Pass me the mouthwash! – oral microbiology

The healthy human oral cavity is one of the most microbiologically diverse habitats in man, arguably only second to the gut in terms of microbial cell numbers and species diversity. It is recognized that the oral microbiota (oral microbiome) includes representatives from all three domains of life; bacteria, archaea and eukarya, however, it is the bacteria which are by far the most numerous colonizers, in both health and disease.

adam roberts

Dr Adam Roberts Department of Microbial Diseases, Eastman Dental Institute


The oral cavity represents a unique, dynamic and challenging environment for microbial inhabitants, and contains multiple distinct ecological niches, ranging from the unique, non-shedding surfaces of the tooth to the various mucosal surfaces on the gums, tongue, cheek and palate. The oral environment is one of the most variable human sites readily colonized by microbes in terms of physicochemical characteristics such as nutrient availability, temperature changes, oxygen potential, shear forces, from the action of the tongue, chewing and eating, and the challenges and opportunities which arise with the constant influx of transient organisms on food.

Bacterial Complexity
The numbers of bacterial species found in the human oral cavity is currently the subject of debate. With the advent of next generation sequencing and the ever-reducing costs of such experimentation, this figure is being constantly revised. Currently, approximately 700 bacterial species have been identified from the oral cavity and these have been curated in the Human Oral Microbiome Database (HOMD) available at: Other studies have put this figure considerably higher however, it must be noted that with next generation sequencing data there is a certain amount of variability in the interpretation of data depending on the various cut-off values used when deciphering the raw data. What is inescapable is that approximately only 50% of oral bacteria present can be currently cultivated in the laboratory.

Oral Biofilms
Many, if not most, species of bacteria in this environment live as part of a multi-species biofilm, commonly known as dental plaque. Biofilm formation on the surface of the tooth begins as soon as the newly exposed surface is covered in the acquired pellicle. The pellicle contains many host proteins and is recognized by the “early colonizers” which bind to the pellicle-covered tooth surface. The early colonizers include, but are not limited to, Streptococcus spp., Actinomyces spp., Capnocytophaga spp., Eikenella spp., Haemophilus spp., Prevotella spp., Propionibacterium spp. and Veillonella spp. These pioneer microorganisms utilize oxygen and condition the environment, allowing colonization by other bacterial species. In subsequent phases, during maturation of the oral biofilm, it is often colonized by Fusobacterium nucleatum which is considered a “bridge” species between the early and late colonizers as it is able to aggregate to members of both groups as well as host molecules within the pellicle. The late colonizers include Actinobacillus spp., Prevotella spp., Eubacterium spp., Porphorymonas spp. and Treponema spp.

Biofilm Resistance
Growth in a biofilm will lead to phenotypic changes in many of the inhabitants including the production of an extracellular polymeric substance (EPS) which is composed of carbohydrates, proteins and nucleic acids, and will often make up the majority of the biomass in a mature biofilm. The EPS affords the inhabitants protection against the external influences and stresses described above. Of clinical relevance is the intrinsic resistance to antimicrobial agents such as antibiotics exhibited by biofilm-growing cells compared to their planktonic, laboratory cultured, counterparts. MIC values have been recorded as being up to 1,000 times more for biofilm growing cells. One explanation for this observation is the increased biomass of the EPS in mature biofilms which prevent antimicrobials, and other molecules, reaching cells deep within the biofilm. A similar effect may also be observed with bacterially derived excreted resistance molecules (such a β-lactamases) which may form locally high concentrations due to impeded diffusion through the biofilm EPS. Biofilms exhibit gradients in nutrient and oxygen concentrations which will result in differing metabolic activities within cells occupying different regions within the biofilm. Subsequently, this will lead to differing susceptibilities and transient resistances to agents which target metabolic processes such as protein synthesis. Finally, many species of bacteria exhibit differential gene expression when growing as part of a biofilm, which can lead to differences in, e.g., membrane transport systems resulting in a phenotypic decrease in antimicrobial sensitivity.

Biofilm Interactions
Growth in a multi-species biofilm leads to some very specific beneficial interactions between some of the microbial inhabitants. Various syntrophic relationships have evolved, e.g., Streptococcus oralis and Streptococcus sanguis reach higher cell densities when grown together in a mucin-based chemostat compared with individual cell densities reached when growing as a single species, suggesting that there is complimentary metabolic activity allowing more efficient utilization of mucin. Fuso. nucleatum has been shown to aggregate with the anaerobic Porphorymonas gingivalis and Prevotella nigrescens which allow them to survive in oxygenated environments.

There are also more intricate relationships within oral biofilms. The biofilm environment is an environment which seems to be conducive to gene transfer leading to increased adaptability of oral bacteria. There are many experimental examples demonstrating horizontal gene transfer within model oral biofilms and circumstantial evidence from the genome sequence of oral bacteria indicates that this process is extremely pervasive in this environment. Indeed recent studies have confirmed that the normal oral flora is a reservoir for transferable antibiotic resistance and many other traits are also likely to be shared amongst the community.

Oral Diseases
The bacteria within the oral cavity are responsible for a range of diseases including the most common diseases in the world, dental caries, apical periodontitis and periodontal disease, which are estimated to affect up to 90% of the global population. These dental diseases are interesting from a causative aspect as, unlike many other diseases which fit Koch’s postulates, dental diseases are often polymicrobial in nature with no single causative species identified.

There are multiple theories regarding the aetiology of dental caries; all of which are concerned with monosaccharide and disaccharide metabolism. The most widely accepted is that a few acidogenic species, such as Streptococcus mutans and Streptococcus sobrinus, are actively involved in the disease. They lower the pH during carbohydrate metabolism leading to an imbalance of mineralization/de-mineralization in the enamel which results in lesions. This gives microbes and their metabolic by-products access to the underlying dentine. At this stage caries are irreversible.
If carious lesions are left untreated the microbes will invade the dental pulp causing necrosis and apical periodontitis will likely result. The bacteria isolated from these primary infections include Actinomyces spp., Bifidobacterium spp., Eubacterium spp., Lactobacillus spp., Rothia spp., Streptococcus spp. and Prevotella spp.


Tooth Anatomy

Periodontitis is a subsequent infection of the soft tissue anchoring the tooth. This is also a polymicrobial disease but the associated species are shifted towards anaerobic, protein-metabolizing bacteria such as Tannerella forsythia, Porphyromonas gingivalis, Trepanema denticola and Aggregibacter actinomycetemcomitans associated with the majority, but not all cases of the disease.

The overall contribution that the oral microbiome makes to human health and disease is beginning to emerge. In addition to the ecological imbalances responsible for many oral diseases, e.g., caries and periodontitis described above, oral microbes have also been shown to be involved with disease at other body sites such as the heart, indicating that the oral cavity may act as a reservoir for bacteria with potential to metastasize to other regions of the body and cause disease. As a more in depth understanding of the dynamic human oral microbiome emerges we will gain insight into its contribution to a range of diseases and will hopefully be in a position to ecologically manage it to a point which promotes health.

Adam P. Roberts, Department of Microbial Diseases, UCL Eastman Dental Institute,

Morgana E. Vianna, Endodontic Unit, UCL Eastman Dental Institute,

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