Oral Microbiome 101: Why Your Oral Microbiome Matters More Than You Think

Did you know your mouth houses more than ~700 strains of bacteria? 

These tiny organisms can influence more than just your teeth and gums – they also affect your gut, skin, and overall health.¹

→ Wait, what? 

Yes, really.

Here’s the thing most people don’t realize: oral health is about far more than avoiding fillings and root canals. The health of your oral microbiome can set the tone for almost everything: from inflammation and disease in the body to the appearance of your skin. 

As a holistic skincare company, this is one of our most foundational pillars: everything in the body is connected. We know skin health is inexplicably linked to overall wellness and vitality. And the health of your mouth, it turns out, is no different. ;) 

That’s why we created a resource specifically for our community. Throughout this post, we’ll explore: 

• Why oral health matters
• How the oral microbiome and skin microbiome are connected
• Simple oral health hygiene + practices to support the oral microbiome

We’re grateful for the opportunity to speak with Dr. Forbes, a certified biological dentist. He provided valuable context and insight on some of the most debated topics in oral health. 

But first, let’s step back and see how this seemingly insignificant microbiome has wide-reaching effects.

Why Oral Health Matters for Whole-Body Wellness

Oral health reflects what's happening inside the body – and in turn, shifts in the oral microbiome can create ripple effects throughout your whole system.

Because while you might think of the oral microbiome as simply your gums and teeth, the oral microbiome actually includes your:¹

• Tongue
• Tooth surfaces
• Buccal mucosa
• Tonsils
• Soft and hard palate
• Lip vestibule

Just like other microbiomes in the body (and throughout nature), diversity is essential for your oral health. A variety of beneficial bacteria helps maintain balance, protect against harmful species, and support healthy oral tissues. But unlike other microbiomes, your oral microbiome is uniquely "vulnerable" because it's so readily accessible.

Anything that comes into contact with your face or mouth can affect the delicate balance of the oral microbiome. That's why supporting a balanced oral microbiome helps keep the "bad guys" at bay – supporting optimal oral health.²

On the other hand, imbalance (aka, “dysbiosis”) contributes to oral health issues, like:

• Gum disease
• Cavities 
• Dry mouth

But it doesn’t stop there. Oral health is deeply connected to your whole-body well-being. It’s even an essential part of your immune defenses. Consider your tonsils, for example – they’re one of your body’s first lines of defense against pathogens. 

Your oral microbiome also plays a role in digestion and gut health. Science continues to confirm an innate connection between the gut and oral microbiome.^1,2 When one is imbalanced, the other is often affected.

One of the most prevalent ways oral health can affect the rest of the body is through bleeding gums. When inflamed gums bleed, bacteria in your mouth gain direct access to your bloodstream since it’s technically an open wound. And as you can imagine, once in circulation, the bacteria can influence other organs and systems throughout your body.¹

Yet here’s the thing most dentists have never explained to us: 

We wouldn’t leave any other part of our body to bleed indefinitely – so why do we so often ignore bleeding gums? 

This is why caring for your oral health and oral microbiome isn’t just about fresh breath or clean teeth. It’s a foundational part of whole-body health. 

Research even shows that oral bacteria can serve as a biomarker for non-oral diseases, like:^1,3

• Cardiometabolic disease
• Gut microbiome disruption 
• Systemic inflammation
• Obesity
• Pancreatic cancer
• Type 2 Diabetes
• Pediatric Crohn's disease
• Heart disease
• Low weight 
• Preterm birth

And while the researchers admit they aren’t sure whether there’s a direct relationship to these conditions, it remains a very interesting connection to consider. 

We also see imbalances in the oral microbiome related to specific skin conditions. 

Skin + Oral Health

While the research continues to unfold, the emerging picture is hard to ignore: what happens in the mouth often echoes on the skin. What begins in the oral microbiome can ripple outward, revealing just how interconnected these systems really are. 

We know that chronic oral inflammation (like periodontitis) can spark immune responses linked to skin flare-ups. A few of the most well-documented examples include:⁴

• Dermatitis – a general sensitized skin condition, shown to be associated with gingivitis (inflamed gums), toothaches, and oral infections. Research reveals that when underlying infections or issues within the oral microbiome are addressed, many see significant improvement. In some cases, they’re even cured.

• Lichen Planus – a painful, itchy, inflammatory condition. Studies show that more plaque accumulation and poor oral health can worsen symptoms. On the flip side, enhanced oral health can significantly improve symptoms.

• Psoriasis – an itchy, inflammatory skin condition with a strong association to a specific streptococcal bacterium within the oral microbiome. Treating this bacterium has been shown to significantly improve, or even cure, psoriasis.⁵   

Together, these show us that the mouth is not a separate entity. It’s part of your body’s larger ecosystem. This invites us to consider a fresh, holistic approach to oral health care. 

