Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, the Netherlands.
Periodontol 2000. 2021 Feb;85(1):210-236. doi: 10.1111/prd.12359. Epub 2020 Nov 23.
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.
本综述旨在提高以微生物组为输出参数的临床研究的质量标准。我们基于 16S rRNA 基因扩增子测序，批判性地探讨了现有口腔微生物组研究中良好质量实践的证据。首先，我们讨论了微生物组图谱分析的有用性。微生物组研究是否真的是回答研究问题的最佳方法？接下来是确定最合适的研究设计、样本量以及应收集的必要数据（研究元数据）的标准。然后，我们评估了在样本采集、运输、储存和 DNA 分离方面的最佳实践的现有证据。最后，提供了可能的测序选项（例如 16S rRNA 基因高变区、测序平台）、处理和数据分析方法以及对有意义的数据存储、共享和报告的要求的概述。
