By Alexander Angeloff, founder of TranscenDental. Educational content, not a substitute for advice from your dentist or doctor.
Your mouth is home to hundreds of species of bacteria, along with fungi and viruses. Together they make up the oral microbiome. When it's balanced, it helps protect your teeth and gums. When it tips out of balance, it drives cavities and gum disease, and research increasingly links it to health beyond the mouth.
In short: a healthy oral microbiome isn't a sterile one. The goal is to keep the helpful species thriving and stop disease-linked species from taking over. That mostly comes down to daily plaque removal, less frequent sugar, enough saliva, not smoking, and avoiding unnecessarily harsh products like strong antiseptic mouthwash for everyday use.
What I brush with every day
What is the oral microbiome?
The oral microbiome is the community of microorganisms living on your teeth, gums, tongue, cheeks and palate, and in your saliva. It's the second most diverse microbiome in the body after the gut. Different surfaces host different communities: the bacteria on your tongue differ from those along your gum line.
In a healthy mouth, these microbes:
- Take up space so harmful species can't easily settle in
- Help keep the pH of plaque from dropping too low
- Convert dietary nitrate (from leafy greens and beets) into nitrite, which the body uses to make nitric oxide
- Train and calm the immune response in the gums
Signs of an oral microbiome imbalance
An imbalance, called dysbiosis, usually shows up as familiar problems:
- Bleeding, swollen gums, the hallmark of gingivitis
- Frequent cavities, often from acid-loving bacteria like Streptococcus mutans thriving on frequent sugar
- Bad breath that brushing doesn't fix, often from bacteria on the tongue or below the gum line
- A white-coated tongue or recurring thrush
- Receding gums and deepening gum pockets in periodontitis
These are also signs to see a dentist, who can tell you what's actually going on.
The mouth-body connection
Gum disease, the main result of oral dysbiosis, has been linked to several conditions elsewhere in the body. Most of these are associations, and researchers are still working out how much is cause and effect:
- Heart disease. Bacteria from gum disease, such as Porphyromonas gingivalis, have been found in arterial plaque (Reyes et al., 2013).
- Diabetes. The link runs both ways: diabetes raises the risk of periodontitis, and periodontitis is associated with worse blood sugar control (Taylor & Borgnakke, 2008).
- Alzheimer's disease. Toxic enzymes from P. gingivalis have been found in the brains of people with Alzheimer's (Dominy et al., 2019), though whether they help cause it is still debated.
- Pregnancy. Periodontal disease has been associated with preterm birth and low birth weight (Xiong et al., 2006).
- Gut health. Mouse studies suggest oral bacteria can colonize the gut and worsen inflammation there (Kitamoto et al., 2020).
The practical takeaway is simple: keeping your gums healthy is worth doing for more than your smile.
What disrupts the oral microbiome
- Frequent sugar and refined carbs. How often matters more than how much, because each exposure feeds acid-producing bacteria.
- Plaque left in place. Undisturbed plaque matures into a community dominated by disease-linked species.
- Dry mouth. Saliva is the microbiome's main regulator. Mouth breathing, many medications and dehydration all reduce it.
- Smoking and vaping.
- Everyday use of strong antiseptic mouthwash. In a small study, a week of chlorhexidine mouthwash reduced the nitrate-converting bacteria and slightly raised blood pressure. Antiseptic rinses have a place, for example after gum surgery, but they're a blunt tool for daily use.
- Antibiotics, which can shift oral as well as gut bacteria.
- Harsh detergents like SLS, which can irritate the lining of the mouth in some people (see SLS-free toothpaste).
What I brush with every day
10% nano-hydroxyapatite, organic birch xylitol and 2% theobromine in a probiotic herbal ferment. No fluoride, SLS or glycerin.
How to improve your oral microbiome
- Disrupt plaque daily. Brush twice a day and clean between your teeth once a day with floss or interdental brushes. Regular disruption keeps plaque young and less harmful.
