Prebiotics are the forgotten ingredient for boosting oral microbiome health. Good bacteria in the mouth need prebiotics just as much, if not more, than probiotics. Prebiotics can prevent cavities, change the pH in the mouth, strengthen teeth enamel, and fight infections. Prebiotics in mother’s breastmilk set the stage for a healthy oral microbiome later in life. One of prebiotics’ award-winning features is they promote the health of many good bacteria in the microbiome, not just a select few. Find out the best prebiotic foods for the oral microbiome. If you don’t like eating a plant-based, whole foods diet, prebiotic supplements can help to nourish friendly mouth bacteria and ward off the bad. Chew prebiotic foods well so that prebiotics can coat your mouth microbes. By building up good bacteria, scaring off harmful bacteria, and boosting immune defenses, prebiotics may be your new best friend in the battle against cavities, gum disease, and bad breath.


Image by klimkin from Pixabay

Dental Probiotics for Oral Health

Before we dive into what prebiotics are best for your oral microbiome, let’s refresh on what these probiotics and prebiotics even are!

Probiotics are little bacteria encapsulated in pills that can promote good health. Think yogurt, but only the fraction containing good bacteria. In the body, probiotics have many, many health benefits, which we can’t delve into here. There are probiotics that you swallow, which support gut health. Dental probiotics may dissolve in your mouth. Either way you take it, probiotics put friendly bacteria into your body.

There are a few different probiotic species that are popular. You may have heard of Lactobacillus rheuteri or Lactobacillus acidophilus, or Bifidobacterium infantis. These are great probiotic bacteria for putting into capsules. The problem is that the oral microbiome has 700+ species. So, while probiotics are great for health, they are a bit like a drop of water in the ocean. Oh, and one more problem- many of the players in the oral microbiome are anaerobic bacteria, meaning they don’t fare well in oxygen.1 That means it’s hard to manufacture probiotics (in oxygen) that are perfect matches for the oral microbiome.

How do you feed the 700+ species of good bugs living in your mouth? How do you grow a robust microbiome that sticks around, even when you aren’t taking probiotics? The answer is prebiotics.


Prebiotics Help Build a Healthy Mouth

Prebiotics and probiotics go hand-in-hand. Prebiotics feed good bacteria. They help good bacteria stick in the body and do their good deeds. Prebiotics are usually hard-to-digest carbohydrates that our bodies don’t use for our own nutrition. The enzymes in our saliva and in our stomachs can’t even break them down.2 You might think of prebiotics as the “bulk” from your diet. Our bacteria however, can make good use of prebiotics through fermentation and the side effect is better health for us.

Prebiotics are usually short-chain or long-chain carbohydrates (polysaccharides or oligosaccharides). Examples include fructooligosaccharides (FOS), galactooligosaccharides (GOS), starch, xylooligosaccharides, inulin, and glucose-derived oligosaccharides.2,3 Dietary fiber is a great source of prebiotics. Many prebiotics are dietary fiber, but not all. Colorful fruits and vegetables also provide prebiotics in the form of polyphenols, or colorful plant chemicals.

The #1 value of prebiotics is they help build up good bacteria, increasing their growth and activity.4 The benefits of having strong levels of good bacteria are countless, but crowding out pathogens (or bad bugs) is one of the most important ones. By boosting good bacteria, prebiotics improve the immune system.3 Good bacteria help to calm inflammation. So, you can see that prebiotics are a vital part of a healthy microbiome.

The crowning glory of prebiotics is they help to grow many, many different kinds of bacteria. They don’t just help certain ones. Because prebiotics can feed many different players in your microbiome, they are arguably much more important than probiotic supplements for achieving overall microbiome health. Probiotic bacteria are available as supplements and include a pretty short list including Lactobacillus species, Bifidobacteria species, Bacillus species, and Streptococcus species. That’s it. But your microbiome has infinite numbers of other bacteria that need your love and support- in the form of prebiotics.

The more prebiotics you eat, the more you feed your good bugs, and the happier you and your bugs are.


