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illustration of a mouth and all the symptoms that stem from it

Many of us watch what we eat, exercise regularly, and get routine medical checkups, yet reach for the dental floss only sporadically. This may be because the mouth seems separate from the rest of the body — a portal meant solely for getting food and drink into our bodies.

Yet nothing could be further from the truth. Oral health affects our heart, joints, and immune system.

“You can’t have true general health unless your mouth is healthy,” explains functional dentist Mary Ellen Chalmers, DMD. Oral health is about more than just teeth and gums, she adds: It includes the mouth’s microbial population, or microbiome.

And what happens in your mouth does not stay there. It literally trickles down to affect the rest of your body, beginning with your gut. The oral cavity is the gateway to the digestive system.

From your mouth and esophagus to your large intestine, your gastrointestinal (GI) tract is a unified system with many highly specialized parts. Taking care of your mouth means taking care of your whole GI tract, and more. Change starts at the top.

Care and Feeding of the Oral Microbiome

Physicians have become more familiar with the gut microbiome — the bacteria, fungi, and viruses that live in the digestive tract and play a critical role in digestion, mood, sleep quality, immune function, and more. But there’s less attention paid to the microbiome in the mouth, even though it plays a key role in keeping the gut microbiome robust and healthy.

“The oral microbiome seeds the gut microbiome,” explains family and sleep-medicine dentist Mark Burhenne, DDS. “We swallow about a liter to a liter and a half of saliva daily, containing trillions of bugs.” This means every time we swallow, we shower the GI tract — particularly the small and large intestines — with microbes from our mouths.

This may sound threatening, since decades of mouthwash and toothpaste commercials have portrayed mouth bacteria as evil microscopic goblins we must eradicate. But it’s the opposite.

Just as diversity in the gut microbiome supports overall health, hosting a variety of friendly bugs in our mouths is far healthier than wiping them out.

“The strategy for the future, in this great age of understanding the microbiome, is to promote and nourish your good bugs instead of trying to kill the bad ones,” notes integrative and functional-medicine researcher Cass Nelson-Dooley, MS, in Heal Your Oral Microbiome.

It turns out the beneficial microbes in our mouths are far better at protecting us from pathogens and bad bugs than even the strongest mouthwash. They do this while helping to regulate the immune response, and they may even create chemicals that contribute to lower blood pressure. Instead of banishing them, we should be throwing them a parade.

If the bacteria in our mouths lack diversity, harmful strains can begin to take over and create oral dysbiosis, explains Burhenne. These harmful bacteria can then cascade down and cause an imbalance in gut bacteria, also known as gut dysbiosis. “We know that the mouth and the gut are linked,” he says. “Oral dysbiosis can impact gut dysbiosis.”

This can lead to problems such as inflammatory bowel disease (IBD).

Interestingly, people with IBD are more likely to have periodontal disease and inflamed gums. Nelson-Dooley points out striking similarities between the two conditions, including an imbalanced microbiome, damage to the lining, and altered immune responses, suggesting that the link between the two is a strong one.

A New Measure of Oral Health

Many dentists don’t consider the oral microbiome’s health, but some have begun to take a different view. “In functional dentistry, we see the mouth as part of the whole ecosystem of the body, and we work to nurture the oral microbiome,” notes Burhenne.

The functional-medicine tenets of oral hygiene include many familiar elements: brushing and flossing; avoiding refined sugar; and getting regular dental cleanings.

But functional dentists go further in their attention to the oral microbiome, recommending their patients avoid alcohol-based mouthwashes that kill good bacteria along with bad, as well as toothpastes that use surfactants and emulsifiers that can damage the oral mucosal lining. (See “How to Avoid Toxins in Your Toothpaste: 12 Ingredients to Ditch Now“.)

Functional dentists also stress the importance of diet and nutrition in promoting a healthy oral microbiome. Vitamins A, D, and K2 are particularly important for healthy teeth. Chewing whole, fibrous foods helps keep jaw muscles strong and toned.

Tongue scraping — removing the film that accumulates overnight with a metal scraper — can help prevent cavities and bad breath while improving digestion and immune function. And breathing through the nose instead of the mouth is also critical, both for proper jaw development and nurturing the oral microbiome. (For more on issues related to breathing from your mouth, see “Should I Breathe Through My Nose or My Mouth?“.)

Like functional medicine, functional dentistry addresses the imbalances at the root of symptoms. Proponents believe it could be game-changing for global health.

