The human oral cavity harbors over 700 bacterial species in complex ecological communities. Advances in DNA sequencing technology have revolutionized understanding of these microbial populations and their roles in health and disease.

The Healthy Oral Microbiome

Healthy oral microbiomes maintain ecological balance through competitive exclusion, nutrient competition, and antimicrobial production. Dominant species in health include Streptococcus, Veillonella, and Neisseria species.

The concept of "core microbiome"—bacterial species present across most healthy individuals—helps define normal microbial ecology. However, significant inter-individual variation exists, influenced by genetics, diet, oral hygiene, and environmental factors.

Dysbiosis in Dental Caries

Caries development involves ecological shifts from health-associated bacteria toward acidogenic and aciduric species. While Streptococcus mutans receives primary attention, caries is a polymicrobial disease involving Lactobacillus, Bifidobacterium, and other acid-producing species.

Research challenges the simple "cariogenic bacteria" model. Studies using 16S rRNA sequencing show caries-associated microbiomes vary substantially between individuals, suggesting multiple pathways to disease. This complexity complicates development of microbiome-based caries diagnostics.

Periodontal Disease Microbiology

Periodontitis involves dysbiotic shifts toward anaerobic gram-negative bacteria. The "red complex" (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia) and "orange complex" (Fusobacterium, Prevotella species) are strongly associated with disease.

However, periodontal health is not simply the absence of pathogens. Health-associated bacteria like Streptococcus sanguinis and Actinomyces species actively suppress pathogen colonization. Therapeutic approaches promoting beneficial bacteria may complement traditional antimicrobial strategies.

Diagnostic Applications

Salivary microbiome testing is emerging as a diagnostic tool. Companies like OralDNA Labs and Hain Diagnostics offer PCR-based tests identifying periodontal pathogens. While these tests detect specific bacteria, their clinical utility remains debated.

A 2025 systematic review found bacterial testing modestly improves periodontal treatment outcomes when combined with antimicrobial therapy. The benefit appears greatest for aggressive periodontitis and refractory cases. For chronic periodontitis, traditional clinical assessment remains the standard.

Therapeutic Approaches

Probiotic interventions aim to restore healthy microbial balance. Lactobacillus and Bifidobacterium strains show promise in clinical trials for caries and gingivitis prevention. A 2023 meta-analysis found probiotic lozenges reduced gingivitis scores by 15-20% compared to placebo.

Prebiotic approaches provide nutrients favoring beneficial bacteria. Arginine-containing toothpastes promote alkali-producing bacteria that neutralize acid and inhibit caries. Clinical trials show arginine toothpastes reduce caries incidence by 20-25% compared to fluoride-only controls.

Future Directions

Personalized microbiome-based risk assessment may enable targeted prevention. Identifying individuals with high-risk microbial profiles before disease develops allows early intervention.

Engineered probiotics designed to colonize oral surfaces and produce antimicrobial compounds are in development. While regulatory and safety considerations remain, these approaches represent potential paradigm shifts in caries and periodontal disease management.

For now, promoting healthy microbiomes through mechanical plaque removal, dietary counseling, and fluoride remains evidence-based practice. Microbiome testing and probiotic adjuncts may benefit select high-risk patients.