Christian Abnet

PhD, MPH

National Cancer Institute

Senior Investigator

IDATA (Learn more about this study)

2018-0020

Dec 18, 2018

Temporal variation in the oral microbiota in the Interactive Diet and Activity Tracking in AARP Study

The human oral microbiota has been found to be associated with some adverse health conditions, but most studies have only included a sample from a single timepoint which generally assumes that the oral microbiota is stable over time. A few studies have evaluated the temporal stability of the oral microbiota, but most of these studies included small sample sizes of predominantly young and healthy participants. Therefore, we propose to conduct a study of the temporal variability in the oral microbiota within the iDATA study. We will include all participants who provided at least one saliva sample in the study (N = ~800). At baseline and after six months, one saliva sample was collected in the morning and one sample was collected in the evening. We will extract DNA from the saliva samples using the QIAsymphony with microbial modifications. The V4 region of the 16S rRNA gene will be PCR amplified and then sequenced using the MiSeq. The sequence data will be processed bioinformatically using DADA2 to create alpha diversity estimates (e.g., observed species, PD whole tree, and the Shannon index), the relative abundance of specific taxa, and beta diversity matrices (e.g., unweighted and weighted UniFrac and the Bray-Curtis dissimilarity index). We will calculate intraclass correlation coefficients (ICC) to estimate the variability over six months and within one day. We will also calculate Dirichlet multinomial mixture models (DMM) to cluster samples into community types and then estimate the transition probabilities between community types. The ICCs will be used to estimate the number of samples to collect per individual in a study and the number of cases required for a nested case-control study within a cohort. We will also conduct analyses using the extensive questionnaire and measurement data to consider associations between diet, physical activity, and other exposures with the oral microbiota.

In this study, we aim to evaluate the temporal variability in oral microbiota over the course of one day and six months from the participants in the iDATA study who provided saliva samples. In addition, we aim to determine associations between diet and physical activity with the oral microbiota. We hypothesize that two samples collected on the same day (i.e., morning and evening) will be more similar than two samples collected over a period of six months. We also hypothesize that the alpha diversity metrics will be fairly stable over six months whereas there will be some temporal variability within the relative abundance of specific taxa and beta diversity.

Analyses of diet, physical activity, and other exposures will be exploratory and will help guide future targeted analyses of these exposures in relation to the oral microbiome.