“One could argue that tooth decay and periodontal disease are [some of the] most common chronic diseases worldwide,” notes Chalmers. “We need a different foundation and modality to address the root causes of these problems.”

A Functional Approach to Oral Health

Suffering from any of these oral-health issues? This guide can help you understand the root causes — and what you can do about them.

Bad Breath

Mask wearing during the pandemic has made us all intimately familiar with the state of our own breath. If you’ve noticed that yours is less than fresh, the cause could be as simple as dehydration — or as complex as a microbial imbalance in the mouth or gut.

To improve your breath, Chalmers recommends more frequent brushing and flossing. If that doesn’t help, she looks for signs of enlarged tonsils, where small stones can form and attract odor-causing bacteria. Infections in the maxillary teeth (those in the upper jaw) can also affect the sinuses and lead to postnasal drip, which can cause bad breath.

Mouth breathing is another common cause of bad breath, notes Burhenne. Saliva helps keep bad bacteria in check, and breathing through the mouth instead of the nose dries out the oral cavity, setting the stage for halitosis. A 2011 Brazilian study found a correlation between mouth breathing and strong odors in children’s breath.

The basics of good breath also include a whole-foods diet. Limit processed and refined carbohydrates, and emphasize fermented, probiotic foods such as kimchi and sauerkraut, as well as prebiotic staples like garlic, onions, asparagus, and leeks. Nelson-Dooley also recommends supplementing with chewable probiotics. (See “16 Prebiotic Foods to Eat Now“.)

Tongue scraping is another useful intervention. “Some studies estimate that 80 to 95 percent of bad breath comes from the buildup of food, bacteria, fungi, and dead cells at the back of the tongue,” says Burhenne.

If the problem persists, the cul­prit may be lurking deeper in the GI ­tract, with yeast or bacterial overgrowth. In that case, working with a functional-medicine provider can help you find and address the root cause. (For more on yeast overgrowth, see “How to Treat Candida Overgrowth“.)


Cavities are the result of teeth-destroying acids made by bacteria, Nelson-Dooley explains. They’re small holes in the surface of the tooth, but if they reach the tooth’s pulp, they may require a root canal.

The cause lies once again in an imbalanced oral microbiome. One bug in particular — Streptococcus mutans — has been implicated in cavities. This bacteria is present in cavity-free mouths as well, but there, friendly bacteria keep S. mutans at bay.

“If you aren’t keeping up with your oral hygiene, if you’re eating sugar, and if your saliva isn’t flowing well, it increases acid in your mouth, which sets off a chain of events that disrupts the bacteria that live on your teeth and causes cavities,” notes Nelson-Dooley. “Dietary changes like cutting out sugar, reducing packaged foods, and eating more veggies are among the most powerful ways to control your oral microbiome and prevent cavities.”

Nutritional deficiencies in magnesium and vitamins D and K2 can also cause decay, adds Chalmers. Celiac disease and gluten sensitivity have been associated with more cavities as well.

If you’re prone to cavities, diet is an important place to start.

Canker Sores

These small ulcers on the soft tissues of the mouth or on the gums aren’t contagious, unlike cold sores. But they can make eating and talking uncomfortable.

They appear to share several root causes with ulcers in other parts of the GI tract, including infection with Helicobacter pylori bacteria and overuse of nonsteroidal anti-inflammatory drugs like ibuprofen. They may also be triggered by harsh oral-care products.

“Canker sores are often the result of modern oral products like toothpaste and mouthwash,” says Burhenne. Many toothpastes contain sodium lauryl sulfate (SLS), a sudsing agent that gives that foamy effect when you brush your teeth.

“That foamy feeling might feel good, but SLS actually strips away the protective lining of the mouth,” he explains. “I can tell when my patients are using a toothpaste with SLS in it because of the sloughing of cheek cells. It’s one of the most recognizable conditions in the mouth.”

Studies have shown that using an SLS-free toothpaste can decrease the frequency of canker sores.

Food intolerances are another common culprit. “With ulcers, I always think about irritation from food sensitivities,” says Nelson-Dooley.

She recommends eliminating gluten from the diet, as well as getting enough amino acids, micronutrients, and essential vitamins and minerals to support the health of mouth tissue.

Lingering Mouth Sores

Mouth sores or lesions that take a long time to heal are more concerning than canker sores, says Chalmers. Any that linger for more than a few weeks may need to be biopsied to rule out oropharyngeal cancer.

