The Oral Microbiome: Critical for Understanding Oral Health and Disease

By Bonnie Feldman, DDS, MBA and Ellen M. Martin

As a dentist trained in the 1980s, I am happy to report that much of what I learned in dental school so many years ago may no longer apply.  New understanding of the microbiome is changing our ideas about health and disease, and is pertinent to our thinking about the role of the oral microbiome in systemic disease, including autoimmune diseases.

Contrary to what I was taught, the goal of good oral hygiene is not simply aimed towards killing the “bad” bacteria, but more reflective of balancing the ecology of the oral microbiome.  On a recent trip to NYC I met with Dr. Gerry Curatola, who seems to agree with this approach in his recent book, The Mouth-Body Connection (1).

Dr. Curatola explains, “Not only do we know that human health depends on maintaining balanced relationship with and within complex communities of microorganisms, but microbes are recognized to contribute to disease in previously unexpected ways… overzealous oral hygiene is being recognized as a cause of disease.” (Curatola, 2017).

The mouth as a gateway

While the mouth is one of the body parts most vital to our health, its significance is often overlooked. In fact, even as I delved into my research on the oral microbiome I was surprised by numerous facts about oral health, despite my background as a clinical dentist.

I was startled to find that nearly half of American adults have periodontitis, the most severe form of gum disease, with gum disease increasing one’s likelihood of meeting ADA guidelines for diabetes screening by an average of 30%.2 Additional statistics are cited below.

Screen Shot 2017-10-12 at 12.23.59 PM

What is the oral microbiome?

Over the past 15 years, microbiologists contributing to the Human Oral Microbiome Database (HOMD) have cultured 68% of an estimated 700 different species of oral bacteria.

The microbiome is highly variable both between and within individuals. Various sectors of an individual’s microbiome show great diversity between compartments in the body; species of bacteria present differ by location (e.g., hair, skin, stomach, and oral cavity, as shown below).

In contrast to the GI tract, in which high level of species diversity is correlated with better health, oral disease is actually associated with an increased diversity and richness of the oral microbiome. The oral cavity, as shown below, varies in species diversity, with additional influence from biofilms and environmental conditions that may hinder or enhance disease.

Screen Shot 2017-10-12 at 12.29.19 PMSource: Frontiers in Microbiology

Why should we care?

New understanding of the oral microbiome is shaping how we think about caries, periodontal and systemic diseases. While the traditional view held that these diseases may be caused by a limited number of causal pathogens, we now think of the oral microbiome as a finely tuned community that determines the balance not only between oral health and disease, but also some systemic diseases (3).

What happens when the oral microbiome is out of balance?

The mouth is positioned as the initial meeting place between the immune system, the gut, the outside environment, microbes, pathogens, toxins and food nutrients. As this first point of contact, the oral microbiome seeds the rest of the GI tract, with a 45% overlap between the microbes found in the mouth and in the colon.

The oral microbial ecosystem is vital to maintaining oral and systemic health. Salivary flow and biofilms on the teeth and soft tissue maintain microbial equilibrium within the oral cavity and protect against manifestation of pathogens. In contrast, disturbing homeostasis of the oral cavity can stir pathogen activity and lead to oral disease.

A healthy oral microbiome can only be maintained with good oral hygiene and a well functioning immune system. As shown in the figure below, poor oral hygiene, immunological disorders, and certain genetic predispositions are major factors that contribute to the initiation of the disease cycle.

Any of the risk factors shown below may cause microbes to either grow abnormally or acquire virulence factors, consequently leading to disease. The key to oral health is maintaining balance within the diverse microbes of the oral microbiome, which may interact both positively and negatively with the host. Cause and effect relative to these ecological shifts in oral microbiome composition are still not entirely well understood as of yet.

Screen Shot 2017-10-12 at 12.24.48 PM

Source: Wiley Online Library

Decay is a polymicrobial disease, influenced by many factors

In dental decay, carbohydrates are fermented to organic acids (shown in red below). These organic acids lower local pH, resulting in net demineralization of the tooth surface and driving dysbiosis in which both acid-producing and acid-tolerating microbiota are present.

