What Is the Oral Microbiome? How to Balance It to Improve Overall Health

The mouth (aka the oral cavity) is considered to be a major gateway to the rest of the body. Oftentimes, what’s happening in the oral microbiome is representative of what’s happening elsewhere in the body.

The oral microbiome is the community of bacteria, fungi, viruses, archaea and other microorganisms that live on the teeth, gums, tongue, cheeks, saliva, tonsils and throat. When balanced, this ecosystem helps protect tooth enamel, support gum health, aid digestion, regulate oral pH and defend against harmful microbes. When disrupted (a state called oral dysbiosis), it may contribute to cavities, bad breath, gum inflammation, bleeding gums, oral thrush and periodontal disease.

It’s believed there are between 300 and 700 different microbial species living in the average human’s mouth. According to an article published in the Journal of Oral and Maxillofacial Pathology, the oral microbiome is the second largest microbial community in humans second to the gut, which is often simply called “the microbiome.”

Microbes populating the mouth play an important role in functions such as digestion, metabolism, blood pressure regulation and maintenance of the structure of the teeth.

How can you take care of the community of organisms living in your mouth? As you’ll learn below, practicing the right type of oral hygiene, eating a healthy diet and consuming probiotics are some of the best strategies.

What is the oral microbiome?

What exactly is a “human oral microbiome”? The oral microbiome refers to the hundreds of billions of microorganisms that live inside of the oral cavity (the mouth).

Most of these microorganisms are bacteria, both the “good” types and the “bad,” while some are yeast, viruses and fungi. Examples of microbes that live in the oral cavity include Streptococcus and Corynebacteria species.

As defined by the Human Microbiome Project, the oral cavity has nine sites spanning the inside of the mouth:

• tongue
• palate
• tonsils
• sub- and supra-gingival plaque on teeth
• keratinized gingiva
• buccal mucosa
• throat
• saliva

Together these microbes form an “ecosystem” that operates similarly to the human gut.

Each part of the mouth has a unique surface and therefore tends to contain its own array of microbes. For example, the tongue contains a different community from what’s on the gums or teeth, due to how their surfaces sustain the life of different microbes.

Dental plaque and the surface of the tongue are especially dense with microbes. They are considered to be “among the densest microbial habitats on Earth.”

How it relates to health

Microbiomes (communities of tiny organisms) actually exist everywhere in nature, and they play an important role in dictating human health and sustaining various ecosystems.

The Human Oral Microbiome Database catalogs the genomes of hundreds of bacterial species found in the human mouth. Within one’s mouth there are some bacteria that contribute to overall health, such as by facilitating digestion, and others that can contribute to problems, such as gum disease, infections and potentially even cancer.

Some of the positive roles that microorganisms living in the oral microbiome have include:

• Carrying out digestive and metabolic processes, which support a normal metabolism (for example, some bacteria participate in nitrate metabolism, which helps support healthy blood pressure)
• Facilitating the process of breaking down foods via saliva and turning nutrients from food into energy
• Transporting ionic minerals from saliva around the mouth
• Supporting remineralization of the teeth
• Carrying oxygen to the gums and soft tissues
• Fighting infections by protecting us from harmful environmental organisms
• Preventing oxidative stress and inflammation
• Removing waste products from the mouth’s surface

Signs of issues

Certain bacteria, viruses and fungi that populate the oral cavity are linked to health concerns that affect various parts of the body, including some you wouldn’t expect, such as heart disease and reproductive issues. That’s because some bacteria are capable of making their way from the mouth into other parts of the body, including the blood vessels and gut.

How do you know if you’re experiencing an imbalance in microbes living in your mouth (also called dysbiosis)?

Oral dysbiosis means the mouth’s microbial community has shifted out of balance. This does not simply mean “bad bacteria” are present.

Many microbes can live harmlessly in a balanced mouth but become problematic when saliva flow, pH, diet, plaque buildup or immune defenses change.

Signs and conditions linked to an unbalanced/unhealthy oral microbiome can include:

• Increased plaque on the teeth that is thick, sticky, smelly and off-white (it can form a film on your teeth in the morning)
• Bad breath
• Bleeding gums and receding gums
• Sensitive teeth
• Mouth ulcers
• Oral thrush, or oral candidiasis, is a fungal condition in which candida fungus (usually C. albicans) overgrows
• Gum disease (periodontitis)
• Cavities and tooth decay (caries)
• Endodontic infections (root canal) and alveolar osteitis (dry
  socket)
• Tonsillitis
• Respiratory infections
• Heart disease and stroke
• Certain types of cancer

What causes an unhealthy oral microbiome?

Common oral microbiome disruptors include:

• Frequent intake of sugar, refined carbohydrates and sugary drinks
• Poor brushing or flossing habits that allow plaque biofilm to build up
• Dry mouth or low saliva flow
• Smoking, vaping or tobacco use
• Heavy alcohol intake
• Frequent use of harsh antiseptic mouthwashes without dental guidance
• Chronic stress, poor sleep and systemic inflammation
• Certain medications or health conditions that affect saliva, immunity or blood sugar

How do cavities relate to your microbiome?

