Oral Microbiome Composition and Health Implications

The human oral cavity hosts a rich and dynamic microbial ecosystem comprising bacteria, fungi, viruses and archaea that inhabit distinct niches such as the tongue dorsum, supragingival and subgingival plaque, and salivary film. A balanced community of microorganisms contributes to the maintenance of oral homeostasis by preventing colonisation by pathogens, modulating local immunity and participating in nutrient metabolism. Perturbations of this equilibrium, or dysbiosis, are linked to dental caries, periodontal disease and mucosal infections, and emerging evidence indicates systemic associations with cardiovascular disease, diabetes and adverse pregnancy outcomes. Technological advances in high-throughput sequencing and metagenomic analysis have revealed a “core microbiome” shared by healthy individuals, alongside a variable component influenced by host genetics, diet, lifestyle and environmental exposures. Understanding these compositional and functional patterns is crucial for developing microbiome-based diagnostics, personalised preventive strategies and novel therapeutics such as oral microbiota transplantation or targeted prebiotic and probiotic interventions.

Research from Nature Portfolio

Large-scale population profiling in Japan has defined a set of 72 core bacterial taxa present in at least three quarters of adults, accounting for over 90 per cent of total salivary reads. Two community types were identified by clustering relative abundances of dominant taxa, and lower phylogenetic diversity correlated with favourable oral health indicators including low plaque burden, absence of active caries, minimal gingival bleeding and non-smoking status. Conversely, a distinct community profile characterised by elevated Neisseria and related genera was associated with younger age, lower body mass index and fewer restorative dental treatments. These findings establish a baseline reference for healthy salivary microbiomes and underscore the relationship between microbiome composition and key clinical measures of oral health.

Oral Microbiome Composition and Health Implications publication trend

The graph below shows the total number of articles in oral microbiome composition and health implications across all publications each year (not limited to Nature Index journals).

Technical terms

Alpha diversity: A measure of microbial richness and evenness within a single sample or habitat.

Beta diversity: A metric comparing compositional differences between microbial communities across samples.

Operational taxonomic unit (OTU): A cluster of closely related sequences used as a proxy for microbial “species” in sequence-based studies.

Core microbiome: The set of microbial taxa consistently present across the majority of healthy individuals.

Dysbiosis: A disrupted microbial community state associated with disease or loss of host–microbe homeostasis.

References

1. Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. Microbiome (2024).
2. Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans. Journal of Oral Microbiology (2023).
3. Characterising healthy Australian oral microbiomes for ‘super donor’ selection. Journal of Dentistry (2024).