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How Much Do We Know About the Oral Microbiome?


Understanding the oral microbiome in health and disease is essential as it will give further directions to explore the functional and metabolic alterations associated with the diseased states, and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine. In this article we explore the development of the oral microbiome, ask what might constitute a ‘healthy’ oral microbiome, and question what still needs to be done in terms of research in order to fully understand the link between the oral microbiome, oral health, and systemic health. 

The Oral Microbiome

The oral microbiome is thought to have the third highest diversity of any microbiome niche, and given its ease of collection has become one of the most well-studied (Dewhirst et al. 2010). Previously, studying the microbiome was limited to the conventional culture-dependent techniques, but the abundant microflora present in the oral cavity could not be cultured. Hence, studying the microbiome was difficult. The emergence of new genomic technologies including next-generation sequencing and bioinformatics has revealed the complexities of the oral microbiome, and has provided a powerful means of studying it. 

The oral microbiome comprises a complex and diverse community of microorganisms living within the oral cavity. It is understood to be the third most diverse and largest after the gut and skin microbiota with over 700 species of bacteria alone (excluding fungi, protozoa and viruses). The microbiome is crucial to the oral health of humans as it is formed of an abundance of bacteria that live on multiple different surfaces: teeth, soft tissues, and mucosa. It is also the first point of digestion and is therefore thought to be crucial in maintaining oral and systemic health (Deo & Deshmukh, 2019). 

Development of the Oral Microbiome

Despite the womb being considered as sterile, recent studies have found colonization by oral microorganisms within the intrauterine environment in as many as 70% of pregnant women, namely Streptococcus spp. and Fusobacterium nucleatum

The development of the oral microbiota is understood to begin after birth, and grows as an infant is exposed to varying microorganisms from its environment. This happens as soon as a baby’s first weeks of life. At birth, a newborn acquires all the necessary species of microbes to keep it healthy, namely Streptococcus salivarius. Within the first year, an infant will go on to develop a more diverse microbiome with Lactobacillus, Actinomycetes and Neisseria (Deo, Deshmukh, 2019).

The increase of microorganisms in the oral cavity is the result of a variety of factors including oral hygiene practices, diet, and environmental factors. As children grow and their teeth begin to emerge, the complexity of the microbiome increases, and the microbial community shifts to reflect changes in the oral environment.

What is a ‘Healthy’ Oral Microbiome?

According to Berg et al. (2020), the term "microbiome" pertains to the collective microbial population residing in a specific environment with unique characteristics. It encompasses not only the microorganisms co-existing in that environment but also their interactions with each other. It is generally accepted that for the microbiome to be healthy it needs to be balanced. 

The concept of a "core microbiome" in oral microbial communities refers to the presence of similar bacterial communities in the mouths of healthy individuals who are not related to each other, regardless of their age or ethnicity. This means that there are certain types of bacteria that tend to be present in the oral cavity of healthy people, regardless of their individual differences.

A healthy microbiome is a barrier to external pathogens and possible exterior aggression. It must be balanced. The balance between bacteria is different between each individual because it depends on multiple factors. However, the species found in individuals overlap (Zaura, et al, 2009). To maintain this balance, oral hygiene with products targeting the microbiome is recommended, meaning the use of products that do not upset the balance of the microbiome. Pre and probiotics can also be interesting ingredients in oral health products for a balanced microbiome (Nanavati et al, 2021). 

An unbalanced oral microbiome can allow the overgrowth of pathogenic bacteria and lead to an oral infection locally in the mouth, for example Filifactor alocis, Porphyromonas, Synergistetes, and Peptostreptococcaceae are genera known to be a causal agent for periodontal disease (Lovegrove, 2004). Amazingly, pathogenic bacteria in the mouth might contribute to systemic diseases, for example, an increase in Fusobacterium and other bacterial species has been found in oral cancer patients and diabetics, reinforcing the importance of a balanced oral microbiome (Matsha, et al, 2020). Ectopic colonization of oral bacteria in other tissues or organs such as the stomach, heart, brain, placenta or even tumors could influence these diseases through an inflammatory response. 

Some recent studies also point to the possible usefulness of the oral microbiome as a treatment for infections of different organs of the body. For example, it has been shown that the use of oral firmicutes spores could help treat C.difficile infections. (Feuerstadt, et al, 2022)

Next steps for research

The link between the oral microbiome and systemic health is still an evolving area of research, thanks to the emergence of sequencing and bioinformatics we are closer to understanding this link. Further research on the correlation between systemic diseases and the oral microbiome is needed in order to gather such consistent and reliable results required to fully understand the important role of oral cavity bacteria.

To date, we have conducted numerous oral microbiome studies. If you are interested in carrying out any research with us and testing your oral care products, you can reach us at


Oral Microbiome: All genomes of microorganisms in the oral cavity (Deo, Deshmukh,2019)

Systemic disease: Disease that impact the whole body 

C. difficile infections: Clostridium difficile, also called C. difficile, is a type of bacteria that can cause a bowel infection

Fusobacterium: Bacteria normally present in the mouth, but can cause infections when  unbalanced

Prebiotics: ingredients that promote the balance of the microbiome

Probiotics: Microorganisms that have health benefits 


Deo, P.N. and Deshmukh, R. (2019) “Oral microbiome: Unveiling the fundamentals.,” Journal of Oral and Maxillofacial Pathology, 23(1), pp. 122–128. Available at:

Feuerstadt, P. et al. (2022) “SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection,” New England Journal of Medicine, 386(3), pp. 220–229. Available at:

Lovegrove JM. Dental plaque revisited: bacteria associated with periodontal disease. J N Z Soc Periodontol. 2004;(87):7-21. PMID: 15143484.

Marsh, P.D. (2000) “Role of the Oral Microflora in Health,” Microbial Ecology in Health and Disease, 12(3), pp. 130–137. Available at:

Matsha, T.E. et al. (2020) “Oral Microbiome Signatures in Diabetes Mellitus and Periodontal Disease,” Journal of Dental Research, 99(6), pp. 658–665. Available at:

Nanavati, G., Prasanth, T., Kosala, M., Bhandari, S.K. and Banotra, P., 2021. Effect of probiotics and prebiotics on oral health. Dental Journal of Advance Studies, 9(01), pp.01-06.

Zaura, E. et al. (2009) “Defining the healthy ‘core microbiome’ of oral microbial communities,” BMC Microbiology, 9(1), p. 259. Available at:


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