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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...

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Detalles Bibliográficos
Autores principales: Zaura, Egija, Pappalardo, Vincent Y., Buijs, Mark J., Volgenant, Catherine M. C., Brandt, Bernd W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
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.
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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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