All About Oral Health and the Oral Microbiome

Dr. Mark Burhenne, DDS is ahead of his time when it comes to dental health. Here’s why I love his approach: He’s all about finding the root cause, meaning he asks “what” is going on as well as “why?” When a dentist looks for the root cause of tooth and mouth troubles, s/he is able to identify the nutrition and lifestyle factors that might be contributing negatively. Every one of Dr. Burhenne’s dental recommendations comes from well-designed, well-conducted, and peer-reviewed research sources.

Here’s why the health of your mouth is so important: we swallow the bacteria in our mouths a zillion times a day and those bacteria seed our gut. If you’re someone who has been trying to get your gut health right for a while now, and all your solutions seem temporary, I recommend going back to the root – your mouth!

Conventional dentistry is AMAZING at restoring smiles…BUT the future of the profession is a NEW standard of care where the oral microbiome, mouth-body connection, epigenetics, and a root cause approach are integrated into how dentists care for their patients’ smiles AND whole body health.

Find the Root Cause of Dental Concerns

Looking for the Root Cause of a dental concern consists of doing anything and everything that needs to be done to help the patient. It goes above and beyond a teeth cleaning or filling a cavity. For example, cavities, gum disease, and bad breath all stem from the incredible ecosystem of bacteria in our mouth, and even in our stomach! Yes, bad breath and the health of your stomach microbiome are linked. Bad breath can be a result of gut dysbiosis. And what’s the root cause of gut dysbiosis? The root cause of gut dysbiosis is eating too many inflammatory foods, stress, poor dental hygiene, toxins (such as pesticides), excessive alcohol intake, antibiotic use, and chronic infections of the sinus, oral cavity, or intestinal tract.

It’s so important for your oral health to boost the good bacteria in your gut by consuming probiotics and probiotic-containing foods such as these fermented foods. A healthy gut microbiome also needs a lot of veggies and other high-fiber foods.

What is the Oral Microbiome?

The oral microbiome is the second largest microbial community in the body after the gut. So what does it even mean? We’ve all heard of “good germs” and “bad germs.” Within the mouth there are good bacteria, friendly bacteria and protective bacteria – and they all essentially mean the same thing. The kinds of bugs that live in our mouth are really important.

What does a healthy oral microbial community look like? According to Dr. Burhenne, a healthy oral microbial community would be made up of billions of good bacteria, with lots of biological diversity (aka: many different species). There would be some fungi and viruses too. But most importantly, the host would have healthy teeth, gums, and mouth lining with no oral health symptoms (cavities, gingivitis, periodontal disease, bad breath, etc).

During pregnancy, researchers know the oral microbiome of a pregnant woman effects the baby. Studies have found mom’s oral bacteria in the infant’s placenta, indicating that oral bacteria may pass through the blood and to the fetus. However, other studies have said the placenta doesn’t have its own microbiome. However, it could be that inflammation from the mouth is affecting the rest of the body of both mom and baby. Also, the baby picks up mother’s oral bacteria in the first two days of life, so it pays off to keep your oral microbiome healthy for you and your baby.

Breastfeeding also plays a role in the health of the oral microbiome. When comparing 3-month-old breastfed and formula-fed infants, research shows the oral microbiome between the two is markedly different. Differences observed include breast milk likely affects establishment of the oral and gut microbiome, and components in breastmilk inhibit growth and attachment of bacteria such as the caries pathogen S mutants. Breastfed children are not immune to cavities or tooth decay, but studies like this demonstrate that breastfeeding has a tremendously important role in establishing the oral microbiome (2).

Your tonsils are part of the oral microbiome and play a role in immune function in the mouth. In tonsillitis, the oral microbiome might be out of balance, overgrowing viruses, bad bacteria, or fungus and causing sore throat and difficulty swallowing. What could be the root cause of that? Investigate the immune system because food sensitivities, allergies, and/or inhalant allergies could be underlying causes of tonsillitis.

Top Three Things for Optimizing Your Oral Microbiome

Here are Dr. Burhenne’s top 3 things you can do to flourish a healthy oral microbiome.

#1: Pay Close Attention to Your Diet

Choose a whole-food, plant-based diet including veggies, fiber, high quality meats, fruit in moderation, fermented foods and home cooked meals. No packaged foods, no sweets or sugar, extreme limit on refined carbs (bread, pasta, rice, baked goods, crackers) and alcohol.