- Clean your tongue with a scraper or your brush.
- Cut down how often you have sugar, and keep sweet things to mealtimes.
- Use xylitol. S. mutans can't use xylitol for energy, and regular xylitol is linked to less of it in plaque. Xylitol also stimulates saliva. An Ora Flora xylitol mint after meals delivers about 3 g of organic birch xylitol plus a postbiotic blend, with no gum base. More in xylitol benefits.
- Eat nitrate-rich vegetables such as leafy greens and beets to support nitrate-converting bacteria.
- Stay hydrated and breathe through your nose where you can.
- Save antiseptic mouthwash for when your dentist recommends it.
- Consider oil pulling as an extra. Small studies suggest it reduces plaque bacteria (see oil pulling benefits).
- Get regular cleanings to remove tartar, which shelters disease-linked bacteria.
The best toothpaste for the oral microbiome
There's no toothpaste proven to "fix" the microbiome, but you can choose one that works with it rather than against it:
- Removes plaque well without harsh antiseptics
- No SLS, for people whose mouths are easily irritated
- Xylitol to make plaque less friendly to S. mutans
- Something for enamel such as hydroxyapatite, so you're not relying on bacteria-killing to prevent decay
That's the approach behind TranscenDental toothpaste: organic birch xylitol as the second ingredient, a probiotic herbal ferment of clove, rosemary and sage, 10% dual-particle nano-hydroxyapatite for enamel, baking soda to neutralize acid, and gum-supporting ingredients like hyaluronic acid and vitamin C. It has no fluoride, SLS, glycerin, silica or charcoal. For more on choosing, see what makes the best natural toothpaste and hydroxyapatite vs fluoride.
Build the full routine: brush with TranscenDental toothpaste, clean between your teeth with our plastic-free bamboo floss, and finish after meals with an Ora Flora xylitol mint (about 3 g of organic birch xylitol each, no gum base or artificial sweeteners). Or get all three together in the Oral Care Trio and save $12.
Oral microbiome testing: is it worth it?
There are two main kinds of oral microbiome test:
- Dentist-ordered tests that use a saliva or gum-pocket sample to look for specific bacteria linked to periodontitis. These can help a dentist or periodontist plan treatment for stubborn gum disease.
- At-home saliva tests sold directly to consumers that sequence the bacteria in your mouth and give a report and suggestions.
Tests can be interesting, but there's no agreed definition yet of a "healthy" oral microbiome, and results can vary with when and how you sample. A test can't replace a dental exam, and the advice that follows is usually the same: clean thoroughly, reduce sugar frequency and treat gum inflammation. If you have persistent gum problems, ask your dentist whether a periodontal pathogen test would change your treatment.
Frequently asked questions
What is an oral microbiome imbalance?
It's when disease-linked bacteria outgrow the helpful ones, usually because of plaque buildup, frequent sugar, dry mouth or smoking. It shows up as bleeding gums, cavities and persistent bad breath.
How do I improve my oral microbiome naturally?
Clean thoroughly every day, have sugar less often, use xylitol, eat nitrate-rich vegetables, stay hydrated and avoid daily antiseptic mouthwash unless your dentist recommends it.
Does mouthwash kill the oral microbiome?
Strong antiseptic mouthwashes reduce good and bad bacteria alike. They're useful short-term but not ideal for most people as a daily habit.
Do oral probiotics work?
Some strains have shown modest benefits for gum health or bad breath in small trials. They're an add-on, not a substitute for cleaning.
Is an oral microbiome test worth it?
For most people, a dental exam tells you more. Dentist-ordered pathogen tests can be useful for persistent gum disease.
Can the oral microbiome affect the rest of the body?
Research links gum disease with heart disease, diabetes, pregnancy complications and more. Many links are associations still being studied, but healthy gums are good for your overall health either way.
What I brush with every day
10% nano-hydroxyapatite, organic birch xylitol and 2% theobromine in a probiotic herbal ferment. No fluoride, SLS or glycerin.
