Why the Oral Microbiome Matters: Insights from an Expert Interview

Contrary to popular belief, oral care is not about eradicating every microbe in your mouth. Many oral microbes support local and systemic health, including cardiovascular function. Preserving microbial balance in the mouth is essential for overall well-being.

We already appreciate the intestinal microbiome’s broad influence on mood, metabolism, immune function, and cognitive health. Yet the oral microbiome—the gateway to the gut—deserves equal attention. The mouth shapes what follows along the digestive tract and has a direct impact on whole-body health.

Antibacterial mouthwashes and other aggressive products can damage oral microbial diversity, which in turn affects the gut microbiome and systemic health. In the following interview, ethnopharmacologist Cass Nelson-Dooley explains the science behind the oral microbiome and the oral-systemic link—how oral health influences the rest of the body.

If any section seems technical, you are encouraged to submit questions through the podcast for future clarification.

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: The U.S. Surgeon General called the mouth a “mirror” of health and disease. If the gastrointestinal tract is a river, the mouth is its headwater—the source that sets the conditions downstream. The oral cavity contains multiple microenvironments—the tongue, hard palate, tooth surfaces above and below the gumline—each hosting distinct bacterial communities. Around 700 species of aerobic and anaerobic organisms form organized biofilms in the mouth, and this ecosystem plays a major role in nutrition, immunity, and systemic physiology.

Dr. Burhenne: Dental training often focuses narrowly on teeth rather than the broader oral-systemic connection. Better collaboration between dentists and physicians would improve diagnosis and treatment.

Some people ask about “leaky gut” and wonder whether an analogous “leaky mouth” exists. Is sublingual absorption for homeopathic remedies the same concept?

Cass Nelson-Dooley, MS: “Leaky mouth” is not an established clinical term; I coined it to describe increased gingival epithelial permeability. Scientific literature does address oral mucosal permeability, and the concept is plausible. Like intestinal permeability, a compromised oral barrier can trigger immune activation, systemic inflammation, and allow microbes or inflammatory molecules access to the bloodstream. The healthy oral mucosa is porous but resilient; when infection or inflammation disrupts that barrier, systemic consequences become more likely.

Dr. Burhenne: Using the term “leaky mouth” helps frame the mouth as part of the same continuum as the gut.

Research shows roughly 45% overlap between bacterial species in the oral cavity and the colon. How should we interpret that overlap, and how are the distinct bacterial subsets specialized?

Cass Nelson-Dooley, MS: The 45% overlap highlights the mouth’s role as a major source of microbes that seed the gut—humans swallow roughly 140 billion oral bacteria daily. While both environments include dominant phyla such as Bacteroidetes and Firmicutes, the oral cavity is characteristically rich in Streptococcus species. Much remains to be learned about specialization: environment, pH, oxygen levels, host factors, and diet all shape which species thrive in each niche. Current research focuses on mapping microbial communities across the alimentary canal and understanding how shifts in those communities affect health.

Dr. Burhenne: This reinforces why the oral environment matters: in addition to brushing and flossing, avoid antibacterial mouthwash, prioritize nasal breathing, consider targeted oral probiotics, and follow a microbiome-friendly diet rich in vegetables and low in processed foods.

How do you define mismatch diseases, and could Streptococcus mutans dominance be considered a mismatch driven by modern diet?

Cass Nelson-Dooley, MS: Mismatch diseases arise when modern lifestyles differ from those that shaped human biology. While Streptococcus mutans and dental caries have existed for millennia, diets high in refined carbohydrates and sugar certainly drive oral dysbiosis, favoring acid-producing microbes and enabling S. mutans overgrowth. Caries development usually follows broader microbial shifts before S. mutans becomes dominant, so diet-driven ecological change is a key factor.

Dr. Burhenne: Cavities are fundamentally a disease of diet, and dentists should increasingly test for dysbiosis at routine visits.

What are the effects of strong bactericidal mouthwashes on the oral microbiome?

Cass Nelson-Dooley, MS: Antibacterial mouthwashes can harm beneficial oral microbes and shift the microbial balance. Evidence suggests routine use may eliminate bacteria that perform beneficial functions, and a study linked mouthwash use to changes that could raise blood pressure. Mouthwash should be used judiciously, reserved for clear indications rather than as a daily, indiscriminate antiseptic.

Dr. Burhenne: Another reason to reconsider daily antiseptic mouthwash.

How does a high-sugar modern diet cause dysbiosis, and what exactly is dysbiosis?

Cass Nelson-Dooley, MS: Dysbiosis means an imbalance in the microbial community that contributes to disease. In the mouth, poor hygiene, high sugar intake, and reduced saliva lower pH and favor acidogenic species. Acid-tolerant microbes proliferate, diversity falls, non-pathogenic streptococci decline, and S. mutans and yeasts can dominate—conditions that promote tooth demineralization and caries. While definitions of a “healthy microbiome” vary, microbial balance and diversity are clearly protective.

Dr. Burhenne: From now on, oral dysbiosis should be considered a source of many dental and systemic problems.