The cause, though, is usually less worrying and easier to address: Metals in fillings and bridges can contribute to mouth sores, particularly when two different metals interact, as with gold bridges and mercury fillings.

“When there are dissimilar metals with different electric potentials, that can set up reactivity and release metal ions that the body can absorb,” explains Chalmers. In some cases, removing just one of the metals can be enough to temper mouth sores and irritation.

Burhenne adds that alcohol-based mouthwash breaks down cell walls of the mouth’s mucosal lining, predisposing you to viral outbreaks, such as cold sores caused by the herpes simplex virus (HSV). “Most of us have these viruses in our mouths, but they don’t necessarily lead to outbreaks unless we’re disinfecting the mouth with caustic ingredients that cause dysbiosis.”

Patterned or Fissured Tongue

Deep grooves or fissures on the top of the tongue can be a sign of gut disturbance, says Chalmers. These grooves often occur alongside patterned or “geographic” tongue, where the tongue’s surface (normally covered by tiny, pinkish-white bumps called papillae) has bare patches with raised red borders.

“Geographic tongue is a great clue for gluten sensitivity and celiac disease,” she says. Chalmers recommends working with a functional-medicine provider to determine the root of the issue and identify food sensitivities or vitamin deficiencies (such as B12) that can contribute.

Oral Thrush

Also known as oral candidiasis, oral thrush is caused by an overgrowth of yeast in the mouth. It’s most commonly found in babies and cancer patients, but others can get it, too.

Candida albicans is the most common fungus in the oral microbiome. When it grows to unhealthy levels, it can form white or yellow patches of bumps on the tongue, inner cheeks, gums, or lips. Root causes include a high-sugar diet, antibiotic use, and mouth breathing, says Burhenne.

“If high candida is a problem in the mouth (or in the gut), you can lower it by cutting foods out of your diet that are high in fungus, such as bread, cheese, beer, corn, and nuts,” explains Nelson-Dooley.

An anti-candida diet minimizes sugar, starch, mushrooms, and vinegar.

Studies also show that Saccharomyces boulardii, a probiotic yeast that can be taken as a supplement, is effective in combating candida overgrowth.

Gum Inflammation, Recession, and Disease

Gums that bleed occasionally may indicate a slight microbial imbalance that can be addressed by a dentist via routine cleaning and a redoubled commitment to flossing and brushing. But Steven Lin, DDS, author of The Dental Diet, suggests that bleeding gums alongside consistent hygiene may be the first sign that your body is experiencing excess inflammation.

When the gums begin to recede, this can create pockets between gums and teeth where bacteria can accumulate. Eventually, the tissue and bone of the teeth and gums can be damaged, ultimately leading to tooth loss.

“With gum recession, we look to see if it’s happening in the presence of inflammation,” explains Chalmers. If there’s no evidence of inflammation, the recession could be the result of orthodontic treatment or structural issues with the bite.

If there is inflammation, it might be a result of pathogenic bacteria burrowing into the gums and causing gum disease. Cytokines are released by the immune system as it battles pathogenic bacteria, says Burhenne.

“[The inflammatory response] melts away your gum tissue — a disadvantage of the complexity of our immune system.”

Regular dental cleanings are your best first defense against the bacteria-laden plaque that commonly irritates gum tissue and can cause it to recede.

For more persistent bacterial issues, some dentists use tools such as diode lasers and ozone therapy (cleaning the periodontal pockets with ozonated water or concentrated ozone gas); this can help eliminate pathogenic bacteria in the gums. These treatments can also disrupt the biofilms that bacteria create to protect themselves from sterilizing mouthwash.

Nelson-Dooley notes that even stress can contribute to tissue loss in the gums and elsewhere. “Cortisol is a wear-and-tear hormone. It’s hard to build healthy tissue in a chronic stress state.”

To take care of your gums:

  • Brush gently with a soft toothbrush.
  • Avoid harsh oral products.
  • Get routine cleanings.
  • Breathe through your nose as much as possible.
  • Look into possible gluten sensitivity.
  • Eat a diet rich in vitamins A and K2, as well as calcium and magnesium.
  • Investigate laser or ozone therapy, which can eliminate pathogens in the gums that scaling or cleaning can miss.
  • Manage stress.

Learn More

Read the other articles in this series:

What Your Body Is Trying to Tell You, Part I

What Your Body Is Trying to Tell You, Part 2

What Your Body Is Trying to Tell You, Part 3

Illustration by: Stuart Briers
Mo Perry

Mo Perry is an Experience Life contributing editor.

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