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Mouth As The Window Into Your Gut And Health

Cass Nelson-Dooley, MS., Guest
Thyroid Nation

Introduction To The Mouth And Gut Connection

While both professions deal with health, dentistry and medicine have diverged such that dentists alone handle oral health while the mouth is often an afterthought for the primary care provider. Yet the mouth is intimately connected with its downstream counterpart, the gastrointestinal tract, as well as systemic health.

The oral cavity serves as a window into the intestinal tract and arguably offers an opportunity to study the complex interaction of the host immune system and microbiome at its epithelial interface.(1)

Far beyond such localized problems as cavities and gingivitis, disease in the mouth is associated with increased risk for heart disease,(2) rheumatoid arthritis,(3) diabetes,(4) and cancers of the head, neck, and esophagus.(5) Therefore, addressing oral health is a necessary component of a comprehensive Functional Medicine approach.

The Mouth as Headwaters of the Gut

Functional Medicine practitioners place a tremendous emphasis on the health of the gastrointestinal tract for overall health, and rightly so. The GI tract influences digestion, absorption, elimination, detoxification, immunity, inflammation, and it houses a microbial population that outnumbers human cells by 10 to 1. By the simple fact of its location—at the beginning of the alimentary canal—the mouth deserves its fair share of attention in primary care.

The mouth is uniquely positioned as the first meeting place between the immune system, the gut, and the outside environment. The mucosal immune system found in the mouth is similar to that of the small intestine.(2) Dendritic cells, lymphocytes, and mucosal-associated lymphoid tissue (in the tonsils and lymphoid follicles) help to sample contents that enter the mouth and determine friend or foe.(6) The resident bacteria in the oral cavity are critical to this process, but until now were given little attention outside of dental circles.

The mouth houses 700 species of bacteria that colonize highly specialized microenvironments: the tongue, hard palate, buccal mucosa, and the teeth in the form of supragingival and subgingival plaque. Given the amount of oxygen that enters the mouth, it may be surprising that approximately 50% of the oral microbiota are anaerobic species and have therefore only recently been identified by next-generation DNA testing technologies.(7) And that’s not to mention the fungi and viruses that also take up residence there.(7)

The mouth can be a reservoir for pathogenic microbes as well as beneficial microbes. Bacteria in the mouth seed the GI tract to the tune of 1 trillion bacteria every day.(8) There is a 45% overlap between the microbes found in the mouth and in the colon.(8) Helicobacter pylori gastric infection has been traced back to dental plaques, and regular dental cleanings have been shown help to reduce H. pylori reinfection.(9) So the oral microbiome is necessary to consider when chronic GI infections are not responsive to common Functional Medicine treatments.

The mouth appears to be a reservoir for nitrate-reducing bacteria, which may contribute to approximately 25% of circulating nitric oxide levels. Thus, treatments that kill all the bacteria in the mouth, such as antibacterial mouthwash, can actually raise blood pressure by killing beneficial oral microflora and reducing nitric oxide production.(10)

TNE-Ad5-FrontIFM educator Mary Ellen Chalmers, DMD, NMD is a functional dentist and board-certified naturopathic physician with a long-standing interest in the oral microbiome. Dr. Chalmers notes that many factors affect oral health, not just the microbiome. She describes the apparent paradox she sees in her clinic: “There are patients who have plaque all over their teeth, and they never get cavities. On the other hand, we have patients who keep their teeth very clean, and we struggle to get their cavities under control.”

In the case of dental caries, Dr. Chalmers explains, microbial dysbiosis, poor diet, and inflammation perpetuate a vicious cycle. She points out,

When talking about decay, we need to consider inflammation in the mouth. Inflammation creates a more opportunistic environment for a microbiome that is destructive to teeth.

Much like the GI tract, terrain is a critical factor for whether or not pathogenic microbes initiate disease in the mouth. Two hundred healthy subjects from the Human Microbiome Project were positive for commonly known periodontal pathogens, yet were asymptomatic, leading authors to speculate that the microbes might be more appropriately reclassified as commensal organisms.(8) Diet, immune system, genetics, inflammation, microbial balance, nutrition, and methylation all interact to affect oral health. Much like the GI microbiota, it seems that oral microbiota promote health when there is high biological diversity,11 whereas lack of diversity is often accompanied by disease and vulnerability to infection.(1,12)

The Oral–Systemic Connection

The link between oral health and systemic health seems undeniable. The U.S. Surgeon General described the mouth as a “mirror of health or disease” and an early indicator of disease in other tissues and organs in the body.(13) Periodontal disease increases the risk for cardiovascular disease,(2) rheumatoid arthritis,(3) diabetes,(4) cancers,(5) and inflammatory bowel disease.(14) Diabetics are three times more likely to develop periodontal disease than non-diabetics.(4,5) Oral pathogens have been found in atherosclerotic plaques(7) and in the joints of rheumatoid arthritis patients.(15) Simple interventions such as brushing and flossing can reduce new cardiovascular events in patients with coronary artery disease(2) and lower inflammatory markers such as CRP.*(16)