Rethinking Traditional Dentistry + Oral Health Protocols 

Conventional dentistry largely relies on fluoride, fillings, and other synthetic solutions. Yet new research into the oral microbiome and the body’s natural ability to heal teeth suggests a more holistic path is possible. 

Fluoride vs. Hydroxyapatite 

Though research is now hitting mainstream news regarding fluoride, this has actually been a conversation for a long time. In 2012, a study found that fluoride affects adults' neurology, among other potential risks.^6,7 (And logically, we could deduce that it would affect kids, too.)

Today, many are switching to Hydroxyapatite. Hydroxyapatite is the primary mineral in teeth and bones, which is why many dentists and experts recommend it as a biocompatible alternative. And many dentists are seeing amazing results with hydroxyapatite without the toxicity concerns fluoride brings. 

However, this conversation raises a few key questions. Thankfully, Dr. Forbes provided valuable insights, drawing on his technical knowledge and clinical experience. 

Q: What’s the real difference between nano and non-nano hydroxyapatite, and is one viewed as safer or more effective from a holistic dentistry perspective?

A: In my experience as a biological dentist, the distinction between nano and non-nano hydroxyapatite is a meaningful one, especially when it comes to patient preferences and comfort around safety. Both forms can be effective, but they work a little differently. 

Because nano-hydroxyapatite is structurally similar to the crystals that make up our enamel, it has an excellent ability to bond with and integrate into tooth structure, supporting deeper remineralization. I’ve seen very good results with nano-hydroxyapatite in patients with early enamel lesions or dentin sensitivity – often with noticeable improvement in comfort and enamel smoothness over time. 

Non-nano hydroxyapatite, on the other hand, has larger particles that don’t penetrate as deeply but still provide strong surface-level remineralization. It creates a smooth, protective layer that supports enamel health beautifully. I often recommend non-nano formulations for children, pregnant, or patients who prefer a more conservative approach when it comes to nanoparticle exposure. 

There’s sometimes concern about whether nano-sized particles could cross biological barriers, like the blood–brain barrier. While the shape and size of these particles can influence their behavior, it’s important to keep this in context. With toothpaste, exposure is localized and superficial – we’re not injecting or inhaling these particles. Based on current clinical evidence and my own practice, the likelihood of systemic absorption or any significant health impact is extremely low. 

For me, the decision between nano and non-nano isn’t about one being “good” and the other “bad.” It’s about matching the right tool to the right patient. Nano-hydroxyapatite can be an excellent, safe option for remineralization and sensitivity, especially when sourced from reputable brands that adhere to strict safety standards. Non-nano is also a great, time-tested alternative for those who prefer to avoid nanoparticles altogether. 

At the end of the day, I trust hydroxyapatite – in both forms – as a biocompatible, effective, and fluoride-free option to support long-term oral health. My role is to educate patients on the differences so they can make informed decisions that align with their health goals and comfort levels.

Q: Some people say hydroxyapatite can hide cavities on X-rays or cause problems like greying teeth. Are these concerns valid?

A: I’ve heard the concerns about hydroxyapatite “masking” cavities, and I understand why that can sound alarming to patients. But in my experience – and based on the current clinical evidence – those claims are often misunderstood or overstated. 

Hydroxyapatite doesn’t hide decay on X-rays in the way some people imagine. It can support remineralization of early, non-cavitated lesions, which may make those areas appear more stable or less pronounced radiographically over time. That’s actually what we want to happen. A true cavity, especially one that’s progressed into dentin, isn’t going to be “covered up” or made invisible by hydroxyapatite. 

X-rays show changes in mineral density, and if a lesion has already broken through the enamel, that will remain visible. If anything, when used properly, hydroxyapatite helps strengthen enamel around these areas, giving us a better chance to stabilize or slow the process, rather than disguise it. 

Regarding concerns such as greying teeth or increased cavities, I haven't seen that in my practice. In fact, I’ve often observed the opposite. Patients who use hydroxyapatite toothpaste consistently – especially as part of a broader oral health routine that includes diet, hygiene, and regular checkups – tend to have stronger enamel, fewer sensitivity issues, and in many cases, fewer early lesions that require intervention. 

It’s also important to remember that no toothpaste is a magic bullet, whether it contains hydroxyapatite, fluoride, or neither. What matters is how it’s used and whether other risk factors are being addressed.

Fillings + Healing Teeth Naturally 

Thankfully, growing evidence shows that teeth have the capacity to remineralize with the proper support. Foundational practices such as simple daily routines, inexpensive products, and consistent oral hygiene can make a meaningful difference for the oral microbiome + oral health.

And while there are times that fillings are necessary, traditional dentistry tends to resort to this option before giving the body a chance (and the right resources) to repair naturally. The fact is, our bodies – and our mouths – are self-healing! 

