How a holistic dentist uses oral microbiome testing to help prevent chronic diseases before they start

You swallow up to 1 trillion bacteria from your mouth every single day.¹ 

Some are beneficial allies that support your immune system, help digest food, and protect against disease.

Others are pathogenic threats that, when allowed to overgrow, trigger the chronic inflammation behind heart disease, Alzheimer's, diabetes, and autoimmune conditions.²,⁷

As a holistic dentist, I don't just look at your teeth. I look at how your oral microbiome — the ecosystem of bacteria in your mouth — affects your entire body. 

Traditional dentistry treats cavities and gum disease. Holistic dentistry asks why they keep happening and addresses the bacterial imbalances driving chronic disease.

In this article, you'll discover what makes holistic dentistry different, how specific oral bacteria contribute to serious health conditions, and why personalized testing changes everything.

Key Takeaways

• Holistic dentists address oral health as inseparable from whole-body wellness, using bacterial testing rather than treating symptoms alone.
• Up to 1 trillion bacteria travel from your mouth to your body daily¹ — beneficial species protect health while pathogenic bacteria trigger systemic inflammation²,⁷.
• Specific harmful bacteria (P. gingivalis, F. nucleatum, T. forsythia) have been found in heart plaques, brain tissue, and throughout the bloodstream, creating disease pathways³,⁴,⁵.
• Oral microbiome testing reveals which bacteria are overgrowing and which are depleted, allowing targeted interventions before chronic diseases develop.
• Periodontal disease significantly increases cardiovascular risk through chronic inflammation affecting your heart, brain, and immune system³,⁶,⁷.
• The goal is bacterial balance, not sterility — nurturing beneficial bacteria while reducing pathogens.

What Makes a Holistic Dentist Different

When I see chronic cavities or recurring gum inflammation, I don't just treat the immediate problem. I ask why it keeps happening.

Traditional dentistry focuses on structures — fixing decay, treating gum disease, repairing damage. 

These interventions are essential, but they miss the bigger picture: 

Your mouth connects directly to every system in your body through blood flow, bacterial transfer, and inflammatory signaling.²,⁷

A holistic dentist takes a different approach:

Root Cause Analysis

As a functional dentist, I often ask the following questions on top of the standard questions conventional dentists ask: 

• Is pathogenic bacterial overgrowth the problem? 
• Are beneficial protective species depleted? 
• Does medication-induced dry mouth allow harmful bacteria to flourish? 
• Are nutritional deficiencies or chronic stress disrupting microbiome balance?

Testing Over Guessing

Rather than applying standardized treatments, I use oral microbiome testing to identify your specific bacterial profile — which pathogens are overgrowing, which beneficial species are missing, and what your disease risks are.

Personalized Protocols

Once we understand your oral ecosystem, we create targeted interventions: specific probiotics to boost beneficial bacteria, dietary changes that feed good bacteria while starving pathogens, and antimicrobial treatments for specific harmful species.

This is functional medicine applied to dentistry — addressing causes, not just managing symptoms.

How Oral Bacteria Affect Your Whole Body

The connection between oral health and chronic disease isn't speculation — hundreds of peer-reviewed studies document these links.

Your oral cavity houses over 700 bacterial species.¹ 

When balanced, beneficial bacteria protect you by maintaining healthy pH, producing vitamins, and keeping pathogens in check. 

When this balance shifts and harmful bacteria overgrow, problems cascade throughout your body.

You swallow up to 1 trillion bacteria daily.¹ 

Beneficial ones support your gut health and immune function. 

But pathogenic species like Porphyromonas gingivalis, Fusobacterium nucleatum, and Tannerella forsythia travel to your gut and beyond, triggering inflammation and disrupting healthy systems.²,⁷

When you have bleeding gums, you've created a direct highway for these pathogens to enter your bloodstream and reach vital organs.⁷

The Research Is Clear

Research found harmful oral bacteria in 78% of atherosclerotic plaque specimens.³ 

When periodontal pathogens enter your bloodstream through inflamed gums, they infiltrate blood vessel walls, trigger inflammation, and contribute to plaque formation that increases heart attack and stroke risk.³,⁴

Research shows people with periodontal disease have significantly increased cardiovascular risk compared to those with healthy gums.⁶,⁷ 

This isn't minor — it's a major, measurable risk factor.

The implications extend to your brain. 

Oral bacteria have been identified in brain tissue of Alzheimer's patients, with P. gingivalis repeatedly appearing in neurodegeneration studies.⁵ 

These bacteria may trigger chronic inflammation that damages brain tissue years before cognitive symptoms appear.

The same chronic inflammation from oral bacterial overgrowth has been linked to diabetes, autoimmune conditions, and pregnancy complications.⁸,⁹

This isn't about creating fear — it's recognizing that oral pathogen overgrowth is solvable when identified early.

Why Testing Changes Everything

Here's the problem with standard dental care: everyone gets the same approach. 

Regular cleanings, fluoride treatments, maybe antibiotic rinses for severe inflammation.

But your oral microbiome is as unique as your fingerprint, shaped by your genetics, diet, medications, stress levels, and health history.¹⁰,¹¹ 

Generic treatments are educated guesses. Oral bacteria testing provides actual answers.

What Testing Reveals

Pathogenic Bacteria Levels: Which disease-causing bacteria are overgrowing? Are you harboring P. gingivalis linked to Alzheimer's? F. nucleatum associated with cardiovascular risk?

