The oral microbiome is a community of bacteria and yeasts that lives in your mouth.
A healthy oral microbiome maintains homeostasis (balance) in the mouth, teeth, and gums.
Imbalances in the oral microbiome can lead to inflammation, dental and gum issues, and oral diseases.
The oral microbiome and the gut microbiome are dominated by different species of bacteria, but they have great influence over each other. For example, a person with gut dysbiosis is more likely to have oral health issues and vice versa.
Improving the oral microbiome or the gut microbiome can have beneficial effects on both the gut and the mouth.
In my podcast episode with Dr. Steven Lin, we discussed the mouth-gut axis, and Dr. Lin pointed out something very interesting: problems in the mouth are a key indicator of disease. Cavities, for example, may have more to do with a lack of fat-soluble vitamins (A, D, E, and K) than too much Halloween candy (though overdoing sweets isn’t recommended either).
It has now been several years since our conversation, and we have a bit more information on another key factor in oral health: the oral microbiome. Considering that oral health represents a snapshot of your overall human health, it makes sense that the state of the oral microbiome would play a significant role in total body well-being.
Research also indicates a relationship between the oral microbiome and the gut microbiome. These two separate but related bacterial ecosystems influence inflammation, digestion, immunity, and more.
In this article, we’ll dig into everything you need to know about the oral microbiome, including its effect on oral health, total body health, the oral-gut microbiome connection, and strategies to improve oral microbiome health.
What is the Oral Microbiome?
Research on the oral microbiome is still in its infancy, so we are currently learning about its characteristics and role in the body. But from what we know so far, the oral microbiome typically exists as abiofilm that helps maintain homeostasis (balance and adequate function) in the mouth and protects the tissues from injury and disease .
After the gut, the oral microbiome is the second largest community of microbes in humans (26%), and between the two, you’ll find over half of all bacteria in the human body (55%) [1, 2].
This means the oral microbiome may be nearly as important as the gut for maintaining overall health and well-being.
According to the Human Oral Microbiome Database, the most common commensal (non-pathogenic and health-supporting) bacterial species found in the healthy oral cavity belong to the following six well-studied bacterial families:
Species of these bacteria can also be found in the gut microbiome, but the oral microbiome is its own distinct community. Some of these bacteria are found everywhere throughout the mouth, while some are relegated to specific areas, such as the cheek tissue and gums, saliva, tongue, tonsils, throat, and dental plaque.
What Factors Affect the Oral Microbiome?
The oral microbiome is influenced by these key factors:
The pH and ion composition of drinking water [1, 3]
Bacterial gene mutations and horizontal gene transfer between bacteria 
To illustrate one of these factors — diet — an observational study found that healthy hunter-gatherers from the Philippines had greater oral microbial diversity than healthy traditional farmers, who in turn had more diversity than healthy Western controls .
All of the participants had good oral health, but the most abundant species of bacteria differed between each dietary group . This shows the variability of the microbiome between people of different health statuses, lifestyles, and other factors .
This also tells us that it’s not necessary to focus on one specific species of bacteria to optimize the oral microbiome since everyone is a little different. Instead, we can take a wide spectrum approach and optimize for an overall healthy bacterial community, just like you would for your gut microbiome.
How Does the Oral Microbiome Affect Your Whole Body Health?
The oral microbiome is essential to protect the mouth from injury or disease . When the microbial balance is disrupted, pathogenic organisms may multiply and cause or contribute to disease in the mouth and elsewhere in the body .
Theoretically, oral dysbiosis may impact overall health when certain oral bacteria produce toxins that damage oral tissues, triggering the immune system to set off inflammation . Inflammation and bacterial toxins in the mouth may then spread elsewhere in the body, especially the lungs and gut, damaging other tissues .
Oral conditions associated with a dysbiotic oral microbiome are periodontal disease (periodontitis), dental caries (cavities), oral cancer, and esophageal cancer .
Systemic (whole-body) diseases related to dysbiosis of the oral microbiome include :
On a smaller scale, having periodontitis often leads to bone and tooth decay. Any oral condition may also lead to fatigue, pain, and other general issues resulting from inflammation and an overactive immune response.
Of course, having a disrupted oral microbiome does not guarantee the development of any of these diseases, especially in the short term. But it is important to maintain good oral hygiene and manage oral health issues when they arise to support your overall health and wellbeing in the long term.
The Oral-Gut Microbiome Connection
Although we don’t always think of it this way, the mouth is part of the digestive system, the first stop on the train where food is initially consumed and partially digested by oral bacteria and enzymes in your saliva.
