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A child’s oral microbiome starts before birth. That’s why the mother’s oral microbiome is critical to the health of her child. Children need a healthy microbiological start because the microbiome is like a tiny garden that, growing slowly within them, will serve them for life. Cavities, mouth sores, and discolored teeth aren’t the only things that good bacteria can combat. A healthy oral microbiome will protect them from infections, lead the way to a comfortable gut, and a strong immune system, defend their lungs, and promote a healthy brain. Build a healthy oral microbiome before, during, and after pregnancy. Even if your child is older, you can still change your child’s oral microbiome for the better. Probiotics, prebiotics, and avoiding unnecessary antibiotics will help give children the best possible start and a long, healthy life.



We are grateful to our sponsor, SuperTeeth, for making this blog possible.

super teeth

I love SuperTeeth’s dental probiotic and prebiotic mint. It delivers a well-researched, beneficial bacteria to the mouth known as Streptococcus salivarius BLIS M18, which reduces cavities, bad breath, and tooth staining. Their toothpaste tastes great and supports a healthy oral microbiome with hydroxyapatite, prebiotics, and CoQ10.

How do children get their oral microbiomes?

Before we dive into where it comes from, let’s take a moment to answer: what is the oral microbiome? The oral microbiome is the collection of bacteria, viruses, and fungi that live in our mouths, most of which are harmless or beneficial. Microbiomes are also found in the gut, vagina, skin, and all over and inside of the body.

For a long time, scientists believed that babies were sterile in the womb. They were microbe-free. But recent evidence shows this notion was completely off. In fact, most of the time the placenta and amniotic fluid that surrounds the baby contain microbes.

What microbes are floating around- and being swallowed by- the baby in utero? The very same microbes that are found in the mother’s oral microbiome!1

So now we know that babies aren’t sterile at birth. But what comes next is an exponential overload of microbial exposures to bacteria, fungi, and viruses. Babies are exposed to microorganisms during birth, with breastfeeding, and from caregivers.

Whether your child receives a healthy oral microbiome or not depends on a handful of factors. The mother is hugely influential in the baby’s oral microbiome. In addition, genetics, the method of birth, breastfeeding or formula, antibiotic use, family members’ microbiomes, and the child’s diet further develop the child’s oral microbiome– for the better or for the worse.

Photo by Larry Crayton on Unsplash

Factors Influencing Your Child’s Oral Microbiome:1

  • Mother’s oral microbiome
  • Genetics
  • Vaginal birth or c-section
  • Breastfeeding or formula feeding
  • Antibiotic use
  • Diet
  • Household members’ microbiomes

Pregnancy and Bacterial Mouth Infections

Having a mouth infection when you are pregnant is a bigger problem than you may realize. Infections in the mouth can reach the unborn child. Oral infections can trigger inflammation throughout the body. They can also stress the mother’s immune system, affecting the fetus. None of this is something you want with a new growing baby.

Unfortunately, being pregnant in itself puts a strain on oral health. Hormones change tissues in the mouth. Many women have bleeding gums and are more susceptible to cavities when they are pregnant. After the baby is born, their oral health problems go away. However, if you have imbalanced mouth bacteria before getting pregnant, then you are in a bigger predicament. Work on improving your oral health before, during, and after pregnancy.

The oral microbiome can affect the health of babies in the womb, infants, and children.1 An imbalanced microbiome and mouth infections can lead to the following problems.

For Pregnant Mothers and Babies in Utero:

  • Infections in the fetus
  • Low birthweight baby
  • Miscarriage
  • Premature delivery
  • Premature labor
  • Stillbirth

For children:

  • Cavities
  • Discolored teeth (yellow or black)
  • Mouth or tooth infections
  • Mouth sores
  • Oral thrush
  • Appendicitis
  • Brain dysfunction
  • Food allergies2
  • Gut dysbiosis
  • Inflammatory bowel disease
  • Heart disease later in life
  • Weak immune defenses
  • Poor lung health


Vaginal Birth or C-Section: Critical for Your Child’s Oral Microbiome

Right out of the gate, babies get a starter pack of bacteria, fungi, and viruses from their mothers.3 How a baby is born affects the oral microbiome and gut microbiome.3 When a baby is slowly descending the birth canal, they get smeared with all of the vaginal microbes that colonize the mother. This is a major first inoculation. Lactobacillus bacteria are high in the vaginal microbiome, and babies born vaginally have high levels of this bug in their feces for the first few days of life. In fact, babies born vaginally end up with a gut microbiota that looks like their mom’s, to the tune of 83 percent similar. And they have a rich, diverse collection of microbes, which is an indicator of microbial health.45

