A New Look at the Oral Microbiome

By Bonnie Feldman, DDS, MBA | Published 5/31/2018 1

blue toothbrush and toothpaste 2048 x 1150

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 be state of the science. New understanding of the microbiome is changing our ideas about health and disease and is particularly pertinent to understanding the role of the oral microbiome in systemic disease, including autoimmune diseases.

Oral microbiome - Biogenics 16 727 x 631

Graphic with permission of Biogenics 16


The oral microbiome introduced

Each of us incorporates a complex ecosystem of bacteria upon and within our bodies, and the collective genomes of all these microbes together are labeled the human microbiome. Each microbiome is distinctive and could identify a person as accurately as fingerprints. thus, while human beings are 99.5% identical in genetic makeup, our microbiomes can be 100% different between individuals. (1)

The mouth contains one of the most significant microbiomes, housing some 700 different species of bacteria that live in different microbial sub-habitats: teeth, tongue, lip, cheek, hard palate, soft palate, and tonsils. The oral cavity is the first meeting place between the outside environment and your immune system, gut, and the signaling molecules they secrete in dealing with the nutrients and toxins of food as well as extraneous microbes (including pathogens) that we encounter.

The oral microbiota can be categorized into three general groups:

  1. Symbiotic (positive relationships)
  2. Commensal (most bacteria that simply live within and on us)
  3. Pathogenic (disease-causing).

Related Content: The Oral Microbiome and Its Links to Autoimmunity

Plaque formation

Recognition of the balance and shifts of these bacterial groups is essential to sustaining an optimally healthy mouth. They are especially important in the formation and understanding of plaque. Dental plaque is a multispecies biofilm that deposits itself as layers onto tooth surfaces (Listgarten, 1976; Flemmig and Beikler, 2011). When saliva interacts with the enamel surface of our teeth, a protective protein layer called the pellicle forms. Aerobic bacteria attach to the pellicle, building a biofilm. These aerobes are typically symbiotes and commensals that form a “buffer zone” that prevents acids in foods and beverages we eat and drink from direct contact with enamel. However, as more microbes attach and the biofilm thickens, it blocks oxygen from deeper layers creating a shift in those deep layers from an aerobic environment to an anaerobic (oxygen-deprived) environment. Anaerobic environments are more hospitable for pathogenic bacteria and, as a result, a shift in bacteria population follows in the direction of more pathogenic.


Oral microbiome - Genome biology 954 x 327

Graphic with permission of Genome Biology

The image above shows the cycle of plaque formation from pellicle formation, initial adhesion to the tooth, maturation of bacteria, microbial imbalance, and dispersion of pathogenic bacteria (from left to right, respectively).


Oral health is no longer about killing “bad” bacteria

Contrary to what I was taught during my time in dental school, the goal of good oral hygiene is no longer aimed at killing “bad” bacteria (and we were taught that all bacteria were bad), but more about balancing the ecology of the microbiota in the oral cavity.

“An unbalanced or unhealthy oral microbiome is like a garden overgrown with weeds”

-Gerry Curatola “The Mouth-Body Connection”


How the oral microbiome affects general health

It is only when the mouth becomes overgrown with pathogens that plaque biofilm can be considered detrimental in terms of general health. When aerobic bacteria are replaced by anaerobic bacteria, they release biologically active agents that can penetrate the lining of the gums and set off an inflammatory cascade.

Due to the rich vascularization of the tissues of the oral cavity, it is easy for pathogens, toxins and other harmful complexes to disseminate to other regions of the body through the bloodstream. New understanding of the oral microbiome is shaping how we think about caries, periodontal and systemic diseases. While the traditional view was that these diseases were caused by a limited number of 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 for some systemic diseases (3).

So far, three pathways linking oral infections to secondary systemic effects have been proposed.

  1. Metastatic Infection: Transient bacteria from oral infections or dental procedures can gain entrance into the blood and circulate throughout the body. Disseminated microorganisms may find favorable conditions, settle at a given site and start to multiply, colonize and infect.
  2. Metastatic Injury: Certain bacteria can produce toxins that, when excreted or introduced into a host body, can trigger many pathological manifestations.
  3. Metastatic Inflammation: Soluble molecules that enter the bloodstream may react with circulating antibodies to produce large complexes that give rise to acute and chronic inflammatory reactions. (4)
Oral microbiome - oral diseases 718 x 626

Graphic with permission of Oral Diseases

That is why it is not only about what goes into your mouth, or how your mouth looks and smells, but what is going on inside your mouth as a microbial ecosystem. Your oral microbiome is affected by a variety of factors, including types of food you eat, stress, aging, genetics/race/ethnicity, gender, even the type of toothpaste you use! Each of these factors contributes to the uniqueness of an individual’s microbiota composition, and practicing consistent oral hygiene and making better lifestyle decisions supports this healthy oral microbiome.


  1. Rob Knight, and Daniel McDonald. “Our Second Genome.” Imagine, pp. 26–29., cty.jhu.edu/imagine/docs/second-genome.pdf.
  2. Lin, Steven. The Dental Diet: the Surprising Link between Your Teeth, Real Food, and Life-Changing Natural Health. Hay House, Inc., 2018.
  3. Zhang, Xuan, et al. “The Oral and Gut Microbiomes Are Perturbed in Rheumatoid Arthritis and Partly Normalized after Treatment.” Nature Medicine, vol. 21, no. 8, 2015, pp. 895–905., doi:10.1038/nm.3914.
  4. Babu, Nchaitanya, and Andreajoan Gomes. “Systemic Manifestations of Oral Diseases.” Journal of Oral and Maxillofacial Pathology, vol. 15, no. 2, 2011, pp. 144–147., doi:10.4103/0973-029x.84477.

    Ellen M. Martin was a co-author of the original story.

Bonnie Feldman, DDS, MBA

Website: http://www.drbonnie360.com

Dr. Feldman is an autoimmune patient advocate and an expert in digital health, the oral and gut microbiomes, and immune-mediated diseases. She is a frequently invited speaker and panelist at national and international conferences including TEDx, SXSW, and Stanford Medicine X.

Currently, she is the Founder and CEO of Your Autoimmunity Connection, a consultancy that through research, consulting, and other professional services, assists clients offer innovative products and services to people with chronic immuno-inflammatory diseases.

Previously, Dr. Feldman was a practicing clinical dentist. As a dentist, she built two dental practices and a consulting business from scratch. Then, armed with an MBA in finance from the UCLA Anderson School of Management, she worked on all sides of the Wall Street equation - sell side, buy side, and investor relations.

Her multimedia work has appeared in numerous online venues such as Forbes, Medium, Tincture, and Thrive Global. She has also been featured in podcasts and documentaries, written various white papers demonstrating deep subject expertise, and created presentations and blog posts that demonstrate her exceptional skills in the art of science storytelling.

Motivated by her desire to help future generations thrive, Dr. Feldman takes her four lenses (dentist, Wall Street analyst, digital health consultant, and patient) to seek out solutions that provide the best of conventional, functional, and digital medicine to improve chronic disease management for all patients.


  • HI Dr. Feldman, My husband just came home from the dental hygienist and said she told him to water floss with 1:1 water and hydrogen peroxide because the latter will kill anaerobic bacteria. This seems like the old “kill bad bacteria” approach you wrote about. Do you agree with this recommendation? Also, what do you think the water flosser for recalcitrant”never flossers?”

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Comment will held for moderation