Temporal variability of oral microbiota over 10 months and the implications for future epidemiologic studies

Authors

• E Vogtmann
• X Hua
• L Zhou
• Y Wan
• S Suman
• B Zhu
• C Dagnall
• A Hutchinson
• K Jones
• B Hicks
• R Sinha
• J Shi
• CC Abnet

Abstract

Few studies have prospectively evaluated the association between oral microbiota and health outcomes. Additional research is required to determine sample sizes and whether multiple samples over time from individuals would strengthen studies, so we evaluated the temporal variability of the oral microbiota from 40 individuals who provided oral samples using the OMNIgene ORAL kit and Scope mouthwash oral rinses approximately every two months over 10 months. DNA was extracted using the QIAsymphony and the V4 region of the 16S rRNA gene was sequenced. We calculated intraclass correlation coefficients (ICC) and Dirichlet multinomial models (DMM), a method of clustering samples into distinct community types. The ICCs for the alpha diversity metrics were high, including for number of observed bacterial species (0.74; 95% confidence interval [CI]: 0.65, 0.82 and 0.79; 95% CI: 0.75, 0.94) from OMNIgene ORAL and Scope mouthwash, respectively. The ICCs for the relative abundance of the top four phyla and beta diversity matrices were lower. For example, the ICC for weighted UniFrac of the Scope mouthwash sample was 0.48 (95% CI: 0.36, 0.61). Three clusters provided the best model fit for the DMM and the probability of remaining in a specific cluster was high (59.5%-80.7%). In conclusion, the oral microbiota appears to be stable over time for multiple metrics, but some measures, particularly the relative abundance of specific phyla and genera, were less stable. We used this information to make stability-adjusted power calculations that will inform future field study protocols and experimental analytic designs.

Scientific Focus Area: Epidemiology

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