If a trusted dental care provider recommends a filling, it’s important to know that not all materials are created equal. Certain options can introduce unwanted toxins or irritants into your oral microbiome/body. If at all possible, avoid materials like: 

• Amalgam
• Older metal alloys 
• Low-quality composites

And this raises an essential question for anyone who doesn’t have access to a biological or holistic dentist:

Q: For people who can’t access a biological or holistic dentist, what safer filling materials or restoration options should they ask about?

A: This is a crucial topic, especially for patients who may not have access to a biological or holistic dental practice but still want safer, more biocompatible options for their dental restorations. In my practice, we’ve never used mercury amalgam fillings. From the beginning, we’ve been committed to materials that are more compatible with the body and support long-term oral and systemic health. 

For most fillings, my go-to option is fluoride-free, BPA-free composite resin. These materials bond directly to the tooth, allowing us to be very conservative and preserve as much natural structure as possible. They’re also metal-free, which is important for patients seeking to reduce potential exposure to reactive or sensitizing materials. 

Porcelain or ceramic restorations are another excellent option, especially for larger restorations, onlays, or crowns. They’re durable, long-lasting, and very well tolerated by most patients. Plus, they offer a natural look that blends beautifully with the surrounding teeth. 

Some patients may also benefit from metal-free hybrid materials, such as high-strength ceramic-composite blends. These can be a great balance between strength and tooth preservation – often a good choice when a full crown isn’t necessary. 

Even if someone isn’t seeing a biological dentist, there are ways to advocate for safer materials. I encourage patients to ask their provider: 

• Is the filling material mercury-free? 
• Is it fluoride-free and BPA-free? 
• How conservative is the procedure – will it preserve as much healthy tooth as possible? 
• Is the material biocompatible for patients with sensitivities?

The reality is, you don’t have to be in a “holistic” office to make better choices. Being informed and asking the right questions can make a meaningful difference in your long-term oral and overall health. Over the years, I’ve seen excellent outcomes with fluoride-free, BPA-free composites and ceramic options – both in terms of function and patient well-being.

Like Dr. Forbes said, even if your dentist follows conventional practices, there are many ways to support your oral health. Here are a few easy tips when visiting your dentist: 

• Say no to fluoride treatments, cleanings with prophy paste or fluoride, sealants, or excessive X-rays  

• Before your appointment, ask if they have a more holistic cleaning method available (many offer pressurized water or salt-based cleanings now)

• If your dentist finds a cavity, ask if they can monitor the area instead of resorting to immediate fillings (and try some natural remineralizing options at home!) 

• If you do need a filling, ask about biocompatible filling materials 

• When it comes to wisdom teeth removal, be cautious and get a second opinion if possible (For more insight on this, check out our episode on jaw health.)

*Tip: If you need/want to find a new dentist, check out the Biological Dentist Directory or the Holistic Dental Association Directory.

While a holistic dentist is ideal, oral health doesn’t end at the dentist’s office. There are also many options for simple at-home practices and over-the-counter products that support oral health.

Simple Ways to Support Your Oral Microbiome Holistically

You don’t need to switch dentists overnight to improve your oral health. Anyone can benefit from a few at-home practices. Here are some simple ways to support oral health hygiene at home beyond brushing and flossing. 

 

→ OIL PULLING – organic, virgin coconut oil can help reduce bacteria, support oral microbiome balance, and even reduce plaque.⁸ All you have to do is swish coconut oil in your mouth for 10-15 minutes a day. (Our holistic esthetician, Courtney, swears by this! Her dentist even noticed a difference.)

*Tip: This is one of the easiest practices to habit-stack with other routines like red light or grounding. ;)

 

→ TONGUE SCRAPING – tongue scrapers are inexpensive to purchase and easy to use! Regular tongue scraping helps remove bacteria buildup, food, and other residue to support a balanced oral microbiome. Best done after brushing. 

 

→ SWITCH TO FLUORIDE-FREE TOOTHPASTE –  as you learned, it’s best to avoid fluoride in your dental care. Whether you choose a hydroxyapatite toothpaste is a personal choice, but there are plenty of non-toxic options to choose from! 

• Living Libations 
• Risewell 
• Zebra 
• Super Teeth 
• Boka
• Pearl 

→ ADD MINERALS TO YOUR ROUTINE – you can add minerals in supplement form, topical, or just add more trace minerals to your food via sea salt. Regardless, adding more trace minerals supports your mouth and whole body. (Win, win!)

• Redmond Real Salt or Celtic Sea Salt
• Bliss Energetics Remineralizing Tooth Putty 
• Pearl Trace Mineral Drops 
• Trace Mineral Concentrace Supplement

 

→ ADD ORAL PROBIOTICS OR TINCTURES – many people see good results with different oils, tinctures, and even probiotics in pill form. 

