The Mouth-Body Connection: Why We Shouldn’t Ignore the Oral Microbiome

Contrary to what you've been told, the goal is not to kill, kill, kill all the germs in your mouth. Some bugs promote good health in your mouth and the rest of your body—like the heart.

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Oral Microbiome

Contrary to what you’ve been told, the goal is not to kill, kill, kill all the germs in your mouth. Some bacteria promote good health in your mouth and the rest of your body—like the heart, for example.

The intestinal microbiome determines so much of our health and well-being. These microbes in our gut have been linked to controlling mental health, weight, and even our resistance to dementia.

But there’s more to the story. The opening to this intestinal tract—the oral microbiome—has long been ignored, but as you’ll see in this interview, the mouth is an absolutely essential part of a healthy gut.

We abuse the precious and delicate environment in our mouths. Antibacterial mouthwashes wipe out microbial diversity, which in turn affects the microbiome in our gut and the health of the rest of our bodies.

In this interview, I am thrilled to introduce Cass Nelson-Dooley, an ethnopharmacologist who brings us the science behind the oral microbiome and the oral-systemic connection, or, in other words, how your oral health impacts the health of the rest of your body.

Bear with us if it’s a bit technical—there’s something you don’t understand, leave in comments and either I or Cass will address it.

Dr. Burhenne: How would you sum up the importance of oral health for the health of the rest of the body?

Cass Nelson-Dooley, MS: I think the US Surgeon General said it best in 2000, that the mouth is the “mirror” of health and disease in the body. If we think of the gastrointestinal tract as a river, then the mouth is the headwater – the source of that river. It sets the stage for everything that comes after in the gastrointestinal tract and in the whole body.

[Tweet “The mouth is the “mirror” of health and disease in the body.”]

The mouth has a variety of microenvironments that host different bacterial populations: the tongue, the hard palate, the teeth, the area around the tooth surfaces, above the gums and below the gums. 700 species (1,2) of aerobic and anaerobic organisms live in the mouth and are organized in biofilm communities.

The mouth is the first meeting place between the alimentary canal (the entire passage along which food passes through the body), the immune system, and the outside world. It’s pretty important!

Dr. Burhenne: This is so well said. Unfortunately, dental training doesn’t emphasize this and many dentists are trained to focus on the teeth instead of the entire oral-systemic connection. I’m looking forward to more collaboration between dentists and other types of doctors, combining our efforts to better aid diagnosis and treatment.

Some of our readers know about leaky gut. But what is leaky mouth? What’s the difference between leaky gut and leaky mouth? A lot of homeopathic medicines are put under the tongue for absorption—is this the same mechanism of leakiness, or is it something different?

Cass Nelson-Dooley, MS: “Leaky mouth” is not a recognized condition to my knowledge. It’s a term that I came up with (in jest, actually) and discussed with Dr. Stephen Olmstead, who co-authored the article on the oropharyngeal microbiome (3), and with Dr. Kara Fitzgerald in our interview on the oral microbiome.

A more scientific description might be gingival epithelium permeability, which has been studied in the literature. Based on our existing knowledge about intestinal permeability, I think leaky mouth is a plausible condition that we should consider, especially when we are trying to understand the oral-systemic disease connection.

We are keenly aware of the disease-producing effects of a damaged intestinal barrier (intestinal permeability) because it triggers the immune system, inflammation, and allows harmful proteins and organisms into the bloodstream. The mucosa (mucous membrane) of the mouth is very porous, even in a healthy person. But when inflammation and infection sets up in the mouth, it could damage the barrier between the oral mucosa and the bloodstream, triggering systemic disease and immune system dysfunction.  

Dr. Burhenne: I actually like the use of your term “leaky mouth” because it helps us think of the mouth in a similar fashion as we do the gut.

There’s a 45% overlap of bacteria population between the mouth oropharynx and colon. How would you categorize that overlap or commonality and how would you characterize the subsets that don’t overlap? How is each set of bugs specialized for that part of alimentary tract?

Cass Nelson-Dooley, MS: The 45% overlap of bacteria in the mouth and colon was one of the most exciting findings I came across in my research. It points to a major contribution by the mouth to the overall gastrointestinal microbiome, which we know is critical for GI health, metabolism, immune function, and even brain function.

You swallow one trillion bacteria every day. I think this is one of the main reasons the mouth is so important. It is continuously seeding the gastrointestinal tract with bacteria.