Does birth mode influence oral microbes like Slackia exigua and subsequent periodontal risk?

Cass Nelson-Dooley, MS: Yes. Vaginally delivered infants tend to have richer and more diverse oral and gut microbiota compared with those delivered by cesarean. Some studies report a higher prevalence of periodontal pathogens such as Slackia exigua in C-section infants. The diverse microbiome acquired at birth may help crowd out potential pathogens, suggesting long-term implications for oral and systemic health.

Dr. Burhenne: The mode of delivery is relevant enough that it may merit inclusion on new patient intake forms.

How important is the oral-systemic connection and what mechanisms might explain links between oral disease and systemic disease?

Cass Nelson-Dooley, MS: The oral-systemic connection is a major frontier. Oral pathogens have been associated with rheumatoid arthritis, inflammatory bowel disease, and atherosclerosis. Periodontal disease correlates with elevated systemic inflammatory markers and pathogens have been found in atherosclerotic plaques. Initiating oral hygiene programs in people with coronary disease has been shown to reduce cardiac events, indicating that improving oral health can positively affect cardiovascular outcomes. Mechanisms likely include microbial translocation, a breached oral barrier allowing inflammatory mediators and microbes into circulation, and downstream effects on distant tissues including the gut and liver. More research is needed to detail causal pathways, but the clinical correlations are strong.

Dr. Burhenne: We have correlation and growing evidence, but elucidating mechanisms will guide targeted interventions.

Why is periodontal disease more common in people with inflammatory bowel disease, and how are the two conditions connected?

Cass Nelson-Dooley, MS: People with IBD are more likely to have periodontal disease, and their oral bacterial profiles differ from those with periodontal disease alone. Dysbiosis and inflammation in the mouth may seed the gut with pathogenic microbes, while systemic inflammation from IBD can affect the oral cavity—causal direction may be bidirectional. Treating periodontal disease alongside IBD is often recommended to improve outcomes for patients with both conditions.

Dr. Burhenne: Collaboration between MDs and dentists is essential to treat inflammatory diseases comprehensively.

What happens when you brush your teeth or undergo a dental cleaning—does that cause bacteremia?

Cass Nelson-Dooley, MS: Brushing and routine dental cleanings commonly cause transient bacteremia. In healthy individuals, the immune system clears these bacteria without issue. But in people with chronic inflammation, dysbiosis, or weakened immunity, the sudden influx of oral microbes into the bloodstream can exacerbate systemic problems. That’s why maintaining oral health is a preventive measure and why clinicians may advise patients to be in good systemic health before invasive dental work.

Dr. Burhenne: Nitric oxide production is important for cardiovascular health and nasal breathing supports that. Does the oral microbiome also contribute to nitric oxide?

Cass Nelson-Dooley, MS: Yes. Certain oral bacteria convert dietary nitrate from leafy greens into nitrite, a step humans cannot perform enzymatically. Oral nitrate-reducing bacteria—such as Veillonella and Actinomyces—can supply a significant portion of systemic nitric oxide precursors. Maintaining those bacteria through diet and by avoiding antibacterial mouthwash supports nitric oxide homeostasis and cardiovascular health.

Dr. Burhenne: Another practical argument against indiscriminate mouthwash use.

How do regular dental cleanings influence reinfection risk for Helicobacter pylori, a stomach pathogen?

Cass Nelson-Dooley, MS: H. pylori can reside in dental biofilms. Patients who receive regular dental cleanings have lower rates of H. pylori reinfection, suggesting that reducing oral reservoirs contributes to more successful eradication and improved gastrointestinal outcomes. This is one example of how oral care affects distal sites.

Dr. Burhenne: That shows gum disease is more than local inflammation—it can impact systemic infections.

When candidiasis appears in the mouth, many clinicians prescribe antifungals but do not address root causes. How should candidiasis be managed more holistically, and what supports a healthy oral microbiome?

Cass Nelson-Dooley, MS: Oral candidiasis often reflects broader gastrointestinal or metabolic imbalances. Integrative approaches focus on diet—reducing sugars and starches—to starve fungal overgrowth, plus targeted antifungals when warranted. Systemic and oral probiotics, including Saccharomyces boulardii, can help rebalance flora. Antimicrobial herbs such as oregano oil or garlic may be useful adjuncts. Regular oral hygiene, optimized salivary flow, a plant-forward low-sugar diet, chewable probiotics or probiotic toothpaste, and nutrient support (vitamins, minerals, CoQ10, glutamine rinses, anti-inflammatory herbal swishes) all help restore a resilient oral ecosystem. Antibiotics and antibacterial mouthwashes should be reserved for true dysbiosis and used sparingly. Addressing underlying factors—food sensitivities, gut dysbiosis, intestinal permeability, hormonal imbalances, nutrient deficiencies, toxicity, and stress—supports long-term oral health.

Dr. Burhenne: Thank you, Cass. This conversation clarifies the vital role of the oral-systemic connection and offers practical steps clinicians and patients can take to preserve oral and overall health.