With nearly one-third of babies in the United States being born by Cesarean section, not all babies get this starter pack, unfortunately. Babies born by C-section have a fecal microbiota that is only 42 percent similar to that of their mothers. Since C-section babies are not getting exposed to their mother’s vaginal microbes, their microbiomes are composed of the bacteria in their environment or the first things they touch or eat (like from the hospital delivery room and the mother’s skin microbiota). The majority of babies that were born by C-section had high levels of the periodontal pathogen, Slackia exigua, but babies born vaginally were free of this microbe. C-section babies also have less diversity in their oral microbiomes than babies born vaginally.45 Babies born by C-section are more likely to have asthma, allergies, and eczema, leading some experts to believe that the commensal bacteria from the mother’s vaginal microbiome is key in preventing these diseases.6

“85% of infants’ oral microbiota resemble their mothers’ in the first six months after birth.1

Breastfeeding for a Healthy Oral Microbiome

Breastfeeding also delivers a package of healthy microbes to the baby’s mouth and gut. Breastmilk is high in probiotic bacteria and the prebiotics needed to feed them! Seeding the newborn gut with mother’s bacteria promotes a healthy response to inflammation, helps introduce it to commensal bacteria, and jumpstarts the immune system. Breastmilk also contains immune-boosting proteins that can prevent the spread of pathogenic bacteria. Secretory IgA from mother’s milk can destroy bacteria and protect the mucosal membranes. Delivering commensal bacteria, the prebiotics that feed them, and proteins that help to prevent dysbiosis means we have yet another thing to thank our moms for!78

Breastfeeding provides all of the nutrients needed to build strong teeth and nourish the mouth. It also helps develop the jaw, the nasal cavity, and alignment of the teeth.9

Breastmilk gives a child a foundation of healthy bacteria that will colonize the gut, the mouth, the skin, and the rest of the body. Nature has designed a magnificent system whereby a mother passes on her microbiome to her child through vaginal childbirth and breastfeeding. Antibiotics, C-section births, and infant formula interfere with the process of transferring mother’s microbiome to her child. These things should be avoided, when at all possible. See below for tips to promote a healthy oral microbiome if vaginal birth and/or breastfeeding are not possible for you and your baby.


The Infant and Childhood Oral Microbiome

The bacteria that colonize the baby’s mouth follow a predictable sequence, timeline, and spatial arrangement in the mouth. But only a subgroup will become permanent residents of the mouth. As the child gets teeth and grows, the oral microbiome grows in diversity and richness.1

The first bacteria that set up in a baby’s mouth are called early colonizers. They lay the foundation for other bacteria to move in later.

Figure. Oral Microbiome Development in Early Childhood. From Xiao et. al.1

Streptococcus bacteria are early colonizers in the mouth. Mostly because (1) they can stick to cells that make up the mouth lining (2) they are high in human breastmilk and (3) breastmilk specifically feeds and grows Streptococcus bacteria.1 Streptococcus salivarius is the species of Streptococcus most often found in the oral cavity of newborn babies and peaks in abundance (10 -15%) around 3 months of age.1

When new teeth come on the scene, everything changes. Researchers say, “the oral ecosystem reforms with the eruption of the first tooth.” With teeth to stick to, new bacteria show up to colonize the mouth. Higher bacteria loads grow on the teeth and tongue, as opposed to the saliva and lining of the mouth.1

By the time a child is three years old, the oral microbiome is complex and continues to build in complexity as the child grows. When primary teeth are replaced by adult teeth, again the child’s oral ecosystem changes significantly.10 Each year the child grows can accompany different microbial communities. Baby teeth have a different bacterial makeup than permanent teeth when they are both present in a child’s mouth.3 Cavities create a distinct microbiome. A young child has greater salivary microbiome diversity than a young adult.3 Once that child grows to be an adult of 18 years old, his oral microbiome is more similar to that of his mother than to his father.

Bacteria in Amniotic Fluid1

  • Streptococcus
  • Fusobacterium
  • Neisseria
  • Prevotella
  • Porphyromonas

Pre-teeth Early and Second Colonizer Bacteria

  • Streptococcus, esp. S. epidermidis and S. salivarius
  • Staphylococcus
  • Fusobacterium
  • Veillonella
  • Lactobacillus
  • Candida
  • Gemella
  • Granulicatella
  • Haemophilus
  • Rothia


After-teeth Bacteria in Toddlers

  • Streptococcus mutans
  • Fusobacteria
  • Tenericutes synergistetes
  • TM7
  • SR1


Boost Your Oral Microbiome Before Pregnancy

Even before birth, you can optimize your microbiome so that it’s in tip-top shape for your baby. Take probiotics during pregnancy to help boost your good bacteria and gut function. A healthy diet low in sugar and refined carbs, rich in vegetables and fruits will help grow your healthy bacteria. Avoid antibiotics before, during, and after pregnancy, when possible.