As far as the groups of bacteria in the mouth versus the colon, we have a lot to learn. Keep in mind, we are talking about trillions of bacteria and thousands of bacterial species. Many researchers focus on a single bacteria and how it acts in the GI tract or mouth. How each set of bugs is specialized for its given part of the alimentary canal is yet to be seen.

Right now, we are characterizing what bacteria live in different parts of the GI tract. Bacteroidetes and Firmicutes are the primary phyla (or supergroups) found in the colon. The mouth also has Bacteroidetes and Firmicutes. Of course, the predominance of Streptococcus is the hallmark of the oral microbiome. It seems evident that Streptococcus is a healthy group of bacteria that colonize the mouth in all people.

Dr. Burhenne: This should alert everyone to the importance of maintaining the proper environment in the mouth. That means not only brushing and flossing, but also eliminating antibacterial mouthwash, encouraging nasal breathing over mouth breathing, taking an oral probiotic supplement, and eating a microbiome-friendly, paleo diet rich in vegetables and avoiding processed foods.

How would you define the term mismatch diseases? Many consider diabetes to be a mismatch disease because our bodies weren’t designed to handle the modern diet. Do you think that the dominance of strep mutans in the mouth could be considered a mismatch disease in people’s mouths today and does it correlate to an increase in caries (cavities)?

Cass Nelson-Dooley, MS: It’s hard for me to say if S. mutans in the mouth is a mismatch disease because dental caries have been with us since ancient times, even when refined sugar was absent from the diet.

However, I think a diet high in simple carbohydrates, refined grains, and sugar is certainly contributing to dysbiosis in the mouth, which eventually leads to S.mutans overgrowth, and dental caries. S. mutans isn’t the only bad guy when it comes to caries.  A number of changes in the oral microbiome happen before S. mutans rises to dominance and damages teeth.

Dr. Burhenne: This is why cavities are a disease of diet. And it also tells me that, one day, dentists need to be testing at the patient’s regular visits for dysbiosis!

We all know what happens when an antibiotic kills bacteria across the board and how this affects the microbiome, but how would you characterize the effects of a very strong bactericidal mouthwash and its effects in the mouth and the microbiome?

Cass Nelson-Dooley, MS: Antibacterial mouthwash should be used with caution because it kills good bugs too. Just like we use oral antibiotics with caution because it can lead to long-term changes in the microbial balance in the gut, we should consider the negative effects of mouthwash to the oral microbiome.

One study showed that using mouthwash eliminated the beneficial effects of healthy oral bacteria and raised blood pressure (4).

Dr. Burhenne: Yet another reason to ditch the mouthwash.  

How does high sugar in the modern diet lead to dysbiosis in the mouth? Could you define dysbiosis for us?

Cass Nelson-Dooley, MS: Dysbiosis refers to an imbalance in microbiota that leads to symptoms or pathology. This is usually used in reference to gastrointestinal dysbiosis by practitioners of integrative and functional medicine.

However, what constitutes a “healthy microbiota” is unknown because there is so much variation between people and their microbes.

Poor oral hygiene, high sugar intake, and low salivary flow change the pH in the mouth. This selects for certain bacteria that like acidic conditions and make acid, which further lowers the pH and contributes to demineralization of teeth.

All in all, it sets up an acidic environment of lower bacterial diversity, where non-pathogenic Streptococcus die out and S.mutans can thrive.

In a more acidic environment, S. mutans and yeast take over, eventually causing dental caries. While the literature doesn’t use the term “dysbiosis” in regards to oral health, the microbial imbalance in the mouth that triggers the development of dental caries, certainly qualifies as dysbiosis.

Dr. Burhenne: And I think from this point on since you’ve said it so well, we should all start considering dysbiosis in the mouth as a source for many oral diseases, as well as affecting the overall microbiome in the intestinal tracts. And as you said, diversity in the mouth is key! Don’t let a mouthwash wipe out that precious diversity.

I ask my patients an essential microbiome question — I ask if they were born vaginally or via c-section and if they were breastfed and for how long. My new patients sometimes find this awkward. I think readers would like to know the connection between slackia exigua and how that relates to how we are born and how this is related to periodontal disease.

Cass Nelson-Dooley, MS: There are many parallels between the oral microbiome and gastrointestinal microbiome. And mode of delivery- cesarean section or vaginal- is another similarity.