Many people are under the impression that certain harmful bacteria cause cavities, but it’s now understood that the causes of tooth decay, cavities and gum disease, such as gingivitis, are actually related to imbalances in the oral microbiome, rather than the presence of bacteria itself.

In other words, certain “pathogenic” bacteria won’t cause problems for someone who has an overall healthy microbiome. However, they can trigger disease in others who lack enough healthy bacteria to counteract the pathogens’ effects.

Experts now believe that when the microbiome shifts from being composed of mostly aerobic bacteria to more anaerobic bacteria (such as Streptococcus mutans and Porphymonas gingervali), this creates a  hypertrophic biofilm inside the mouth, which makes tooth erosion and gum disease more likely to develop.

Why is there a connection between the oral microbiome and cancer?

Oral cancer is thought to develop in part due to the effects of harmful bacteria in the mouth. Some studies suggest that a common type of mouth bacterium known as Fusobacterium nucleatum may also be involved in the development of colon cancer.

This type of bacteria seems capable of penetrating the cheeks and invading the immune system, most of which is located in the gastrointestinal tract. By contributing to inflammation and free radical damage, bacteria like Fusobacterium nucleatum may play a role in the development of cancer.

How to balance oral microbiome

Maintaining homeostasis in the oral microbiome can help prevent some types of bacteria and microbes from “behaving badly” and contributing to disease.

Wondering, “How can I improve my oral microbiome?”

The goal is not to sterilize the mouth. A healthy oral microbiome depends on balance, diversity, saliva flow, proper pH and regular removal of excess plaque biofilm.

Here are steps you can take to help improve the health of your second largest microbiome:

1. Practice smart oral hygiene

While cleaning the inside of the mouth too much can actually contribute to problems, proper “interdental cleansing,” which includes flossing, brushing with natural toothpaste and sometimes the use of picks, is thought to help support balance within the oral environment.

Some harsh or overused oral care products may alter the balance of microbes in the mouth, especially strong antiseptic mouthwashes used daily without a specific reason. That said, oral care needs vary.

The American Dental Association notes that toothpastes with cavity-prevention claims and the ADA Seal contain fluoride, and fluoride remains widely recommended for cavity prevention. If you are cavity-prone, have gum disease, have dry mouth, wear braces or have had recent dental work, ask your dentist which toothpaste and mouthwash are best for your oral health goals.

Some experts recommend avoiding products such as detergent-based toothpastes and alcohol-containing/antiseptic mouthwashes, including those that are made with these questionable ingredients:

• Sodium laurel sulfate (SLS)
• Sodium fluoride
• Triclosan
• Artificial sweeteners (such as sodium saccharin, aspartame, xylitol and erythritol)
• Artificial color dyes (often made from coal tar)
• Propylene glycol
• Diethanolamine (DEA)
• Microbeads (tiny solid plastic particles)

A simple oral microbiome-supporting routine looks like this:

1. Brush twice daily with a soft-bristled toothbrush.
2. Clean between teeth once daily with floss, interdental brushes or picks.
3. Clean the tongue gently if you notice coating or bad breath.
4. Drink water regularly to support saliva flow.
5. Limit frequent snacking on sugar or refined carbohydrates.
6. Use mouthwash only when it fits your needs, and choose the type based on your dentist’s guidance.

2. Consume probiotics

Probiotic supplements and probiotic foods can help populate the mouth with friendly bacteria, much in the same way as how they support gut health. They work by creating a protective biofilm that supports the health of teeth and gums and reduces inflammation, while blocking bad bacteria from reaching enamel or vulnerable tissues.

They may also help alter the pH of the mouth to stop cavity growth and improve saliva quality to support remineralization of enamel.

Research on oral probiotics is promising but still developing. A 2026 umbrella review of meta-analyses found that certain probiotic strains were associated with modest reductions in cariogenic bacteria, such as Streptococcus mutans, and improvements in halitosis measures, but the authors noted that results vary by strain, dose, delivery format and study quality.

In other words, oral probiotics may be useful as an add-on to brushing, flossing and dental care, but they should not replace standard oral hygiene or professional treatment.

What is the best oral probiotic to take? Dentists believe that oral microbiome probiotics are most effective when delivered directly to the mouth in lozenge, milk or chewable form.

Oral microbiome probiotic strains considered most beneficial to oral health (which should be taken for at least two to three months) include:

• Lactobacillus salivarius
• L. reuteri
• Streptococcus salivarius K12 and M18
• L. sakei
• L. brevis
• L. acidophilus
• L. rhamnosus
• L. reuteri
• L. casei
• Bifidobacillus
• S. thermophilus

The main differences between gut probiotics and oral probiotics comes down to the specific types of organisms included in each, although there is some overlap. While gut probiotics are usually taken in tablet/capsule form, oral probiotics can be taken as drinks, mouth washes, lozenges and chewable tablets.