If you are planning to get pregnant, or already are, you are in a perfect position to optimize your child’s dental health. You simply do this by optimizing your microbiome. It doesn’t require a lot of work because we all have microbiomes, naturally. But if you have signs of an unhealthy, or imbalanced, microbiome, then you need to restore health as soon as possible. You can look for signs all over the body to help figure out if your microbiome is healthy.

Telltale clues that you have an unhealthy microbiome are:

  • Bad breath
  • Bleeding gums (before pregnancy)
  • Cavities
  • Gum disease
  • Mouth sores
  • Root canal infections


Other signs of dysbiosis are urinary tract infections, bladder infections, vaginal yeast infections, or bacterial vaginosis. In the gut, imbalanced bacteria can show up as constipation, diarrhea, irritable bowel syndrome, gas, bloating, heartburn, abdominal pain, or stomach pain. If you have any of these symptoms, then your microbiome is likely out of balance.

It turns out that a mother’s microbiome can directly influence her child’s mouth years later. Contrary to popular advice, infections are not only the result of harmful bacteria. They are also, and perhaps more importantly, the result of a weakened defense system and a weak microbiome. Instead of waiting until your child gets a tooth cavity, avoid cavities all together by boosting your microbiome during pregnancy. By giving your child a healthy dose of probiotic bacteria, you will give her dental health and protection from infections later in life.

How to Change Your Child’s Oral Microbiome


If you have a baby who is eating solid foods for the first time, choose the foods you introduce carefully. Don’t give them sugar or cereals, but instead veggies and fruit to help them cultivate a garden of beneficial bacteria. Take the time to prepare a homecooked, whole-foods diet with vegetables, fiber, nuts, seeds, healthy fats, and healthy meats. Avoid antibiotics while you’re nursing and avoid them for your toddler.

Perhaps you already had your baby and fed your baby. He or she is a rambunctious 9-year-old now. It’s not too late! Even though you can’t change what you did before or during pregnancy, or how the baby was fed early on, you can cultivate a healthy garden of good bacteria for your child now. You can feed your child a microbiome-nourishing diet, like the one described in the recommendations below. You can give dental probiotics and oral probiotics (for gut health). Fermented foods like kim chee, kefir, sauerkraut, or pickles further boost the microbial communities in the mouth and gut.

Prebiotic foods are the food that friendly bacteria eat. Boost your child’s friendly mouth bacteria with nitrate-rich prebiotic foods such as leafy greens, beets, beet juice, red spinach, fennel, parsley, and Chinese cabbage. They will just love those foods, right? Consider hiding them in smoothies if you think they won’t like beets. Xylitol is also an oral prebiotic, a cavity-fighter, and a natural anti-Candida sweetener. Since you are trying to build the oral bacteria, encourage more time chewing so that these foods can have more contact with the teeth and gums.

Prebiotic Foods for the Oral Microbiome

  • Asparagus
  • Banana
  • Beets or beet juice
  • Chicory root
  • Chinese cabbage
  • Fennel
  • Garlic
  • Green plantain
  • Jerusalem artichoke
  • Leafy greens
  • Leeks
  • Onions
  • Parsley
  • Red spinach
  • Rocket
  • Xylitol


Image by Sabrina B. from Pixabay

Antibiotics Promote Oral Thrush and Bad Mouth Bacteria

At every turn, parents are confronted with whether to give their children antibiotics or not. Antibiotics are vital for treating pathogenic bacterial infections. But there is a flip side. Antibiotics kill friendly bacteria and encourage harmful fungi such as Candida to grow out of control. They also help bad bacteria rise to power and become antibiotic-resistant.

Candida, or yeast, is a prime suspect in the development of childhood cavities. Candida works together with Streptococcus mutans to promote cavities in children.1 It’s also a key player in oral thrush, an overgrowth of Candida in the mouth. Oral thrush symptoms in children include cracks at the corners of the mouth, trouble eating or drinking, painful tongue or gums, and an unpleasant taste in the mouth.

We are emerging from a time when antibiotics were given out like lollipops. How many people today are struggling with chronic dysbiosis, immune suppression, and fungal overgrowth because they had too many antibiotics as children? Luckily there is much more caution exercised with antibiotics today, but we aren’t completely done with it. Antibiotics are still used excessively and without consideration of the consequences (or the real cause of symptoms).

Ear infection is one of the most common reasons for children’s antibiotic prescriptions. Yet many ear infections improve on their own without antibiotics. Viruses can also cause ear infections. Remember, antibiotics kill bacteria, not viruses. So, antibiotics are useless for a viral ear infection.

Chronic ear infections in babies and children can also be a sign of food sensitivities, so exercise caution when introducing allergenic foods into your baby’s diet (such as wheat, dairy, corn, and soy). Limiting allergenic foods can help to reduce infections and unwanted antibiotics. Dairy is my number one suspect for recurrent ear infections and strep throat infections.

If your child has recurrent ear infections, antibiotics and “getting tubes put in” are not the answer. There is a root cause that needs to be investigated with a functional medicine provider so that ear infections stop happening. While you line up the right help, consider removing dairy from the diet and giving your child Streptococcus salivarius K12 probiotics for ear, nose, and throat health.

In this day and age, parents have to be stewards of their children’s microbiomes. Yes, there is a time and a place for antibiotics. But only when a bacterial infection has been proven or in an emergency when there is no time to determine the cause. Treating every childhood ear infection, sore throat, and cough with antibiotics is an outdated strategy. It is devastating to the microbiome and can set up chronic fungal infections, immune weakness, and susceptibility to other pathogenic infections.


Probiotics for Mouth Infections

Probiotics are friendly bacteria that support health and are sold as dietary supplements. Probiotics for the gut and for the mouth have a number of benefits for health. They can change the environment of the mouth to foster growth of beneficial bacteria, while crowding out harmful bacteria. They can improve the body’s natural immune defenses and protect from infection. Probiotics help to overcome the damage that antibiotics do to the microbiome.

Probiotics for gut health can improve inflammation in the gut, regularity, and reduce gut infections. They are widely available and come in capsules, which are taken by mouth. Examples of probiotics for gut health include Lactobacillus species, Bifidobacteria species, Bacillus species (or spore-based probiotics), Streptococcus species, and the newcomer, Akkermansia muciniphila. Maintenance doses are 50 billion colony forming units/gram (CFU/g) daily. Therapeutic doses go up to 250-400 B CFU/g, under the supervision of a practitioner.

Dental probiotics are probiotics specifically intended for the mouth. Even though they are sometimes called “oral probiotics,” I prefer the term “dental” to avoid confusion with probiotics taken orally for gut health. Dental probiotics are chewed up or they melt in the mouth so as to deliver more probiotic bacteria directly to the teeth and gums. They can improve the oral environment so that healthier bacteria grow in the mouth. They can calm inflammation and ward off infections. They even reverse black staining on children’s teeth.

Dental probiotics usually contain Lactobacillus species and/or Streptococcus species. Of special note is the bacteria Streptococcus salivarius, which is well known to promote oral health (M18 strain) and ear, nose, and throat health (K12 strain). It is an early colonizer found in breastmilk and in babies’ mouths naturally, which supports its safety of use. Typical doses are 3-6 B CFU/g per day. SuperTeeth sells a S. salivarius M18 dental probiotic and prebiotic for adults and children.

For Mothers Who Cannot Have Vaginal Births and/or Breastfeed

Despite our best efforts, however, children are born by C-section and/or can’t breastfeed at alarmingly high rates. There are some things you can do to simulate the microbiome transfer that normally happens during vaginal birth and breastfeeding.

One technique to restore a baby’s microbiome after C-section delivery is called vaginal seeding, whereby gauze is placed into the mother’s vagina where it absorbs the mother’s vaginal fluid (and good bacteria). When the baby is delivered, the gauze is removed and then brushed over the newborn’s mouth, nose, and skin. A very small study showed that vaginal seeding “rescued” the C-section infant’s microbiome11 and restored it so that it more closely resembles that of babies born vaginally. Pretty incredible! I did it with my daughter. Some doctors discourage this practice, saying that there is not enough evidence to support it. They believe pathogenic microbes in the mother’s vaginal fluids could present harm to the newborn. Instead, they encourage at least six months of breastfeeding to overcome the depletion of microbes caused by the C-section birth.

Mothers who can’t breastfeed should consider using donor human milk. Human breast milk is actually recommended by the American Academy of Pediatricians for all premature infants because it reduces the risks of blindness, blood infections, gut infections, and death in these vulnerable babies. When breast milk isn’t available, they recommend pasteurized human donor milk over formula. Dairy and soy infant formula can’t even compare to the sublime health- and microbiome- benefits of human milk for our babies.

What if your child is already 5 years of age or older? Birthing and infant feeding are water under the bridge. You can still fix your child’s oral microbiome with the recommendations below.