• Supreme Nutrition Oral Supreme
• Super Teeth Dental Probiotic 

→ BRUSH TWICE OR MORE PER DAY – if you don’t already, adding an extra brushing session or two after meals or snacks can help support oral health. It’s almost too easy to do, but don’t underestimate the impact! 

 

→ DITCH THE MOUTHWASH FOR A HOLISTIC ALTERNATIVE – many mouthwashes on the market can be quite astringent and wipe out too much bacteria, including the good stuff. (It’s all about balance, not nuking!) Natural alternatives can provide the same benefits, sans the harsh astringents. 

• Baking soda rinses 
• Briotech Mouthwash 

→ DIET AND LIFESTYLE CHANGES – from diet to sleep habits and hydration – these choices matter, and the benefits also create a beautiful ripple effect! 

• Reduce sugar intake + never leave sweets (or carbs) sitting on your teeth. 

• Prioritize hydration, as it supports saliva production, which protects tooth enamel. 

• Try mouth taping at night (if you’re a good candidate) to help encourage nose breathing. This, in turn, prevents the mouth from drying out overnight and disrupting your oral microbiome. 

• Eat nutrient-dense, whole foods (preferably organic or regenerative foods, which have a higher density of vitamins/minerals.
  

Here’s what Dr. Forbes had to say about diet: 

Q: Are there specific foods or nutrients you recommend for supporting oral health and the oral microbiome?

A: Nutrition plays a huge role in oral health – far more than many people realize. In my experience, a well-supported oral microbiome and strong, resilient teeth start with what we eat and how we nourish the body as a whole. You can’t out-brush or out-toothpaste a nutrient-deficient diet. 

I often encourage patients to focus on whole, nutrient-dense foods, ideally organic or regeneratively grown when possible. These foods tend to be richer in vitamins, minerals, and healthy fats that directly support enamel strength, gum health, and a balanced oral microbiome. 

Vitamins A, D, and K2 are particularly powerful for oral health. They work synergistically to support proper mineralization of teeth and bones, healthy salivary function, and a balanced immune response in the mouth. 

Foods like grass-fed butter, pasture-raised eggs, wild-caught fish, organ meats, and full-fat dairy (for those who tolerate it well) can be excellent sources of these fat-soluble vitamins. Healthy fats – from sources like avocado, olive oil, grass-fed animal fats, and wild-caught fatty fish – are also essential. They help the body absorb fat-soluble vitamins and support the body’s natural remineralization processes. 

I also encourage incorporating mineral-rich foods such as leafy greens, sea vegetables, bone broth, and properly prepared nuts and seeds. These provide calcium, phosphorus, magnesium, and trace minerals that support tooth strength. 

And, of course, limiting ultra-processed and refined sugars makes a huge difference in maintaining a healthy oral microbiome. When patients make these dietary shifts, I often see meaningful changes not just in their teeth but also in their gum health, saliva quality, and cavity risk. Supporting the mouth starts with supporting the whole body – and that’s something we see reflected repeatedly in both research and real-world outcomes.

 

When you bring these gentle practices into your daily rhythm, oral care shifts from a task to a form of nourishment. Little by little, they help create the internal environment your oral microbiome needs to thrive.

Nurturing the Ecosystem Within

Oral health is about more than avoiding cavities – it’s an opportunity to nurture the delicate ecosystem of your mouth in ways that ripple through your entire body. With simple, holistic practices, you can strengthen your smile and your overall vitality.

The oral microbiome is a powerful reminder that everything is connected. And that even the smallest shifts can bring big changes to your well-being.

XO

 

**This post is designed to inform and empower you, but it is not a substitute for professional medical or dental care. Nothing here should be interpreted as medical advice or used to diagnose, treat, cure, or prevent any condition. Always consult with a qualified healthcare or dental provider about your personal health needs.

---

Sources: 

1. National Library of Medicine | A Practical Guide to the Oral Microbiome and Its Relation to Health and Disease
2. National Library of Medicine | Exploring the Oral-Gut Linkage: Interrelationship Between Oral and Systemic Diseases 
3. National Library of Medicine | The Oral-Gut Microbiota Axis: A Link in Cardiometabolic Diseases 
4. National Library of Medicine | The Association Between Oral Health and Skin Disease
5. National Library of Medicine | Throat Infections Are Associated With Exacerbation in a Substantial Proportion of Patients With Chronic Plaque Psoriasis
6. National Academies | Fluoride in Drinking Water: A Scientific Review of EPA’s Standards (2006)
7. World Health Organization | Chemical Safety and Health: Inadequate or Excess Fluoride
8. National Library of Medicine | Oil Pulling for Maintaining Oral Hygiene – A Review

 

---

Pin this blog post to your wellness Pinterest board for future inspo: