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Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies.

ABSTRACT: Background: Few studies have prospectively evaluated the association between oral microbiota and health outcomes. Precise estimates of the intrasubject microbial metric stability will allow better study planning. Therefore, we conducted a study to evaluate the temporal variability of oral microbiota.Methods: Forty individuals provided six 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 amplified and sequenced using the MiSeq. To estimate temporal variation, we calculated intraclass correlation coefficients (ICCs) for a variety of metrics and examined stability after clustering samples into distinct community types using Dirichlet multinomial models (DMMs).Results: The ICCs for the alpha diversity measures 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. Three clusters provided the best model fit for the DMM from the OMNIgene ORAL samples, and the probability of remaining in a specific cluster was high (59.5%-80.7%).Conclusions: The oral microbiota appears to be stable over time for multiple metrics, but some measures, particularly relative abundance, were less stable.Impact: We used this information to calculate stability-adjusted power calculations that will inform future field study protocols and experimental analytic designs. Cancer Epidemiol Biomarkers Prev; 27(5); 594-600. ©2018 AACR.

SUBMITTER: Vogtmann E

PROVIDER: S-EPMC5932224 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies.

Vogtmann Emily E Hua Xing X Zhou Liang L Wan Yunhu Y Suman Shalabh S Zhu Bin B Dagnall Casey L CL Hutchinson Amy A Jones Kristine K Hicks Belynda D BD Sinha Rashmi R Shi Jianxin J Abnet Christian C CC

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 20180223 5

<b>Background:</b> Few studies have prospectively evaluated the association between oral microbiota and health outcomes. Precise estimates of the intrasubject microbial metric stability will allow better study planning. Therefore, we conducted a study to evaluate the temporal variability of oral microbiota.<b>Methods:</b> Forty individuals provided six oral samples using the OMNIgene ORAL kit and Scope mouthwash oral rinses approximately every two months over 10 months. DNA was extracted using t ...[more]

PMID: 29475969

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Project description:Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno's fixative, Scope mouthwash, and nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an alternative method. DNA was extracted using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno's fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno's compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno's showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno's fixative.IMPORTANCE We compared four different oral collection methods for studying the human oral microbiome: an OMNIgene ORAL kit, Scope mouthwash, nonethanol mouthwash, and Saccomanno's fixative. Our study shows that the type of the collection method can have a large impact on the results of an oral microbiome analysis. We recommend that one consistent oral collection method should be used for all oral microbiome comparisons. While Scope and nonethanol mouthwashes are less expensive and provide results similar to those with OMNIgene, Saccomanno's fixative may be unfavorable due to the microbial differences detected in this study. Our results will help guide the design of future oral microbiome studies.

Project description:BackgroundThe threats to health, associated restrictions and economic consequences of the COVID-19 pandemic have been linked to increases in mental health difficulties for many. Parents, in particular, have experienced many challenges such as having to combine work with home-schooling their children and other caring responsibilities. Yet, it remains unclear how parental mental health has changed throughout the pandemic or what factors may have mitigated or compounded the impact of the pandemic on parents' mental health.MethodsWe examined monthly survey data from two linked UK-based longitudinal studies: COVID-19: Supporting Parents, Adolescents and Children during Epidemics' (Co-SPACE) and COVID-19: Supporting Parents and Young Children during Epidemics' (Co-SPYCE). Data from 5576 parents/carers of 2-17-year-old children collected between April 2020 and January 2021 was analysed using mixed-effect modelling and latent class growth (mixture) modelling.ResultsParental stress and depression, but not anxiety, were higher during the periods of restrictions. This pattern was most pronounced for parents with primary-school-aged children, those that worked at home or had other adults in the household. Being younger, reporting secondary or below education, working out of home, having secondary-school-aged children or children with special education needs (SEN)/neurodevelopmental disorders (ND) further moderated whether, how and when parental mental health symptoms changed. Although around three quarters of parents reported consistently low mental health symptoms, a substantial minority reported consistently high or increasing symptoms of anxiety, stress and depression. The latter were more likely to be parents who were younger than average, were a single adult in the household, had a pre-existing mental health diagnosis or had a child with special educational needs or a ND.ConclusionsThese findings emphasise how different personal circumstances and pre-existing inequalities shaped how parents were affected by this unprecedented global pandemic and highlight the need for support and consideration to meet the needs of families in the future.

Dataset Information

Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies.

Publications

Temporal Variability of Oral Microbiota over 10 Months and the Implications for Future Epidemiologic Studies.

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