However, the microbial communities in the mouth and the gut are dominated by different species of bacteria and yeasts, making each their own distinct environment. A 2021 literature review explained that the oral cavity is dominated by Firmicutes-type bacteria, whereas the stool tends to be dominated by Bacteroidetes .
The microbes in the mouth and gut can still greatly influence each other, but they also act independently and have distinct effects on your health. They are separated by what’s called the oral-gut barrier.
The Oral-Gut Barrier
The oral-gut barrier is a combination of gastric acid in the stomach, bile acids in the duodenum (first part of the small intestine), and a strong intestinal wall, all of which keep oral bacteria from colonizing the gut (2).
We know that, although the mouth and gut are connected parts of the digestive tract, the oral-gut barrier keeps their communities of microbes surprisingly distinct. However, if the oral-gut barrier is dysfunctional, oral organisms can move directly into the gut or secrete metabolites into the gut and vice versa (2).
It’s possible that oral bacteria may transfer to the gut much more than we thought ; however, it’s still not clear whether oral bacteria are able to colonize the gut or if they simply pass through .
How to Improve Your Oral Microbiome
There are many ways to improve and maintain oral microbiome health, including dental hygiene tools, probiotics, diet, antioxidants, and stress management.
Dental Hygiene Tools
Dental hygiene tools include:
Interdental tooth cleaning devices such as interdental brushes, floss, wooden or rubber/plastic toothpicks, and water piks
All of these tools are generally helpful for oral health with slight differences.
A 2022 review compared the effects of rubber bristled interdental cleaners, interdental brushes, dental floss, and manual tooth brushing alone on plaque and gingivitis.
Plaque scores and gum bleeding scores were the same between rubber bristled interdental cleaners, dental floss, and interdental brushes. Rubber bristled cleaners were better than dental floss and interdental brushes at cleaning hard-to-reach places.
Overall, rubber bristled interdental cleaners used for 4-6 weeks were slightly better than dental floss and interdental brushes for gingivitis and reducing plaque, and people tended to prefer them to floss or other interdental brushes .
Another study found that toothbrushing plus mouthwash containing essential oils (eucalyptus, menthol, methyl salicylate, and thymol) was significantly better than brushing with or without flossing alone at improving plaque levels and gum health in people with gingivitis .
Probiotics for Oral Health
The data on gut-focused probiotics for oral health is another sign of the intimate connection between the gut and oral microbiome. Many studies found that gut-focused probiotics improved oral health, by reducing:
Oral candida (16)
The bacteria Streptococcus mutans (17) (18) (19)
Other oral pathogens (20) (21) (22)
Plaque formation (23)
Periodontitis (24) (20) (25)
A systematic review and meta-analysis assessed 12 clinical trials to understand the effects of probiotics on Candida numbers in oral and palatal samples. Overall, probiotics can help reduce oral Candida counts, especially in people who wear dentures, possibly by creating oral biofilms, changing the pH, and making hydrogen peroxide .
Two additional reviews found that probiotics are helpful for treating chronic periodontitis (10, 11). And several other studies showed that probiotics were able to reduce pathogens that may cause other oral health issues [12, 13, 14, 15, 16, 17]. One of these studies showed that subjects who ate yogurt containing Lactobacillus reuteri for 2 weeks had up to 80% less S. mutans in their saliva, the overabundance of which may lead to cavities .
Overall, standard (gut-focused) probiotics appear to have beneficial effects on the oral microbiota. We don’t have enough evidence yet to know whether “mouth-specific” probiotics are better for the oral microbiome than standard probiotics, but encouraging research has been conducted using probiotic mouth rinses for periodontal disease , plaque , and halitosis (bad breath) .
That said, there is so much evidence that regular, gut-focused probiotics are beneficial for the oral microbiome that there is less need to go searching for an oral-specific probiotic formula.
At the Ruscio Institute, I typically recommend Probiotic Triple Therapy as part of our foundational health protocol. Triple Therapy combines the three subsets of probiotics – a multi-species Lactobacillus & Bifidobacterium blend, S. boulardii (a probiotic yeast), and soil-based probiotics – for a well-rounded spectrum of probiotic coverage. We find that most people see benefits from this therapy, even if other probiotics have failed them before.
If you want to learn more about the types of probiotics and why Probiotic Triple Therapy may be more effective than any single probiotic species, click here.
