Oral Microbiome: What It Is and Why It Matters

The oral microbiome is the community of bacteria and other microorganisms that live in your mouth. It's one of the most diverse microbial communities in the body, and most of it is a normal, stable part of a healthy mouth. Researchers link problems such as cavities and gum disease to harmful shifts in that community, which are associated with factors like frequent sugar intake, reduced saliva and plaque buildup. Much is still unknown, and the most reliable ways to support oral health remain the everyday basics of oral care.

What Is the Oral Microbiome?

The term "microbiome" refers to the community of microorganisms that live in a particular part of the body. The oral microbiome, sometimes called the mouth microbiome or oral microbiota, is the community that lives in the mouth.

According to a 2016 review in the British Dental Journal (opens in a new tab), the mouth houses the second most diverse microbial community in the body, with more than 700 species of bacteria.

Where Microorganisms Live in the Mouth

The mouth isn't one uniform environment. The 2016 review describes several distinct habitats that support significantly different microbial communities:

• Teeth. Teeth are the only natural surfaces in the body that don't shed, so bacteria can build up on them as dental plaque, a structured community called a biofilm.
• The gumline. Bacteria also live in the gingival crevice, the small space between the gums and the teeth.
• Soft tissues. Unlike teeth, the surfaces of the tongue, cheeks and palate shed, and they host different communities.
• Saliva. Saliva also contains very large numbers of microorganisms.

The National Institutes of Health's Human Microbiome Project (opens in a new tab), which studied 242 healthy adults, collected nine samples from different areas of the mouth and throat, including saliva, cheek, gums, palate, tongue and two plaque sites. It found that most oral habitats are dominated by Streptococcus bacteria.

How Diverse Is the Oral Microbiome?

Diversity here means both how many kinds of microorganisms live in the mouth and how much they differ between people. The Human Microbiome Project found that the microbes in each body habitat "vary widely even among healthy subjects." In other words, there isn't one fixed "healthy" oral microbiome that everyone shares.

Oral Microbiome vs Gut Microbiome

The mouth and the gut are very different environments, and researchers study their microbial communities separately. The Human Microbiome Project, for example, sampled the mouth, gut, skin and other body areas as distinct habitats.

This matters when you read about microbiome research. Findings about the gut microbiome, or about probiotics studied for digestion, don't automatically apply to the mouth. For background on how probiotics and prebiotics relate to the gut, see our guide to prebiotics vs probiotics for gut health.

What the Resident Oral Microbiome Does

Most of the microorganisms that normally live in the mouth aren't harmful. The 2016 review describes several roles researchers attribute to the resident community:

• Keeping out unwanted microorganisms. A stable resident community helps prevent disease-promoting microorganisms from invading and growing.
• Interacting with saliva. Components of saliva help regulate the oral microbiome.

"Balance" and "Imbalance": What These Terms Mean

You'll often see the oral microbiome described as "balanced" or "imbalanced." Researchers use the term dysbiosis for a disruption of the oral ecosystem's usual equilibrium. The 2016 review explains that in dysbiosis, disease-promoting bacteria can take hold and contribute to conditions such as cavities, gingivitis and periodontitis.

This idea is often described as the ecological plaque hypothesis: oral disease occurs when environmental changes shift the natural balance of the microbial community, rather than simply because certain bacteria are present.

These terms have limits:

• There's no single healthy profile. Because oral microbes vary widely among healthy people, "balance" doesn't mean matching a standard list of species.
• Balance isn't something you can measure at home. A product or test that claims to show your microbiome is "out of balance" isn't the same as a dental diagnosis.
• The concept describes a process, not a quick fix. Shifts in the community are linked to ongoing conditions in the mouth, such as diet, saliva and plaque control.