Research shows that infants born vaginally have more bacteria and more diverse bacteria in the mouth and in the gut, than infants born by cesarean.

Infants born by cesarean were found to have a higher prevalence of the periodontal pathogen, Slacki exigua, in the oral cavity. So far, we believe that the infants born vaginally were also exposed to S. exigua, but that their rich diversity of oral microbiota helped crowd out the pathogen (5).

Dr. Burhenne: I almost feel this is so important that it should be on my new patient form! How were you delivered shows how complex the cause of periodontal disease is. 

One of the most important things, since I left dental school almost 30 years in dentistry, is the recognition and the knowledge that there is a mouth-body (oral-systemic) connection. I think for many people they may know about it, but they don’t really understand how important it is and how it actually happens, or what to do about it. I would also say that a lot of dentists and even physicians don’t understand the actual mechanism.

How would you rate the importance of the oral-systemic connection and how would you explain the mechanism of that connection?

Cass Nelson-Dooley, MS: I think this is the real frontier of oral microbiome research. Studies show a clear link between oral disease and systemic disease.

Oral pathogens have been found in rheumatoid arthritis and inflammatory bowel disease is more common in people with periodontal disease.  

The most well-known connection is between the mouth and the cardiovascular system. Good oral hygiene decreases your risk for heart disease while poor oral hygiene increases circulating inflammatory and heart disease markers in the blood. Oral pathogens have even been found in atherosclerotic plaques, especially Streptococcus sanguinis, Prevotella gingivalis, Fusobacterium nucleatum, Neisseria and Treponema forsythia (2). 

In people with coronary artery disease, simply beginning an oral hygiene program reduced their cardiac events. This shows that instituting oral hygiene practices changes cardiovascular health in real time. It seems like improving oral hygiene should be recommended for people who have had cardiac events, in addition to changes aimed at improving their diets and activity levels.

We don’t know all the answers about how or why this happens but I think it could relate to the “leaky mouth” concept discussed earlier. Infection in the mouth and a breached barrier, may lead to systemic circulation of inflammatory signals in the body and immune dysfunction, causing problems at distant sites. It could also lead to inflammation in the alimentary canal, which would affect the GI and possibly the liver.

Dr. Burhenne: In summary, we know there’s a correlation and the studies support it but we have to figure out how it’s actually happening. These mechanisms have to be found out and discussed before we find the solutions to the problem.

What is the connection if someone has periodontal disease and an increase in inflammatory bowel disease (IBS)? Is that the oral systemic connection at play?

Cass Nelson-Dooley, MS: People with inflammatory bowel disease are more likely to have periodontal disease and their bacterial patterns are different than people who have periodontal disease only. The two conditions may have similar underlying pathologies. Of course these two sites are connected by the alimentary canal and dysbiosis and inflammation in the mouth likely influences physiology in the colon. A mouth that is sick is seeding the entire GI tract with bad bugs every day. It could be the oral-systemic connection at play.

A mouth that is sick could also be introducing unhealthy bacteria into the bloodstream every day. In the reverse, inflammatory bowel disease may be increasing circulating inflammatory signals in the bloodstream, affecting the mouth. We don’t know what is cause and what is consequence, but researchers suggest treating periodontal disease at the same time as treating inflammatory bowel disease to help the patient that struggles with both.

Dr. Burhenne: This is why I’ve created a form for MDs when treating inflammatory diseases to consider periodontal disease. The form allows them to interact with the dentist and confirm diagnosis of periodontal disease. This is where the collaboration between MDs and dentists is absolutely necessary for functional treatment.

I tell all my patients that they have to be healthy when they come in for a cleaning. The reason I say that is because having their teeth cleaned causes a bacteremia. What is the actual response to brushing one’s teeth or having them cleaned at the dentist?

Cass Nelson-Dooley, MS: This is a very interesting phenomenon that helps us understand how the oral-systemic connection works. Just brushing your teeth causes bacteremia. In a healthy person, the body can handle and clear the surge of bacteria in the bloodstream.

But someone who is already struggling with inflammation, dysbiosis, or other chronic illnesses may reach the tipping point with a cleaning or invasive dental procedure because it introduces so much bacteria into the bloodstream.

Dr. Burhenne: As a sleep medicine dentist, I tell my patients how important nitric oxide is to the body, how it reduces blood pressure, and how it affects the blood vessels. I specifically refer to their ability to breathe through the nose. However, I have read that the microbiome in the mouth also contributes to the amount of nitric oxide in the body. How is this so?