#2: Closed-mouth breathing

Breathing through your mouth while you sleep not only reduces the quality of your sleep, but it disrupts the balance of your oral microbiome and makes you more prone to tooth decay. The mouth is for eating, tasting, and talking, and the nose is for breathing and smelling. When our bodies, or body parts, begin to operate outside their intended function, problems arise.

During mouth breathing, air is forced through the airway at a larger volume than when you breathe through your nose. And when you breathe in air at such a high volume, the collapsible airway tends to collapse.

Children who mouth breathe can have numerous health issues, including abnormal facial growth and development, misaligned teeth, and poor sleep habits that can cause exhaustion and poor mental processing skills (3, 4).

#3: Oral hygiene and dental cleanings

We all know this one – brush, floss, and go to the dentist every six months.

When You Eat and What You Eat Both Matter for Your Teeth Health

Children (and adults too) who snack or graze all day have a much higher risk of developing dental cavities.
Why? Mastication (chewing food) is the beginning of the digestive process and to break down our food the pH of the mouth lowers, or becomes more acidic.

If we are nibbling, sipping, and snacking all day, our mouths stay in a constant state of acidity, never getting a chance to recover. This can negatively affect our oral microbiome and ultimately lead to enamel loss or dental decay.

Explained another way, our teeth need a break! Buffer meals with plenty of water and be mindful of spacing out snacks so teeth get a chance to remineralize in between meals.

  • Allow 2-3 hrs between meals and snacks and attempt an eating schedule.
  • ”Organized eating” helps balance the health of our oral cavity and also our GI tract.
  • Sip on water in between to stay hydrated and satiated and shoot for foods with fiber, healthy fat, and protein to stay full longer.

Little changes to your eating and snacking routine can have big impacts on overall health! Here are 9 foods to support a healthy mouth and healthy teeth.

Is Mouthwash Healthy? A Functional Dentist Answers

Dr. Burhenne is announcing to please stop using mouthwash! Most mouthwash formulations can actually CAUSE cavities, dry mouth, and bad breath.
Why? Because they damage the oral microbiome. Most mouthwash contain alcohol as one of the first ingredients, which dries out the mouth and causes a whole host of issues with both dental and overall health...

Reasons to avoid using mouthwash:

  • Mouthwash may actually cause more cavities. Teeth need to be bathed in saliva in order to remineralize. A dry tooth = a tooth that can't protect itself against demineralization.
  • Think of what you already know about gut health. Those "friendly" bacteria are necessary for a healthy gut, and even have downstream effects elsewhere in the body, including on mood and mental health. Imagine the effect of an antibacterial mouthwash on your oral microbiome, which is the headwaters to the gut!
  • Don't let the minty flavor fool you; they may smell great but they don't address the root cause of bad breath (like a tongue scraper or working with a functional dentist!)
  • That "burn" is due to ingredients that irritate the gums, teeth and tongue. The sensitive tissues inside your mouth, the oral mucosa, are very delicate. Think of how doctors say never to douche—same advice applies. This is a sensitive environment that does NOT need to be disinfected! Burning and drying out these tissues can also worsen bad breath, cause mouth ulcers, and cause imbalances in pH levels.
  • If a mouthwash is colorful, it’s likely because of artificial color, which I recommend skipping.

Trying to disinfect the mouth is the WRONG approach (1). We want to NOURISH, not disinfect, the delicate ecosystem of bacteria in the mouth. Ditch the mouthwash altogether, or switch to a safe one. Dr. recommends the following “natural” brands: RiseWell Alkalizing Mouthwash, TheraBreath, Georganics mouthwash and mouthwash tablets, Lumineux

I hope this information helps guide you to in taking care of your oral microbiome.

Kelly Harrington, MS, RDN

Registered Dietitian Nutritionist for Healthy Goods


  1. Bescos R et al. Effects of Chlorhexidine mouthwash on the oral microbiome. Scientific Reports 10, article number: 5254 (2020).
  2. Holgerson PL. Oral microbial profile discriminates breastfed from formula-fed infants. J Pediatr Gastroenterol Nutr. 2013 Feb; 56(2):127-136.
  3. Basheer B. Influence of mouth breathing on the dentofacial growth of children: a cephalometric study. J Int Oral Health. 2014 Nov-Dec; 6(6):50-55. 
  4. Benninger M, Walner D. Obstructive sleep-disordered breathing in children. Clin Cornerstone. 2007;9 Suppl 1:S6-12. 
  5. AsktheDentist on Instagram 
  6. Dr. Mark Burhenne at Ask the Dentist 

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