Periodontal disease increases gastric cancer, pancreatic cancer, head and neck cancer (four-fold) and tongue cancer (five-fold). In people who do not brush their teeth, the risk of esophageal cancer is doubled. On the other hand, good dental hygiene practices can reduce a person’s risk of oral cancers by 62%.(5)


Periodontal disease and inflammatory bowel disease (IBD) often present as comorbidities, and it’s been suggested that they have similar immunopathogeneses.(17) Those with IBD and periodontal disease are more likely to have opportunistic bacteria in inflamed gums(14) and are also more likely to have elevated Saccharomyces cerevisiae antibodies.(1) While the arrow of causation has not been determined, disruption of the microflora, mucosal health, and immune responses is evident in both sites along the alimentary canal.(1,18)

The mouth is uniquely positioned as the first meeting place between the immune system, the gut,… Click To Tweet

Mechanisms Explaining the Oral–Systemic Link

While swallowing pathogens or inflammatory cytokines may be one way disease spreads from the oral cavity to the GI tract, bacteremia may be another route whereby the mouth can influence extraoral sites. The gums are actually more porous than the GI lining.(19) Bacteria rush into the bloodstream with each brushing, and oral bacteria have been found in the blood following dental procedures.(7) One hypothesis is that the periodontium presents a large, inflamed surface area that is rich in dysbiotic microbes. Frequent, transient bacteremia exposes the system to chronic, low-grade inflammation.(5)

GRAVES-AD1The teeth extend through the oral mucosa, leaving a vulnerable point of entry in the protective epithelial barrier of the mouth. In 2013, Dr. Chalmers coined the term “leaky mouth” to describe the breach of this barrier. It is a natural extension of the concept of intestinal permeability (“leaky gut”), whereby the epithelial barrier of the Gl tract permits harmful proteins and organisms to pass into the bloodstream. The mucosa of the mouth is very porous, even in a healthy person, but low-grade inflammation and infection in the mouth could further damage the barrier between the oral mucosa and the bloodstream, making it more “leaky.” This could trigger permeability, immune dysfunction, inflammation, and ultimately, systemic disease.(20)

Applications for Clinical Practice

The World Health Organization recommends that oral disease prevention should be integrated with chronic disease prevention, as the two are intimately linked.(21) Incorporating oral health measures into clinical practice can improve cardiovascular disease outcomes,(2) rheumatic joint pain,(3) and hemoglobin A1c.(4) Likewise, authors have suggested that balancing the oral microbiome may, in fact, treat systemic disease,(22) and that addressing oral inflammation should be an integral part of treating inflammatory bowel conditions.(18)

The mouth should be considered a major potential contributor to dysbiosis, inflammation, and possibly barrier dysfunction. Cavities, gingivitis, periodontal disease, root canals, chronically elevated C-reactive protein (CRP)*, and frequent dental work are clues to the practitioner that oral disease could be holding back progress on other health fronts. Chronic GI dysbiosis that has not responded to typical Functional Medical interventions may have its origins in the mouth.


Commonsense clinical recommendations include regular brushing, flossing, and dental cleanings. A low-sugar, plant-based, anti-inflammatory diet and healthy salivary flow will encourage healthy bacterial populations. Chewable probiotics, probiotic toothpaste, chewable CoQ10, and overall adequate nutrition can support the oral tissue. Treatments to heal a “leaky mouth” may be similar to those designed to heal and seal the GI mucosa.(23)

Oral antibiotics should be used with caution, and antimicrobial mouthwash should be used judiciously as it can kill beneficial bacteria. Dr. Chalmers urges dentists and Functional Medicine practitioners to work together when treating dysbiosis of the mouth or gut:

Oral and gut infections should be handled in an integrated fashion. For example, if we are going to treat infections in the mouth with antibiotics, we have to consider the health of the gut first. There has to be a coordinated approach between Functional Medicine practitioners and dentists to address infections in the mouth and gastrointestinal tract.


The mouth is uniquely positioned as the first meeting place between the immune system, the gut, the outside environment, microbes, pathogens, toxins, and nutrients. Accordingly, the mouth deserves to be placed next to the GI tract as paramount in the body’s immune and inflammatory response and in maintaining microbial balance. Luckily, the oral cavity is imminently accessible for both treatment and monitoring. In conditions of oral disease, GI disease, or systemic inflammation, consider the health of the oral microbiome, the oral mucosa, and the oral hygiene of the patient.

*Special thanks to Stephen Olmstead, MD, and ProThera, who jumpstarted this conversation with their fully referenced newsletter on the topic.24

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About the Author

Dr-Cass-Nelson-DooleyCass Nelson-Dooley, M.S.
is the owner of Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley served as a Medical Education Specialist for almost eight years at Metametrix Clinical Laboratory and then Genova Diagnostics. She enjoys teaching, presenting, writing, and researching how to address the underlying causes of disease, not just the symptoms. Cass received the Fulbright Scholar award to study medicinal plants in Bocas del Toro, Panama. She currently lives in the Atlanta area and enjoys Zydeco and Cajun dancing on the weekends, owing to her Louisiana roots. Her favorite food is dark chocolate. For more information, check out Facebook and Twitter. You can read this original article here that was featured on

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Questions or anything to add about the link between the mouth and the gut? We want your thoughts, please. You might just help someone else in need.


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