Stability of healthy subgingival microbiome across space and time

Abstract

The subgingival microbiome is one of the most stable microbial ecosystems in the human body. Alterations in the subgingival microbiome have been associated with periodontal disease, but their variations over time and between different subgingival sites in periodontally healthy individuals have not been well described. We performed extensive, longitudinal sampling of the subgingival microbiome from five periodontally healthy individuals to define baseline spatial and temporal variations. A total of 251 subgingival samples from 5 subjects were collected over 6–12 months and deep sequenced. The overall microbial diversity and composition differed significantly between individuals. Within each individual, we observed considerable differences in microbiome composition between different subgingival sites. However, for a given site, the microbiome was remarkably stable over time, and this stability was associated with increased microbial diversity but was inversely correlated with the enrichment of putative periodontal pathogens. In contrast to microbiome composition, the predicted functional metagenome was similar across space and time, suggesting that periodontal health is associated with shared gene functions encoded by different microbiome consortia that are individualized. To our knowledge, this is one of the most detailed longitudinal analysis of the healthy subgingival microbiome to date that examined the longitudinal variability of different subgingival sites within individuals. These results suggest that a single measurement of the healthy subgingival microbiome at a given site can provide long term information of the microbial composition and functional potential, but sampling of each site is necessary to define the composition and community structure at individual subgingival sites.

High conservation of the dental plaque microbiome community across populations with differing subsistence strategies and levels of market integration

“…Further, no associations between dental plaque taxonomic composition and subsistence strategy were identified. These findings are consistent with recent archaeogenetics studies showing the long-term stability of dental calculus microbial communities within diverse human populations extending back to the late Pleistocene 30,31 , as well as experimental studies examining dental plaque changes over short and medium time frames 32,33 .…”

“…No members of the Baka or Nzime communities had dental fillings (or other hardware such as crowns or dentures). All noted health conditions on anterior teeth, both in the maxilla (tooth numbers 11,12,13,21,22,23) and mandible (tooth numbers 31,32,33,41,42,43), were recorded collectively for the anterior dental plaque sample, and all health conditions on posterior teeth, both in the maxilla (tooth numbers 14-18, 24-28) and mandible (tooth numbers [34][35][36][37][38][44][45][46][47][48], were recorded collectively for the posterior dental plaque sample. Dental health summary plots are provided in Supplemental Figures S2 and S3 and in the R markdown file on the github page 02-scripts.backup/Cameroon_taxonomy_oral_health.Rmd.…”

Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology

“…Instead of patterns relating to sample site, time period, or dental health, the samples appear to maintain individuality. This pattern of stable microbial signatures in dental plaque is a known phenomenon, with individual teeth having relatively stable communities over months-long time scales (Tamashiro et al, 2021). Despite high variability in profiles across teeth within an individual, plaque from any one tooth in an individual is more similar to other teeth in the same individual than to teeth in other individuals (Tamashiro et al, 2021).…”

“…This pattern of stable microbial signatures in dental plaque is a known phenomenon, with individual teeth having relatively stable communities over months-long time scales (Tamashiro et al, 2021). Despite high variability in profiles across teeth within an individual, plaque from any one tooth in an individual is more similar to other teeth in the same individual than to teeth in other individuals (Tamashiro et al, 2021). This pattern of individuality is also captured in ancient dental calculus (Fagernäs et al, 2022), where there is relatively high variability across teeth in an individual, yet samples from one individual are more similar to each other than to samples from another individual.…”

Long-Term Analysis of Resilience of the Oral Microbiome in Allogeneic Stem Cell Transplant Recipients

“…Other important factors that contribute to maintaining oral homeostasis include the chemical sensing of pathogenic microorganisms, salivary derived immunoglobulins (S-IgA), (glyco)proteins, and colonization resistance [2]. The oral microbiome is chemically and physically challenged several times a day, but despite these challenges the composition of the oral microbiome is fairly stable over time [6,7].…”