In contrast, in health, (shown in blue below) a more complex and balanced pattern of metabolism involves the catabolism of salivary proteins and glycoproteins, with the generation of alkali to neutralize any acid products.

Upon low salivary clearance, overly frequent snacking, smoking, and presence of other risk factors, demineralization outweighs remineralization and results in a net mineral loss, which eventually presents itself in the form of tooth decay.

Traditional caries-associated species include Streptococci mutans and Lactobacillus species.  Increasing evidence now points to the roles of Actinomyces, Bifidobacterium, and other Gram-positive rod species play important roles in the community.

Screen Shot 2017-10-12 at 12.25.07 PMSource: British Dental Journal

Polymicrobial Synergy and Dsybiosis in Periodontitis

Recent advances in metagenomic, metatranscriptomic, and mechanistic studies suggest a new model of periodontal disease, as shown below. In this model, disease results from polymicrobial synergy and dysbiosis, which perturbs the balance from homeostasis to disease in oral and extra oral sites (6).

Screen Shot 2017-10-12 at 12.26.20 PM

Source: US National Library of Medicine National Institutes of Health

Recent research suggests that Potassium may be a key signal in host-microbiome dysbiosis in periodontitis, and may also point to the role of changing diet to prevent periodontal disease progression (7).

Autoimmune Disease and the Oral Microbiome

New published data indicates that changes in the symbiotic and dysbiotic interactions of the core and variable microbiome are associated with a number of autoimmune diseases, as shown below.

Changes in the oral microbiome due to the host’s environment, genetic susceptibility, diet, and smoking may contribute to the pathogenesis of Sjogren’s syndrome, rheumatoid arthritis, systemic lupus, erythematosus, and Crohn’s disease. (Read here to find out the microbiome’s role in these diseases.) There is a delicate balance between the immune system and the composition of microbiota leading to dysbiosis, or microbial imbalance, and autoimmune progression (8).

Interested in delve deeper into the role of the oral microbiome in autoimmune health? Explore this curated bibliography of recent research publications.

Click here for more autoimmune resources.

To learn and engage more… attend a session at the 5th Microbiome R&D and Business Collaboration Forum. See what it’s all about here!



[1] Curatola, Gerald P. et al., “The Mouth-Body Connection: a 28-Day Program to Create a Healthy Mouth, Reduce Inflammation, and Prevent Disease throughout the Body,” Center Street, (2017).


[2] Strauss, S. M., et al., “The dental office visit as a potential opportunity for diabetes screening: an analysis using NHANES 2003-2004 data.” Journal of Public Health Dentistry (2010): 70: 156–162.

[3] Zhang, Xuan et al. “The Oral and Gut Microbiomes Are Perturbed in Rheumatoid Arthritis and Partly Normalized after Treatment.” Nature Medicine 21.8 (2015): 895–905.  

[4] Zarco, Vess et al. “The Oral Microbiome in Health and Disease and the Potential Impact on Personalized Dental Medicine.” Oral Diseases 18.2 (2012): 109–120.

[5] Dewhirst, Floyd E. “The Oral Microbiome: Critical for Understanding Oral Health and Disease.” Journal of the California Dental Association 44.7 (2016): 409–10.

[6] Hajishengallis, George. “Periodontitis: from microbial immune subversion to systemic inflammation,” Nature Reviews Immunology (2015): 30–44.


[7] Yost, Susan et al. “Potassium is a key signal in host-microbiome dysbiosis in periodontitis,” PLOS Pathogens (2017): e1006457.

[8] Nikitakis, N. G., et al. “The autoimmunity–oral microbiome connection.” Oral diseases (2016).


  1. This is a terrific overview of the oral microbiome and offers a better understanding of the beneficial and essential role of the microbial community in our mouths that has long been misunderstood….and mistreated. It also sets the table for novel approaches in treatments and greater systemic health! Thank you Dr. Bonnie.

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