Sep 18, 2022 - minute readminutes read

What Is Oral Microbiome? A Simplified Guide to Understanding Your Mouth’s Ecosystem 

Ecosystems organically take form in a vast assortment of places, both in nature and within our own bodies. It’s one of the cool things about biology and life. You might be surprised by the complexity of the ecosystem within your own mouth.


To understand this ecosystem and why it’s important to dental care, you’ll first want to understand the concepts of biomes and microbiomes.

Biomes are communities of flora and fauna that form in response to the conditions of their natural environment. Those environmental conditions will dictate what type of biome develops – for instance, a dry, arid climate fosters the flora and fauna of a desert biome. As conditions change, the flora and fauna present can change, too.

What, then, is a microbiome? Much like their larger counterpart, microbiomes are communities of organisms that flourish within their given environment, but on a microscopic scale.

And rather than being located within a broad geographical region, they’re found in smaller spaces – such as on our bodies and even inside our mouths.

The oral microbiome

While it may be off-putting to think about having a vast number of microscopic organisms residing inside our mouths, those microbes will be there whether we think about them or not. So, in the best interest of personal health, it’s worth having at least a passing familiarity with what a healthy oral microbiome looks like.


The human mouth is host to roughly 700 varieties of microorganisms. In total, the population of an average oral microbiome is roughly 6 billion microbes. No, that was not a typo! We each carry the equivalent of three-quarters of the world’s population in microbes inside our mouths.


These microbes consist of bacteria, viruses, and fungi. The important thing to remember is that, for the most part, the oral microbiome exists in a state of symbiosis, with the microorganisms having a healthy balance and beneficial exchanges with one another.


Much like violets growing in dappled forest floors and woodpeckers nesting in hollow branches, the organisms within the oral microbiome have places they call home as well. For example, some thrive on hard surfaces like teeth, while others prefer soft tissues like the tongue and oral mucosa.

Numbered among the vast population of microorganisms residing in the oral microbiome are several beneficial microbes that work day in and day out, helping maintain balance in our bodies.

Some good bacteria can be added to help tip towards a beneficial balance. Indeed, probiotics are live microorganisms which when administered in adequate amounts confer a health benefit to the host, according to FAO and WHO joint definition.

Probiotics have been identified as having a net-beneficial impact on the well-being of the host. Probiotic supplements are expected to positively modify the microbiome by bringing more beneficial bacteria, either to strengthen or restore it. When these probiotics reach our guts, they aid with digestion. In the oral microbiome, they fight against harmful microbes that threaten our oral – and whole-body – health.

Harmful microbes

The impact of harmful microbes that fester and multiply is much more noticeable since they disrupt our well-being.

Some negative health effects caused by harmful microbes in our oral microbiome include:

●      Bad breath

●      Plaque

●      Tooth decay

●      Gum disease

Whereas a healthy oral microbiome is the norm, this is a very delicate balance, and when the harmful bacteria are allowed to flourish instead, that’s when health problems begin to manifest. Oral health problems can be an early indicator of greater health issues, like cardiovascular disease and diabetes. 

Inside the matrix

No, this is not a pop-culture reference – well, not exactly. Much like the Matrix from the movies, the matrix in the oral microbiome shields the organisms it plays host to, but that’s where the similarities end.


Biofilm is a thin layer of microorganisms, such as bacteria, that coat the surfaces of their environment. Once a biofilm is established, a matrix forms to protect the communities of bacteria.

In the oral microbiome, the matrix houses both beneficial and harmful microbes, enabling those bacteria to establish a stronghold – for better or for worse. Plaque is a biofilm that contains an accumulation of bacteria that are responsible for gum inflammation and decay.

Feeding the biofilm

These matrices eventually develop systems that ensure bacteria in the biofilm are supplied with nourishment. As part of their digestive process, bacteria release enzymes. Some of these enzymes turn sugars into acids, which promote the development of caries.

Maintaining a healthy balance in the oral microbiome

The key to maintaining a balanced oral microbiome is practicing good oral hygiene, limiting the accumulation of bacteria and limiting the amount of nourishment that reaches the biofilm within the matrix.

Stop feeding harmful bacteria

Harmful microbes thrive on sugars, so limiting sugary foods and drinks is a good start. Brushing and cleaning interdentally between meals also removes the food source for these microbes.

Practice a complete oral care ritual

By making complete oral care part of your twice-daily ritual to remove plaque, you can play a proactive part in balancing your oral microbiome.

This ritual consists of:

1.  Cleaning between your teeth with interdental cleaners like floss, picks, and special brushes.

2.  Brushing your teeth correctly and thoroughly with the right toothbrush and toothpaste.

3.  Rinsing your mouth to remove remaining debris.

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