Children’s Oral Health and the Oral Microbiome

Mothers and fathers, there is a tiny garden in your baby, one that you don’t realize is there. That garden will grow and change and ultimately influence the health of your child’s mouth but also her heart, her immune system, her brain, and her lungs. That tiny garden is the oral microbiome. If you are already thinking about how to keep your child’s gut microbiome healthy, then this is the natural next step. Giving your child a healthy oral microbiome starts even before the baby is conceived. The oral microbiome shifts and changes in infants, growing in richness and diversity as they grow. Learn what you can do to give your child the best possible start with a healthy oral microbiome. Your child will reap the benefits now, later, and long after you’re gone.


Tips to Promote a Healthy Oral Microbiome in Children


For Mothers Before and During Pregnancy:

  1. Eat a healthy diet that is low in sugar, low in processed foods, high in homecooked, whole foods that are plant- and fiber-rich, with healthy fats, and healthy meats.
  2. High-quality multivitamin-mineral or prenatal.
  3. Optimize the health of gut, oral, and vaginal microbiomes. If your microbiomes are imbalanced, get this checked out, tested, and treated before getting pregnant, or as soon as possible.
  4. Dental probiotics, such as SuperTeeth’s dental probiotic and prebiotic.
  5. Dental prebiotics.
  6. Avoid unnecessary antibiotics whenever possible.
  7. Avoid unnecessary C-section births.
  8. Use non-toxic oral care products and regular dental hygiene.
  9. Avoid antiseptic mouthwashes.
  10. Enhance nasal breathing, not mouth breathing.


For Babies and Children:

  1. Choose breastmilk or donor milk instead of infant formula.
  2. If problems arise with breastfeeding, have the baby checked for tongue tie.
  3. If baby was born by c-section, then extended breastmilk feeding, probiotics, and diet are all the more important to “rescue” the microbiome.
  4. Feed children a healthy diet that is low in sugar, low in processed foods, high in homecooked, whole foods, plant- and fiber-rich, with healthy fats, and healthy meats.
  5. Dental probiotics, especially S. salivarius M18 and/or K12 for ear, nose, throat. For babies and young children, consult with a functional medicine provider or functional/biological dentist before use.
  6. Dental prebiotics.
  7. Avoid unnecessary antibiotics.
  8. Anti-Candida diet for oral thrush or cavities, if needed. Consult with a practitioner before use.
  9. Provide nutrition and vitamins for oral health, with oversight of a practitioner.
  10. Non-toxic oral care products for children and regular dental hygiene.
  11. Watch for mouth breathing and address with dentist if present.
  12. Test the oral microbiome, if needed.
  13. Find an integrative and functional medicine practitioner for your child, especially if there are chronic ear infections, respiratory infections, or other chronic symptoms. Do not accept antibiotics and surgery as the only solution.


About Our Sponsor

SuperTeeth is one of the first natural oral health brands that addresses the root cause of oral disease – bacteria. Formulated with guidance from a holistic nutritionist and dentist, their line of probiotic and prebiotic oral care products harness the power of beneficial bacteria and shift the oral microbiome to a healthier state. SuperTeeth’s commitment to creating toxin-free products with alternative and equally-effective ingredients to those used in traditional oral care products makes achieving optimal oral health possible in a completely natural way.


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  2. Moreno CM, Boeree E, Freitas CMT, Weber KS. Immunomodulatory role of oral microbiota in inflammatory diseases and allergic conditions. Front Allergy. 2023;4:1067483. doi:10.3389/falgy.2023.1067483
  3. D’Agostino S, Ferrara E, Valentini G, Stoica SA, Dolci M. Exploring Oral Microbiome in Healthy Infants and Children: A Systematic Review. Int J Environ Res Public Health. Sep 10 2022;19(18)doi:10.3390/ijerph191811403
  4. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. May 16 2017;474(11):1823-1836. doi:10.1042/BCJ20160510
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  6. Huang YJ, Marsland BJ, Bunyavanich S, et al. The microbiome in allergic disease: Current understanding and future opportunities-2017 PRACTALL document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. J Allergy Clin Immunol. Apr 2017;139(4):1099-1110. doi:10.1016/j.jaci.2017.02.007
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  8. Martin CR, Ling PR, Blackburn GL. Review of Infant Feeding: Key Features of Breast Milk and Infant Formula. Nutrients. May 11 2016;8(5)doi:10.3390/nu8050279
  9. Scardina GA, Messina P. Good oral health and diet. J Biomed Biotechnol. 2012;2012:720692. doi:10.1155/2012/720692
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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.