Authored by Kathryn Kos, M.Ed., NTP

Mouth Microbiome: As the gateway to your body, the mouth is an incredibly important aspect of health. It is not, however, just a door into the body, and is its own room known as a microbiome. Today we will explore how the oral microbiome can incite health or disease depending on the balance of bacteria found in it, and ways to support the good bacteria and minimize the bad.


The Microbiome of Your Mouth

Microbiome refers to the microorganisms in a particular living environment. You may be more familiar with the concept of gut microbiome because the importance of gut health has taken off lately. However, the body has a wide range of different microbiomes, and your mouth has one as well.

The oral microbiome is particularly essential because it’s one of the first points of contact between the outside world and your inner world. The oral microbiome is a significant, involved microbial community that contains ‘good’ and ‘bad’ bacteria. Bacteria is good or bad, depending on if it promotes human health or not.

The now old school of thought was labeled the Germ Theory, whereby all bacteria in the mouth were harmful and needed to be killed off. This belief was held about bacteria in general– but as microbiome science has taken off, we now understand that health is rooted in a delicate balance of bacterial health.

The old mentality of killing off all bacteria is what led to the anti-bacterial push for all biomes. Antibacterial soaps were developed, as were antibiotics. The oral biome was hit with strong mouthwashes and toothpaste-like Listerine and Colgate—to kill off all these ‘germs.’ This shift led to a generation of very sick humans and drug-resistant superbugs.

Germ Theory-Debunked

We now know that humans are made of more bacterial cells than human cells. Unfortunately, a generation of healthcare rooted in the ‘Germ Theory’ led to the overuse of sanitizing products without realizing the ill health effects this has on our symbiotic bacteria.

The Germ Theory lead to a western medical paradigm that has had a profound effect on the health of our beneficial bacteria. However, most nutrition and health advice comes primarily from Doctors trained in these germ theories. With the emergence of “The Human Microbiome Project,” we now know how imperative bacteria is to keep us both alive and in good health. Through modern advancements, researchers are uncovering more evidence against these Germ Theory beliefs, and we are gaining a stronger understanding of the importance of a healthy microbiome, especially in the mouth!

Our Mouth Microbiome Needs to be In Balance

Bacteria behave like people. If the environment is right, they behave in a beneficial and effective health-promoting way. What we discovered in the mouth is that these bacteria, when they’re in balance, do amazing things like transport calcium and phosphorus from saliva to teeth, and oxygenate to your gums. The oral microbiome is an essential part of our immune system. Your mouth microbes promote remineralizing your teeth when it’s in balance.

Your Mouth Microbiome is the Best Indicator of Your Health

Healthy mouth bacteria balance is associated with better health and longevity. Our oral bacteria is the “gateway” to our gut bacteria. Studies are indicating a distinct link between the health of our mouth bacteria and disease processes in the body. An imbalance of oral bacteria is associated with:

  • Rheumatoid arthritis
  • Inflammatory bowel disease (IBS)
  • Cardiovascular disease
  • Alzheimer’s and dementia
  • Mental Health

Gingivitis (bleeding gums) is a common sign that there is a bacterial imbalance in your mouth.

How Can We Effectively Detox Our Mouth and Fill it with Beneficial Bacteria?

Like with any of your microbiomes, or any environment with living biology—finding balance means removing the bad all the while promoting the good. With too aggressive a “kill the bad” approach, you run the risk of also killing off the good. And vice-versa, with an only “put in the good” strategy, you run the risk of also feeding the harmful bacteria.

Taking Out The Bad

Using harsh agents like the Acetaldehyde (a toxic by-product of alcohol found in Listerine) has been shown to bioaccumulate in the mouth. These agents have linked to oral cancer as well as the destruction of the good bacteria in your oral biome.

Ideally, you want to altogether avoid harsh, toxic, or anti-bacterial agents like:

  • Fluoride
  • Alcohol
  • Chlorine
  • Triclosan
  • Propylene Glycol
  • Sodium Lauryl Sulphate (SLS)
  • Diethanolamine (DEA)
  • Parabens
  • Artificial Sweeteners

These ingredients are commonly found in conventional oral care products like toothpaste, mouthwash, and dental floss. Thankfully there are so many natural health companies making non-toxic versions of these products to help you clean your mouth without stripping it of good bacteria or introducing any unnecessary toxins.

In terms of diet and lifestyle, avoiding processed foods (like white sugar, flour, and seed/ vegetable oils) as well as smoking will do wonders to protect your oral biome.

Mouth Microbiome: My favorite toothpaste?

I like to use a non-fluoride based periobiotic toothpaste. My favorite brand is Designs for Health

Putting In The Good

Taking care of your mouth microbiome also requires a nourishing approach to help feed and support the good bacteria in your mouth. Some of these habits include:

  • Eating a wide range of organic plant foods
  • Eating enough fat-soluble vitamins (A, D, E, and K) from high-quality pasture-raised animal proteins and fats
  • Eat probiotic-rich foods (like sauerkraut, kefir, and yogurt)
  • Take an oral probiotic

Other habits that are useful for keeping your oral biome in balance are brushing after meals, flossing once a day, oil pulling, and scraping your tongue using a copper tongue scraper.


Your mouth microbiome is a home to live bacteria that can either help promote or harm your health. The balance of ‘good’ to ‘bad’ bacteria depends on your lifestyle and habits. Outdated concepts like the Germ Theory gave rise to the anti-bacterial movement that wreaked havoc on the human biome. Today, we know that by cultivating good habits, we can support our oral microbiome and whole-body health. Good habits include eating a whole diversified food, organic diet, consuming probiotics, taking an oral probiotic, and keeping good dental hygiene practices using non-toxic products.


Bourgeois, Denis, et al. “Periodontal Pathogens as Risk Factors of Cardiovascular Diseases, Diabetes, Rheumatoid Arthritis, Cancer, and Chronic Obstructive Pulmonary Disease—Is There Cause for Consideration?” Microorganisms, vol. 7, no. 10, Sept. 2019, p. 424., doi:10.3390/microorganisms7100424.

Ciancio, Sebastian G. “Alcohol-Containing Mouthwashes.” Australian Dental Journal, vol. 54, no. 2, 2009, pp. 179–182., doi:10.1111/j.1834-7819.2009.01116_3.x.

Gao, Lu, et al. “Oral Microbiomes: More and More Importance in Oral Cavity and Whole Body.” Protein & Cell, vol. 9, no. 5, 2018, pp. 488–500., doi:10.1007/s13238-018-0548-1.

Gomez, Andres, and Karen E. Nelson. “The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.” Microbial Ecology, vol. 73, no. 2, 2016, pp. 492–503., doi:10.1007/s00248-016-0854-1.

He, Jinzhi, et al. “The Oral Microbiome Diversity and Its Relation to Human Diseases.” Folia Microbiologica, vol. 60, no. 1, 2014, pp. 69–80., doi:10.1007/s12223-014-0342-2.

Lin Dr, Steven, et al. “Good Bacteria in the Mouth and Gut Flora.” Dr. Steven Lin, 23 July, 2018,


Source:  Your Mouth Microbiome

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  1. I could add that another good measure to keep a mouth non-toxic and clean is to refrain from cussing and to say nice things.


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