Benefits of Prebiotics for the Mouth

  • Activate the immune system5
  • Crowd out pathogens
  • Increase friendly mouth bacteria
  • Turn off inflammation5,6
  • Tune the immune system for better performance
  • Build the mouth lining

There is one more term you may have heard: synbiotics. A synbiotic supplement is a combination of probiotics and prebiotics- the good bugs in a capsule together with the prebiotic food that can help them thrive.

Prebiotics Promote Oral Health: How?

Prebiotics can ward off cavity-causing bacteria by binding to the pili (hairs on the surface of the cell), making it hard for them to attach to the teeth or gums. Prebiotics can increase the lysozyme enzyme, which kills off bad bugs by destroying their bacterial cell walls.2 They may boost immune system fighters such as secretory IgA, IL-10, and interferon-gamma. They may also calm down the inflammatory response to pathogens. 2,5,7

Prebiotics to Prevent Cavities

Some dentists suggest prebiotics as a solution to chronic oral health problems. Konde and colleagues said, “Prebiotics offer a simple, safe, and economical regimen to prevent dental caries.”2

In children with high numbers of decayed teeth, eating 40 grams of red banana twice daily for one month significantly lowered Streptococcus mutans in saliva. Strep mutans, or S. mutans, is the bacteria that overgrows in people with lots of dental cavities (or dental caries). The lowering effect of prebiotics on Streptococcus mutans was similar to probiotics and synbiotics, showing that prebiotics alone had a powerful effect. Red banana is rich in prebiotic fructooligosaccharides (FOS).2

In one study, prebiotics FOS and GOS significantly inhibited S. mutans. Lactobacillus acidophilus probiotics and prebiotics worked in tandem to crowd out S. mutans.4


Prebiotics are Superstars for Gut Health

Loads of research has shown us that prebiotics help good bacteria in the gut thrive while stamping out the bad. When prebiotics arrive in the gut, they are selectively fermented by gut bacteria. The byproducts of bacteria, such as short chain fatty acids, can do wonders for the gut lining and the microbiome or feed other friendly bacteria in the gut (called cross-feeding). They can prevent overgrowth of bad bugs, boost the health of your gut lining, and prevent cancer.8

Some people with gut disorders may not tolerate certain prebiotics well, at least until they are healthier. If you are one of those, work with your integrative and functional medicine practitioner to fine-tune a diet that builds your good bacteria without flaring up your gut symptoms.

While there are droves of studies about probiotics for gut health, brain health, metabolism, and more, prebiotics are a relatively newer topic of study. Prebiotics for the gut microbiome are relatively well understood. However, there is still much more to learn about how prebiotics benefit the oral microbiome.6


Why are your good bacteria so great?9

In case you forgot why your microbiome deserves so much tender loving care, here are the amazing services that your good bacteria provide to your body 24/7. So, let’s show them some love!

  • Activates the immune system
  • Breaks down toxins
  • Crowds out bad bacteria and pathogens
  • Helps develop the mucosal barrier
  • Helps to metabolize bile acids
  • Produces antimicrobial substances and antioxidants
  • Produces short-chain fatty acids
  • Promotes a healthy immune defense
  • Synthesizes vitamins

Breastmilk Prebiotics

The very first prebiotic you ever had was from your mother’s breastmilk or from infant formula. It’s a necessary ingredient for growing babies. Breastmilk is high in probiotic bacteria and the prebiotics needed to feed them!

Known as human milk oligosaccharides, these prebiotic oligosaccharides make up a huge proportion of breastmilk. Just like other prebiotics, babies can’t digest them. Yet they are vital for feeding and growing beneficial bacteria in the baby’s microbiome, such as Bifidobacterium spp. and friendly Streptococcus species. Even better, they prevent harmful pathogens from infecting the baby. Babies who breastfeed have a very different oral microbiome than babies who do not breastfeed. Prebiotics might be one reason why.10

Prebiotic Foods

One of the most powerful ways to shift your microbiome is to eat more plant-based foods and fiber rich in prebiotics. Bacteria love living in the mouth- there is a constant stream of yummy food. Above all, the microbiome likes plant-based foods. A fiber-rich diet of vegetables and prebiotics is hog heaven for good bacteria.