Supplementing or increasing antioxidants in your diet may be beneficial for oral microbiome health.
A 2019 review evaluated 15 clinical trials to find out how effective antioxidants are as an addition to standard periodontitis treatment. The antioxidants tested included:
Chicory leaf extract
Tea tree oil
Overall, antioxidants – especially lycopene and green tea – were helpful in standard periodontal treatment by reducing oxidative stress on the periodontal tissues . Specifically, periodontitis patients who took antioxidants had less overall inflammation and improved gum attachment, plaque levels, and gum irritation.
I don’t know about you, but drinking green tea (preferably organic) sounds like a pretty low-cost and enjoyable way to improve your oral health to me!
Consider Xylitol and Erythritol
Xylitol and Erythritol are artificial sweeteners that have a reputation for possibly reducing dental plaque, disrupting pathogenic biofilms, and acting as oral prebiotics (foods/substances that promote healthy bacteria).
A systematic review looked at several microbiology studies on the effects of xylitol or erythritol chewing gum or candies on Streptococcus species and other oral microbes in kids and adults. Streptococcus species likely cause cavities.
Overall, the sweetener xylitol likely reduces levels of Streptococcus species (and probably reduces cavities). However, xylitol may not have the oral prebiotic properties to affect the overall microbiota. The effects of erythritol require further study (22).
Optimize Your Diet
Several diets have been studied for their effects on the oral microbiome and oral health.
Multiple studies have found that a generally healthy diet that includes at least five servings a day of fruits and vegetables is protective against periodontal disease and tooth loss [23, 24].
According to a review of 18 observational studies, a vegetarian diet may be associated with a higher risk of tooth erosion, but its relationship to cavities or the number of natural teeth was unclear .
With most patients at the Ruscio Institute, we initially recommend a Paleo or low-FODMAP diet, depending on their symptoms and health goals. These are both anti-inflammatory diets that promote a healthy microbiome and include plenty of fruits and vegetables, so it’s reasonable to say they would also promote oral health.
After a short term on one of these diets, the goal is always to expand your food options as much as possible without triggering symptoms. Besides staying away from processed foods most of the time, you don’t always need to be on a restrictive diet to promote oral health or health in general.
As an additional short-term therapy, a 2022 study found that an elemental diet was helpful as a preventive treatment for oral mucositis (inflamed tissue in the mouth) in cancer patients undergoing chemo- or radiotherapy. An elemental diet uses a pre-digested meal replacement shake for some or all meals to support easier digestion and heal the gut. However, RCTs and observational studies found the elemental diet reduced the risk of developing oral mucositis in patients with GI cancer and esophageal cancer, but not oral cancer .
Alongside the high risk of lung, mouth, and throat cancer, smoking isn’t so great for your oral microbiome either.
A 2022 observational study compared the oral, respiratory, and intestinal microbes of 24 current smokers, 27 ex-smokers, and 27 never-smokers.
Current smokers had lower microbial diversity but greater numbers of microbes in the mouth, lungs, and gut. This means that smokers were likely already experiencing dysbiosis, an imbalance of unhealthy vs. healthy bacteria, or trending in that direction. Ex-smokers had microbial diversity more similar to never-smokers. Overall, smoking makes oral and gut dysbiosis more likely .
Managing excessive stress is essential to healing from any condition, and oral health is no different.
A 2022 systematic review and meta-analysis reviewed 25 observational studies (total participants unknown) to understand the association between psychological stress, anxiety, and periodontitis. Psychological stress was highly and significantly correlated with periodontitis .
Another study found that people with aggressive periodontitis had an average of 53% higher salivary cortisol levels than healthy people. High cortisol levels may negatively affect the teeth and gums, worsening the progression of periodontitis .
It’s likely that you already know what activities help you destress, but if you’re looking for inspiration, try activities that incorporate gentle movement like yoga, stretching, walking, or dance. Of course, options like cognitive behavioral therapy or guided meditation are also available if you feel you need extra guidance.
For a Healthy Oral Microbiome, Focus on Both Oral and Gut Health
While the oral microbiome is its own environment with different species of bacteria than the ones in your gut, the state of the gut microbiome still has a significant impact on oral microbiome balance (and vice versa).
When you have the foundations of a healthy diet, good sleep, and stress management in place, Probiotic Triple Therapy is a logical next step to improve both gut and oral health by modulating the microbiome. Additional therapies may include increasing antioxidants, trying a different interdental tooth cleaning device, or certain gums and mouth rinses containing xylitol.
The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.
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