Bacteria make up the largest proportion of the oral microbiome

Most of the microorganisms in the oral microbiome are bacteria. The Human Oral Microbiome Database (HOMD) currently lists 774 bacterial species as part of the oral microbiome.

These bacteria are not evenly distributed throughout the mouth. Instead, they form communities in the form of biofilms, inhabiting various ecological oral niches. These niches, which roughly include the tongue, saliva, teeth, and mucosal surfaces, create unique microenvironments that support bacterial survival.

Common misconception: We have good and bad bacteria. 
The truth: Bacteria are not inherently good or bad. Instead of "good" bacteria genetically becoming "bad" species, it is more about a change in their behaviour or environment. Harmless bacteria can become problematic when conditions shift — like increased sugar intake leading to acid production and cavities, or low oxygen levels allowing gum disease-causing bacteria to thrive.

Here is how it works:

1. Opportunistic pathogens (pathobionts): Many bacteria in the mouth that are normally harmless, or even beneficial, are considered opportunistic pathogens or pathobionts. This means they have the potential to cause disease when the conditions become favourable.
2. Environmental shift (dysbiosis): The oral microbiome exists in a delicate balance. When this balance is disturbed – a state called dysbiosis – bacteria that are usually "good" or neutral can seize the opportunity to become problematic. This doesn't involve a change in their DNA, but rather a change in how they function or interact within the community.

What causes this shift?

• Altered pH levels: Like those caused by frequent sugar intake.
• Varied nutrient availability: Often influenced by dietary changes.
• Different oxygen levels: Especially critical in gum pockets.
• A weakened host immune system.
• The protective biofilm structure.
• The presence of keystone pathogens, which can drive the entire community toward disease.

An overview of the most important bacteria

Most bacteria in the oral microbiome belong to seven phyla — broad taxonomic groups that categorise bacteria based on shared genetic and physiological characteristics: Actinomycetota (Actinobacteria), Bacteroidota (Bacteroidetes), Bacillota (Firmicutes), Fusobacteriota (Fusobacteria), Pseudomonadota (Proteobacteria), Saccharibacteria (TM7), and Spirochaetota (Spirochaetes).

Each phylum contributes to the delicate balance of the oral microbiome. However, if the environment inside the mouth changes in ways that benefit the disease-causing microbes, this equilibrium breaks down, leading to an imbalance (dysbiosis) that can contribute to oral diseases like caries or periodontitis.

1. Actinomycetota (Actinobacteria)

• Key genera: Actinomyces, Corynebacterium
• Oral location.
  • Supragingival plaque (especially along the gingival margin)
  • Tooth root surfaces (especially in root caries)
  • Tongue dorsum
• Role in oral health: Early colonisers that help initiate plaque biofilm.
• Pathogenic potential: Can cause root caries and actinomycosis (chronic abscess-forming infection).

2. Bacteroidota (Bacteroidetes)

• Key genera: Porphyromonas, Prevotella, Tannerella
• Oral location:
  • Subgingival pockets
  • Periodontal tissues
  • Tonsillar crypts
• Role in oral health: Anaerobic organisms; some are normal residents, others opportunistic pathogens.
• Pathogenic potential: Major contributors to periodontitis, with virulence factors that break down tissue and evade immune response.

3. Bacillota (Firmicutes)

• Key genera: Streptococcus, Veillonella
• Oral location:
  • Supragingival plaque
  • Tongue surface
  • Buccal mucosa
  • Saliva
• Role in oral health:
  • Streptococcus initiates plaque biofilm (e.g., S. mitis, S. salivarius)
  • Veillonella consumes lactic acid produced by Streptococcus, moderating acidity
• Pathogenic potential:
  • S. mutans drives dental caries through acid production.
  • Some species promote biofilm imbalance under high-sugar conditions.

4. Fusobacteriota (Fusobacteria)

• Key genera: Fusobacterium
• Oral location:
  • Subgingival plaque
  • Periodontal pockets
  • Interproximal spaces
• Role in oral health: Acts as a “bridge species” allowing other bacteria to co-aggregate in the maturing biofilm.
• Pathogenic potential: F. nucleatum linked to periodontitis and even systemic diseases (e.g., colorectal cancer).

5. Pseudomonadota (Proteobacteria)

• Key genera: Neisseria, Haemophilus, Aggregatibacter
• Oral location:
  • Tongue dorsum
  • Hard palate
  • Saliva
  • Aggregatibacter: Subgingival plaque, especially in deep pockets.
• Role in oral health:
  • Neisseria and Haemophilus are early colonisers, maintaining oral homeostasis.
• Pathogenic potential:
  • A. actinomycetemcomitans is highly aggressive, especially in localized aggressive periodontitis.

6. Saccharibacteria (TM7)

• Key genera: Candidatus Saccharibacteria
• Oral location:
  • Subgingival biofilms
  • Associated with other bacteria (epibionts)
• Role in oral health:
  • Lives in symbiosis with other bacteria, affecting biofilm stability and immune response.
• Pathogenic potential:
  • Emerging evidence links it to periodontitis, but its role is still being defined.

7. Spirochaetota (Spirochaetes)

• Key genera: Treponema
• Oral location:
  • Deep periodontal pockets
  • Necrotic pulp tissues
  • Subgingival plaque
• Role in oral health:
  • Low abundance in health; increases in periodontal disease
• Pathogenic potential:
  • T. denticola is a key late coloniser in advanced periodontitis, contributing to tissue destruction.

While bacteria dominate, other microorganism groups play crucial roles too. Each type interacts within the biofilm community, influencing microbial balance, immune responses, and overall oral health:

Fungi

In addition to bacteria, the oral microbiome includes more than 100 fungal genera, with Candida and Malassezia being the most predominant. Candida albicans is associated with dental caries, particularly in children with early childhood caries, due to its ability to interact with Streptococcus mutans and reinforce cariogenic biofilms....

Archaea

Although less common than bacteria and fungi in the mouth, archaea play a key role in how other microbes work. The most common type, Methanobrevibacter oralis, acts as a "hydrogen scavenger," meaning it consumes the hydrogen gas that many bacteria produce when they break down food. By removing this hydrogen, archaea enable those bacteria (like Prevotella and Veillonella) to keep working efficiently, ultimately influencing the overall health and balance of the oral microbiome.

Viruses

The oral virome consists mainly of bacteriophages, which regulate bacterial populations through predation. Recent studies suggest that the diversity and abundance of phages in the oral microbiome are greater than previously thought, indicating their potential role in modulating microbial ecology and influencing oral diseases.

Protozoa

Protozoa are single-celled eukaryotic microorganisms that can be either free-living or parasitic. While they are less studied than bacteria and fungi in the oral microbiome, some protozoa have been associated with periodontal disease.

The most common oral protozoa include:

• Entamoeba gingivalis – Found in dental plaque and subgingival biofilms, often in individuals with periodontitis. It can ingest host immune cells, contributing to inflammation.
• Trichomonas tenax – A flagellated protozoan found in dental plaque, particularly in patients with poor oral hygiene and periodontal disease.

Although their exact role in oral health and disease is still being explored, protozoa may contribute to biofilm dynamics, inflammation, and tissue destruction in periodontal infections.