Boost friendly mouth bacteria with nitrate-rich prebiotic foods such as leafy greens, beets, beet juice, red spinach, fennel, parsley, and Chinese cabbage. Xylitol is also an oral prebiotic, a cavity-fighter, and a natural anti-Candida sweetener.

To build the oral bacteria, spend extra time chewing so that these foods can have more contact with your teeth and gums. I thought it was funny how one dental clinic said it, “chew more fiber to create an ‘oral garden mulch’ to feed good bacteria.” Carly Zanatta and Wendy Ward recommended eating, chewing, and drinking (with pulp) prebiotic foods for the oral microbiome.

Prebiotic Foods for the Oral Microbiome 2,11-14

Prebiotic foods should be eaten as part of a balanced, whole foods diet containing vegetables, meats and/or other proteins, healthy fats, complex carbohydrates, fruits, nuts, and seeds. If you aren’t sure about beets, check out my favorite Prebiotic Beet & Potato Salad Recipe below.

  • Asparagus
  • Banana
  • Beets*
  • Celery*
  • Chinese cabbage*
  • Fennel*
  • Garlic
  • Leek*
  • Lettuce*
  • Meats†
  • Nuts†
  • Onion
  • Parsley*
  • Seafood†
  • Seaweed†
  • Seeds (esp. pumpkin) †
  • Spinach*
  • Red banana
  • Tomato
  • Watermelon†

*These high-nitrate prebiotic foods can also work together with the oral microbiome to lower blood pressure! Recently, inorganic nitrates were shown to halve long-term cardio and kidney outcomes in a 2023 trial presented at the European Society of Cardiology Congress.

†These foods contain the prebiotic arginine, which can feed the oral microbiome.


Prebiotic supplements

How many servings of vegetables and fruits do you eat every day? If you don’t eat a wide range of vegetables and fiber-containing foods all day long, then good bacteria in your mouth may be starving. Prebiotic supplements can help you build up your healthy oral bacteria. You can find prebiotic supplements as powders or in pills. The large majority of prebiotic supplements are designed to boost the gut microbiome. Dental prebiotics are still not as easy to find, but they can come in powders or lozenges.

Prebiotics can change dental biofilms, which are simply the bacterial communities living on your teeth. Prebiotics encourage beneficial bacteria to grow and crowd out bad bacteria. Arginine, nitrate, and urea are well-known dental prebiotics that build up good bugs. See more about them below. Nitrate, beta-methyl-D-galactoside, and N-acetyl-D-mannosamine are dental prebiotics that promoted healthier mouth bacteria and reduced pathogens (A. actinomycetemcomitans, F. nucleatum, and P. gingivalis).6,15,16


Arginine is an amino acid prebiotic that promotes remineralization of teeth.17 It’s naturally occurring in the mouth saliva at 50 umol/L. Certain mouth bacteria are good at breaking down arginine. When they do, they produce ammonia, which makes the mouth more alkaline. Remember how cavities happen in an acidic pH environment in the mouth, rich in bacteria that make acid and love acid? By shifting to a more basic pH in the mouth, arginine helps to fight cavities.17

Some major mouth bacteria use arginine for food, such as Actinomyces species, Streptococcus sanguinis, S. gordonii, S. parasanguinis, and S. mitis.17 When people don’t have these kinds of bacteria in their mouths, it is a risk factor for developing cavities.