Factors That Can Influence the Oral Microbiome

The 2016 review identifies several modifiable factors linked to dysbiosis, including:

• Frequent sugar intake. NIDCR explains that tooth decay begins when bacteria come into contact with sugars and starches and form acids that attack tooth enamel (NIDCR (opens in a new tab)).
• Reduced saliva. According to NIDCR (opens in a new tab), saliva contains minerals that help keep teeth strong, helps keep harmful germs in check and washes away food particles. Hundreds of medicines can reduce saliva, and dry mouth increases the risk of tooth decay.
• Poor oral hygiene and gum inflammation. The review lists inadequate oral hygiene and gingival inflammation among these factors. NIDCR notes that plaque not removed every day can harden into tartar (NIDCR (opens in a new tab)).
• Smoking and acidic drinks. The review lists cigarette smoking and excessive consumption of acidic drinks and refined sugar among lifestyle factors linked to dysbiosis.

What We Know About Cavities and Gum Disease

This is where the evidence is strongest, because the role of bacteria in these conditions is well established:

• Cavities. NIDCR explains that decay-causing bacteria form acids from sugars and starches, which can lead to a cavity. At an early stage, tooth decay can be stopped or reversed.
• Gum disease. NIDCR describes plaque as "a sticky, colorless film of bacteria" and notes that plaque buildup can cause tooth decay and gum disease (NIDCR (opens in a new tab)). NIDCR describes gum disease as an infection that causes inflammation of the tissues that hold the teeth in place, and notes that early gum disease (often called gingivitis), caused by plaque buildup, can often be reversed by daily brushing and flossing (NIDCR (opens in a new tab)).

Research also suggests the picture is more complex than "bacteria cause disease." The 2016 review notes that the presence of a biofilm alone isn't sufficient for periodontitis to develop.

Association Isn't Causation: The Mouth and the Rest of the Body

You may see headlines linking oral bacteria or gum disease to conditions elsewhere in the body. The 2016 review notes that oral bacteria have been proposed to play a role in a number of systemic diseases, but many of these links come from studies that show an association, not proof that one causes the other.

Heart disease is a well-studied example. A 2012 American Heart Association scientific statement (opens in a new tab) concluded that observational studies support an association between periodontal disease and atherosclerotic vascular disease, independent of known confounders, but "do not, however, support a causative relationship."

Similarly, the 2016 review describes a relationship between periodontitis severity and complications of diabetes, while noting that more research is needed to determine whether the periodontal microbiota has any direct effect on diabetes. Treating your gums is important for oral health in its own right, but these associations don't show that changing the oral microbiome prevents or treats other diseases.

What Science Still Doesn't Know

Oral microbiome research is moving quickly, but important questions remain open:

• What a "healthy" oral microbiome looks like for any individual, given how widely it varies among healthy people.
• Which changes in the community cause disease and which are a consequence of it.
• Whether deliberately changing the oral microbiome, for example with probiotics, can prevent or treat oral or other diseases. Research on oral probiotics is still limited; our guide to oral probiotics and what the evidence says covers that research in detail.
• How findings about oral bacteria and other diseases should be interpreted, since most are associations.

Evidence-Based Habits for Oral Health

There's no established way to deliberately reshape your oral microbiome to treat disease. The habits with the strongest support are the basics that control plaque and protect your teeth and gums:

When to See a Dentist

According to NIDCR, signs of gum disease include swollen, red or bleeding gums, gums pulling away from the teeth, loose or sensitive teeth, pain when chewing and persistent bad breath. If you notice any of these, or have a dry mouth that doesn't go away, see a dentist. NIDCR notes that only a professional cleaning can remove tartar, and that gum disease needs treatment from a dentist or dental hygienist.

Regular check-ups matter even without symptoms, because early tooth decay can be stopped or reversed.

The Bottom Line

The oral microbiome is a diverse community of microorganisms that lives on your teeth, gums, tongue and in your saliva. Most of it is a normal part of a healthy mouth. Cavities and gum disease are linked to harmful shifts in that community, which are associated with factors such as frequent sugar intake, reduced saliva, plaque buildup and smoking.

Much is still unknown, including what a healthy oral microbiome looks like for any one person and how oral bacteria relate to other diseases, where most findings are associations rather than proof of cause. The most reliable steps remain the basics: brushing with fluoride toothpaste, cleaning between your teeth, limiting sugar, avoiding tobacco and seeing a dentist regularly.