Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting

Abstract

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.

Microbial Screening Reveals Oral Site-Specific Locations of the Periodontal Pathogen Selenomonas noxia

“…Based upon these results, this may be the first description of the presence of this organism among additional oral sites, suggesting the presence of this organism at these specific biofilm locations may be more commonplace than previously though and may be similar to other studies of gram-negative periodontal pathogens that aggregate in developing or existing biofilms on teeth and the tongue [28][29][30]. In fact, recent studies have postulated that enrichment of periodontal pathogens may first occur in developing biofilm prior to the development of subgingival inflammation, gingivitis or periodontal diseasesuggesting more detailed analysis of these oral sites may be needed in future studies [31][32][33].…”

Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions

“…Importantly, metadata does not only refer to sample attributes, but also to sample preparation and processing [128]. The variability of metadata can limit the conclusions, since the observed patterns might not be attributable to a certain factor(s) [129,130] that should also be considered when selecting study subjects. In this context, we call attention to the necessity of validating metadata submitted to public repositories by providing immediate and informative feedback to the submitting researchers [128].…”

Microbiomics: Were we all wrong before?

“…However, when omics methods are used to examine human samples, additional considerations—for example, study design, defining primary outcome variables, sample types, positive and negative control groups of subjects, confounding and covarying variables, sample biomass, sample collection methods and material, sample processing and storage, biological and technical variates, adequately powered studies, sufficient metadata, etc—become critically important. Zaura et al 36 provide us with a roadmap for clinical research involving the oral microbiome based on the currently available evidence. From their work, we learn how to get most out of this exciting type of research.…”