In clinical studies, arginine can inhibit cavities onset and progression. Multiple studies show arginine prebiotic decreases the development of cavities. However, because of private company involvement, the findings are not 100% conclusive.17

Arginine together with fluoride improves the strength of enamel and dentin, balances the oral microbiome, and prevents cavities.18 In cell studies, arginine was able to reduce biofilms and promote good oral bacteria. It also inhibited Streptococcus mutans (S. mutans) growth, stopped it from making toxins, and made it harder for S. mutans to stick to things.17


Nitrate encourages a healthier oral microbiome balance by helping good bugs grow and pushing out bad bacteria.19 We get 80% of nitrate from dietary vegetables and nitrate is high in lettuce and beetroot. Specifically, nitrate helps to increase Rothia and Neisseria species. It wards off periodontal pathogenic genera such as Porphyromonas, Fusobacterium, Prevotella, Leptotrichia and Alloprevotella. It reduces gingivitis and bad breath. It prevents cavities by making the pH in the mouth more basic, producing ammonia, and burning up lactic acid.19


Urea is also a prebiotic for the oral microbiome. Healthy people have 3-10 mmol/L urea in their saliva. Certain bacteria can break down urea to make ammonia (NH3) and bicarbonate (HCO3-). These bacteria contain an enzyme called urease. Increasing urea in the mouth can reduce Lactobacillus bacteria, inhibit cavities, and prevent cavities. Urea-containing chewing gum neutralized acids in plaque. Unfortunately, it doesn’t seem to work in daily life. When adding it to a mouthwash or chewing gum, urea doesn’t seem to help fight cavities or other oral health problems.17


Don’t Forget Prebiotics When Building Your Healthy Oral Microbiome

Good bacteria living in your mouth can ward off nasty mouth infections, and cavities, tune the immune system, and keep a healthy mouth lining. People are therefore looking for ways to nourish these friendly microorganisms that live in the mouth, known as the oral microbiome. This new approach is gaining momentum and the research backs it up. Even some dentists will admit that the traditional way of using antimicrobial methods to control cavities doesn’t always work for the long haul.17 We discussed how prebiotics promote a healthy mouth and what prebiotic foods can boost the good bacteria in your mouth.

Take These Steps to Boost Your Oral Microbiome with Prebiotics

  • Eat a whole foods diet with colorful veggies and fruits, rich in prebiotic foods such as beets, onions, celery, banana, lettuce, and spinach.
  • Chew your food more times so your oral microbiome can soak up the benefits
  • Increase your fiber (shoot for 25 – 35 grams/day unless fiber gives you gastrointestinal distress)
  • Take dental prebiotics or gut prebiotics (swish in the mouth first)
  • Take dental probiotics
  • Breastfeed babies or give donor milk, when possible
  • Introduce your children to the flavors of vegetables, fruits, and whole foods and don’t give up even when they reject them


Prebiotic Beet & Potato Salad Recipe

(Ethiopian Beet & Potato Salad)

Chock-full of prebiotics, this is my favorite beet dish. It makes a delicious summer salad with tangy flavors of lemon and mustard, blended with earthy beet flavors, and balanced with the mild and satisfying weight of potatoes. It also has a kick if you add the jalapeno. Great for the oral microbiome and for blood pressure, too. Served cold or warm.

  • 1 lb yellow potatoes, peeled and diced
  • 1 lb red beets
  • 1/4 c fresh lemon juice
  • 2 Tbsp peanut oil (or olive oil)
  • 1/2 md onion (yellow or red), finely diced
  • 1 jalapeño chile, seeded and finely diced (optional)
  • 1/4 tsp kosher salt, to taste
  • 1/4 tsp yellow mustard seeds
  • 1 pinch fenugreek powder


  1. Wash and trim the beets, and simmer in a medium saucepan for about 35 – 45 minutes (depending on size), or until you can easily pierce them with a fork. Remove the beets from the liquid and remove skins with a paper towel. Cut into bite sized pieces.
  2. Meanwhile, in a separate saucepan, gently simmer the potatoes for 20 – 25 minutes, or until tender. Drain the potatoes, and let them dry out a little in the warm pot.
  3. While the beets and potatoes are cooking, dice the onion and jalapeño, and place them in a large serving bowl with the lemon juice and oil. When the potatoes have dried off a little, add them (still warm) to the onion mixture, and gently combine. Add the beets, and stir through until everything is a lovely pink shade.
  4. Toast the yellow mustard seeds just until they start popping, then pour them over the salad, along with the salt and fenugreek powder. Stir well to combine.
  5. This can be made a day or two in advance. Keep tightly covered in the refrigerator.




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Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.