Ideally, look for an oral probiotic supplement with a high strain count (CFUs), such as at least 3 billion CFUs. Try taking it in the morning prior to eating.

3. Eat a nutrient-dense diet

Our diets are a major way in which we take in microorganisms from our environments. For instance, eating plant foods like veggies and fruits provides us with not only nutrients, but also some dirt, water and bacteria.

Some foods help beneficial bacteria thrive, while others promote the growth of pathogens and unfriendly bacteria. Foods to emphasize in your diet are those that are alkalizing, anti-inflammatory and high-antioxidant foods.

The following foods should be eaten regularly in order to support oral health:

• Green leafy vegetables
• Berries, citrus fruits and other fruits
• Cruciferous veggies like broccoli, kale, cauliflower, etc., plus all over fresh veggies
• Organically raised meat, poultry and eggs
• Wild-caught fish
• Healthy fats like olive oil, avocado, nuts and seeds
• Algae and seaweed
• Probiotic, fermented foods like yogurt, kefir, kombucha, sauerkraut, and dill pickles
• Prebiotic foods including onions, leeks, dandelion greens, garlic, artichokes, chicory root, asparagus, jicama, apples and flaxseeds
• Plenty of water, herbal teas and green/black tea, and coffee in moderation

For oral microbiome health, frequency matters. Sipping sugary drinks or grazing on refined carbohydrates throughout the day repeatedly feeds acid-producing bacteria and keeps the mouth in a more acidic state. Pairing carbohydrates with protein, fiber and healthy fats, and drinking water after meals, may help reduce the impact on oral pH.

You want to avoid consuming too much sugar and refined carbohydrates, especially from sugary beverages and highly processed foods. Certain types of bacteria thrive on a high-sugar diet and then contribute to tooth- and gum-related diseases, such as erosion of enamel and tooth decay.

A diet high in refined carbohydrates and sugar can also cause a shift in the oral microbiome from slightly alkaline to a more acidic, which makes it more susceptible to infections and other issues.

4. Approach oral health holistically

It may not seem obvious that there’s an association between lack of exercise, chronic stress and poor oral health, but we know that a generally unhealthy lifestyle and lots of stress can lead to a decrease in saliva, which affects which types of microbes that populate the mouth.

Changes in saliva impact how well microbes carry minerals like calcium and phosphorus from saliva to the teeth enamel and can also create a more acidic environment in the mouth that changes the overall ecosystem. Stress can trigger dry mouth, loss of appetite, TMJ, teeth grinding, and other issues affecting the mouth and jaw.

Managing stress and getting enough exercise are both important for keeping inflammation under control. Exercise and other mind-body practices, such as yoga and mediation, can help decrease the stress-induced, inflammatory flight-or-fight response that leads to a compromised immune system.

Exercise is also beneficial for boosting circulation and detoxification via the lymphatic system, which helps keep the teeth, gums and tissues in the mouth in good shape.

Frequently asked questions

What is the oral microbiome?

The oral microbiome is the community of microorganisms that live in the mouth, including bacteria, fungi, viruses and archaea. These microbes live on the teeth, gums, tongue, cheeks, saliva, tonsils and throat.

What are signs of an unhealthy oral microbiome?

Possible signs include chronic bad breath, increased plaque, bleeding gums, gum recession, sensitive teeth, cavities, oral thrush, mouth ulcers, dry mouth and recurring gum inflammation.

How do you restore the oral microbiome naturally?

You can support a healthier oral microbiome by brushing and flossing consistently, limiting added sugar, eating nutrient-dense and prebiotic-rich foods, staying hydrated, avoiding tobacco, managing dry mouth, and using oral care products that fit your dental needs.

Are oral probiotics good for the oral microbiome?

Oral probiotics may help support the oral microbiome, especially for bad breath and cariogenic bacteria, but benefits appear to depend on the specific strain, dose and delivery method. Lozenges, chewables and other products that stay in contact with the mouth may be more relevant than capsules swallowed quickly.

Is mouthwash bad for the oral microbiome?

Not always. Some mouthwashes can be useful for plaque, gingivitis, cavities or dry mouth, but strong antiseptic rinses may not be necessary for everyone. The best choice depends on your oral health needs, so ask your dentist if you should use one regularly.

Conclusion

• The human oral microbiome refers to the community of tiny microbes that live in the human mouth, which includes the teeth, tongue, palate, inside cheeks, plaque, throat and gums.
• Experts believe that different parts of the mouth have different bacterial communities, and the way these communities interact with one another is very important for our overall health.
• To help maintain oral homeostasis, use gentle/natural cleansers in the mouth as well as floss, eat a healthy diet and avoid too much sugar, increase your intake of probiotics, and exercise and manage stress.
• In short, the oral microbiome is not just about the mouth. It is connected to digestion, immune function, inflammation, nitric oxide production, gum health and tooth enamel protection. Supporting it means creating an oral environment where beneficial microbes can thrive and harmful biofilms are kept in check.