Beneficial Species Status: Are protective bacteria like Streptococcus salivarius present in adequate numbers to maintain balance and compete with pathogens?

Overall Balance: A healthy mouth contains hundreds of bacterial species working together. 

Low diversity means vulnerability to pathogenic takeover. High diversity means beneficial bacteria can outcompete harmful ones.

Disease Risk Markers: Specific bacterial profiles correlate with increased risk for cardiovascular disease, diabetes, autoimmune conditions, and neurological disorders.

This transforms dental care from reactive to proactive — identifying imbalances when they're easily correctable, before years of contributing to chronic disease.

I recently worked with a patient experiencing bleeding gums despite excellent oral hygiene, along with persistent fatigue and elevated inflammatory markers. 

Her oral microbiome test revealed high levels of pathogenic P. gingivalis and F. nucleatum while showing critically low levels of beneficial protective species.

We created a targeted protocol: specific probiotics to increase beneficial bacteria, dietary modifications to reduce pathogen-feeding sugars, and natural antimicrobial compounds for her specific bacterial overgrowth. 

The goal was restoring balance, not eliminating all bacteria. 

Her symptoms improved significantly as beneficial bacteria recolonized and pathogens decreased to healthy levels.

This is the power of personalized testing. 

Your Next Steps

Understanding the oral-systemic connection is empowering. 

You're not helpless in the face of chronic disease risk.

If bleeding gums, persistent bad breath, recurring cavities, or unexplained fatigue frustrate you, your oral microbiome balance might be the missing link. 

Pathogenic bacteria may be overwhelming your beneficial bacteria right now, creating inflammation that will manifest as disease later.

Testing reveals exactly which bacteria need support and which need reduction. 

No more trial-and-error with supplements that might harm beneficial bacteria while missing actual pathogens.

The Orobiome Testing Package provides everything: 

• at-home testing, laboratory analysis, 
• licensed dentist consultation explaining your results, 
• personalized healing protocol for your unique bacterial profile, 
• plus complete access to the Gateway to Health documentary series.

For the complete science, watch the Gateway to Health series.

Hosted by Dr. Pedram Shojai with interviews from myself and leading researchers, this 7-episode series explores how your mouth affects your heart, brain, and immune system. 

Watch free for 10 days.

Your mouth is the gateway to your health. 

The question is: are beneficial or pathogenic bacteria dominating your oral microbiome right now?

Testing provides answers. Answers enable action. Action — restoring bacterial balance —  prevents disease.

The choice to optimize your oral microbiome isn't just about better dental health. 

It's about cultivating beneficial bacteria that protect your heart, brain, immune system, and future while keeping pathogenic species in check.

About the Author

Dr. Elmira Shojai is a Doctor of Dental Surgery with over 15 years of hands-on clinical experience revolutionizing how we understand the connection between oral health and whole-body wellness.

After graduating from the University of the Pacific, consistently ranked among the world's most prestigious dental schools, Dr. Elmira spent over a decade in active clinical practice in California, where she treated thousands of patients and discovered patterns conventional dentistry was completely missing.

Time and again, she witnessed patients with perfect oral hygiene developing gum disease, recurring cavities, and chronic bad breath — symptoms that pointed to deeper systemic issues.

She saw patients with heart disease, diabetes, and autoimmune conditions who had severe oral infections that no one had connected to their declining health.

These clinical observations led her to functional dentistry and oral microbiome science.

In May 2025, Dr. Elmira made a pivotal decision: transition from one-patient-at-a-time clinical practice to leading Gateway to Health as Chief of Dental Programs, where she could scale her impact to reach thousands.

She now oversees a nationwide network of licensed dentists who provide personalized consultations based on cutting-edge oral microbiome testing — the same testing she wishes she'd had access to throughout her clinical career.

Featured as a leading expert in the Gateway to Health documentary series alongside her husband, Dr. Pedram Shojai (NYT bestselling author and founder of The Urban Monk), Dr. Elmira brings real-world clinical experience to every educational resource, protocol, and patient consultation.

Her mission is clear: bridge the dangerous gap created when medicine and dentistry split in the mid-1800s, and help people understand that the mouth isn't separate from the body — it's the gateway to systemic health.

Sources

1. Oral microbiome: Unveiling the fundamentals. Journal of Oral and Maxillofacial Pathology. 2019.
2. Oral Microbiome: A Review of Its Impact on Oral and Systemic Health. Microorganisms. 2024.
3. Detection of oral bacteria in cardiovascular specimens. Oral Microbiology and Immunology. 2009. 
4. Oral Health and Cardiovascular Disease. The American Journal of Medicine. 2024. 
5. Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Science Advances. 2019. 
6. Periodontal therapy for the management of cardiovascular disease in patients with chronic periodontitis. Cochrane Database of Systematic Reviews. 2014.
7. The Oral Microbiome and Its Role in Systemic Health: Bridging the Gap Between Dentistry and Medicine. Cureus. 2025.
8. Risk factors for periodontal disease. Periodontology 2000. 2013.
9. Term stillbirth caused by oral Fusobacterium nucleatum. Obstetrics & Gynecology. 2010.
10. Genetic influences on the human oral microbiome. BMC Genomics. 2017.   
11. Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study. Scientific Reports. 2020.