Journal
PERIODONTOLOGY 2000
Volume 85, Issue 1, Pages 210-236Publisher
WILEY
DOI: 10.1111/prd.12359
Keywords
16S rDNA amplicon sequencing; clinical study design; dental plaque; metadata; microbiome; saliva
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This review aims to improve the quality standards of clinical studies with microbiome as an output parameter. It discusses the existing evidence for good quality practices in oral microbiome studies, including study design, sample collection, data processing, and interpretation.
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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