 |
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author | Zaura, Egija Pappalardo, Vincent Y. Buijs, Mark J. Volgenant, Catherine M. C. Brandt, Bernd W. |
author_facet | Zaura, Egija Pappalardo, Vincent Y. Buijs, Mark J. Volgenant, Catherine M. C. Brandt, Bernd W. |
author_sort | Zaura, Egija |
collection | PubMed |
description | With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided. |
format | Online Article Text |
id | pubmed-7756869 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-77568692020-12-28 Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting Zaura, Egija Pappalardo, Vincent Y. Buijs, Mark J. Volgenant, Catherine M. C. Brandt, Bernd W. Periodontol 2000 Review Articles With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided. John Wiley and Sons Inc. 2020-11-23 2021-02 /pmc/articles/PMC7756869/ /pubmed/33226702 http://dx.doi.org/10.1111/prd.12359 Text en © 2020 The Authors. Periodontology 2000 published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Articles Zaura, Egija Pappalardo, Vincent Y. Buijs, Mark J. Volgenant, Catherine M. C. Brandt, Bernd W. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title | Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title_full | Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title_fullStr | Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title_full_unstemmed | Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title_short | Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting |
title_sort | optimizing the quality of clinical studies on oral microbiome: a practical guide for planning, performing, and reporting |
topic | Review Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756869/ https://www.ncbi.nlm.nih.gov/pubmed/33226702 http://dx.doi.org/10.1111/prd.12359 |
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