Evaluation of periodic stability of the oral microbiome from a healthy cohort using 16S ribosomal RNA gene sequencing analysis

Abstract

ObjectivesThe use of 16S ribosomal RNA gene sequencing analyses has rapidly increased in clinical oral studies. However, cohort-based clinical research has not sufficiently accounted for the periodic stability in oral microbiota. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention-free “healthy” cohort. Materials and MethodsWe obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at monthly (T1) and quarterly (T2) intervals for 16S ribosomal RNA gene sequencing analysis. ResultsWe observed that taxonomic profiling had a similar pattern of dominant genera, namely Rothia, Prevotella, and Hemophilus, at all-time points. Shannon diversity revealed a significant increase from T0 (p<0.05). Bray Curtis dissimilarity was significant (R=-0.02, p<0.01) within the cohort at each time point. Clustering revealed marked differences in the grouping patterns between the three-time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers. ConclusionOur observations confirmed presence of periodically different stable states within the oral microbiome in an intervention-free healthy cohort. Accounting for multi-stability will improve the understanding of future research and facilitate identifying and classifying the reliable markers of diseased, healing, healed, and healthy states.Clinical relevanceThe high periodic variation within a healthy cohort demonstrated the presence of multiple stable states within an individual. Clinical research using RNA gene sequencing for comparison should adopt microbiome specific selection criteria for careful classification of a health-associated group.