Cass Nelson-Dooley, MS: Certain oral bacteria convert nitrate to nitrite from the leafy greens we eat in the diet. Humans cannot do this biochemical step so we rely on oral bacteria to help us make nitric oxide. Amazingly, these bacteria in the mouth may contribute up to 25% of systemic levels of nitric oxide. Veillonella and Actinomyces appear to have the strongest nitrate-reducing activity. Given the important role of nitric oxide in healthy cardiovascular function and blood pressure regulation, we have to promote these bacteria by eating leafy greens and avoiding antibacterial mouthwash, when possible.

Dr. Burhenne: Another good argument against mouthwash!

The profession of dentistry is a big proponent of prevention. I read that if a patient has regular cleanings every six months, they have a lower chance of reinfection by the H. pylori bug – a bug that causes ulcers in the stomach, indicating that people with regular cleanings are less susceptible to having ulcers. What’s the connection there?

Cass Nelson-Dooley, MS: H.pylori can be a very stubborn infection to get rid of. It turns out that H.pylori lives in dental biofilms in the mouth. When people had dental cleanings, they were less likely to get reinfected with H.pylori. This is just one example of how bacteria in the stomach and gastrointestinal tract are directly influenced by the bacteria in the mouth. When patients have chronic gastrointestinal dysbiosis, it may be originating in the mouth and they should be evaluated for periodontal disease.  

Dr. Burhenne: This is wonderful, Cass. This gives me more to talk about with my patients who think gum disease is only inflammation in the gums. It’s so much more than that!

Often I see yeast infections in the mouth—candidiasis— and as a dentist, the only thing I can do is recommend an antifungal. I feel that that’s not enough to help a patient because it really doesn’t address the root cause. What is candidiasis in the mouth? How does it come about and how would you recommend a more functional approach, rather than just prescribing an antifungal? What other treatments help to maintain a healthy oral microbiome?

Cass Nelson-Dooley, MS: Integrative medicine generally addresses candidiasis as a systemic issue, originating from the gastrointestinal tract. The primary treatment is to remove starches and sugars from the diet to starve out fungus. Antifungals can also be used. Other natural treatments include high dose oral probiotics, the friendly yeast, Saccharomyces boulardii, and even antimicrobial herbs (for example, oregano oil or garlic).

Of course, flossing, brushing, and regular dental cleanings help to maintain a healthy oral microbiome. A plant-based, low-sugar diet is recommended. Chewable probiotics or probiotic toothpaste can be used to replenish beneficial bacteria in the mouth. Addressing other oral health issues, especially poor salivary flow, can encourage a healthier oral environment.

Consider treatments for the mouth such as a glutamine rinse, anti-inflammatory herbal swish, chewable CoQ10, and vitamins and minerals to promote immune function. Antibiotics and antibacterial mouthwash (even herbal) should be used only when there is oral dysbiosis.

A gluten-free diet may be of benefit because gliadin is known to cause intestinal permeability in all people (6). With stubborn infections, addressing other imbalances in the body may be important to help normalize the patient’s oral microbiome: food sensitivities, gastrointestinal dysbiosis, intestinal permeability, nutrition, hormones, toxicity, and stress, to name a few.

Dr. Burhenne: Thank you, Cass, this has been a wonderful and informative interview. You have helped so many people and doctors to better understand the ever-increasing importance of the oral systemic connection.

Read Next: What Exactly Is the Mouth-Body Connection?



  1. Meurman JH, Halme L, Laine P, von Smitten K, Lindqvist C. Gingival and dental status, salivary acidogenic bacteria, and yeast counts of patients with active or inactive Crohn’s disease. Oral surgery, oral medicine, and oral pathology. May 1994;77(5):465-468.
  2. He J, Li Y, Cao Y, Xue J, Zhou X. The oral microbiome diversity and its relation to human diseases. Folia microbiologica. Jan 2015;60(1):69-80.
  3. Nelson-Dooley C, Olmstead SF. The microbiome and overall health part 5: the oropharyngeal microbiota’s far-reaching role in immunity, gut health, and cardiovascular disease. ProThera, Inc. Practitioner Newsletter. Reno, NV: ProThera, Inc.; 2015:1-4.
  4. Hyde ER, Andrade F, Vaksman Z, et al. Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. PLoS ONE. 2014;9(3):e88645.
  5. Lif Holgerson P, Harnevik L, Hernell O, Tanner AC, Johansson I. Mode of birth delivery affects oral microbiota in infants. Journal of dental research. Oct 2011;90(10):1183-1188.
  6. Fasano A, Sapone A, Zevallos V, Schuppan D. Nonceliac gluten sensitivity. Gastroenterology. May 2015;148(6):1195-1204.

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  1. I assume sublingual alcohol based extracts would affect the oral microbiome. Would you suggest a probiotic rinse daily if one is using these? Or another approach?

    • Cass Nelson-Dooley says:

      Hi Carolyn,
      I would also suspect that alcohol extracts could affect the oral microbiome. But bacteria can grow back rather quickly. I imagine the impact would be minor compared to swishing with mouthwash. But it might be good to replenish healthy bacteria with chewable probiotics, or even probiotic toothpaste. You might take a look at The Natural Dentist Healthy Gums rinse. It doesn’t contain alcohol.

  2. Cass Nelson-Dooley says:

    Dear Reader,
    I’d like to make a correction to a statement in this interview: that I coined the term, “leaky mouth.” I recently spoke with a functional dentist, Dr. Mary Ellen Chalmers, who says that she coined the term “leaky mouth” in an interview with the Institute of Functional Medicine in 2013. This is a case of great minds thinking alike. 🙂 The term is relatively new and most doctors haven’t heard of it. In parallel, I suggested the term this year as a natural extension of the concept of “leaky gut” which is widely understood in the integrative and functional medicine field. Hopefully “leaky mouth” or “leaky gums” will be a phrase that is more recognized in the future with our awareness of the oral-systemic connection.
    Thank you,
    Cass Nelson-Dooley, M.S.

    • Juan Giuseppe says:

      I find this repord, and i think it also refer about “leaky mouth”:

      It has been known for many years that oral bacteria
      can enter the bloodstream. In particular, in
      cases of severe gingivitis and periodontitis, the
      inner epithelial lining of the periodontal pockets
      is ulcerated and shows loss of epithelial lining
      integrity (Schenkein and Loos 2013 ; Loos 2005 ;
      Tonetti and Graziani 2014 ). This ulcerated pocket
      epithelium may add up to 8–20 cm 2 (Loos 2005 ;
      Nesse et al. 2008 ). It is called periodontal
      infl amed surface area and forms an easy porte
      d’entrée for the bacteria, bacterial toxins, and
      other antigenic components residing in the
      subgingival area (Loos 2005 ; Nesse et al. 2008 ).

      Anne Marie Lynge Pedersen, Oral infections and general health, Springer, Switzerland, 2016.

  3. If possible, I may be even more worried about my 23 year old bite restoration now that I’ve read your interview. I have an onlay and 8 failed crowns (with decay) that need to be replaced. I have a big recession and attachment problem that requires extensive pinhole grafting. I can’t afford to pay for the dental and periodontal work I need done this time. I’ve had extensive dental work done in the past. I’ve had an upper palate expander, 3 sets of braces, upper jaw surgery, 4 quadrant crown lengthening surgery, 4 single tooth implants (to replace baby teeth), 8 crowns and an onlay. I need help. I can’t keep walking around with a mouthful of decay and a giant recession and attachment problem. It’s bad for my health. Do you know anyone that can help me? Please think about it, ask around and let me know. Happy Holidays!
    Many Thanks!

  4. What connections have been made to things we are exposed to, but may be unaware of? Like the antimicrobials used in cleaning products, fragrances, personal care products, pesticides, paint, etc. must affect the oral microbiome.

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  6. David T Eberiel says:

    About a year and a half I noticed a difference in the appearance of the surface of my tongue and with that my ability to distinguish tastes is being interfered with. I’ve seen an ENT and she prescribed Nystatin for 14 days, along with a probiotic and eating yogurt and foods like sauerkraut. Nothing changed. I haven’t noticed any other changes and am relatively healthy. I am located in Eastern Massachusetts. The ENT is willing to refer me to someone who can help, but she doesn’t know who or what type of specialist. Can you make a suggestion? If you have questions, I’d be happy to answer them.

    • Mark Burhenne, DDS says:

      Hi there David! I would look into the possibility of Candida (I have some info on here) and also get in to see a good functional dentist. He/she may refer you to see a functional medicine practitioner to perform tests to figure out the root cause of your issues. I wish you all the best!

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