11 Steps To Better Oral Microbiome Health That May Reduce Your Risk Of Chronic Disease

As a functional medicine physician, I spend a lot of time discussing the importance of the gut microbiome and its connection to nearly all chronic diseases.

However, the gut isn’t the only part of the body with its own microbiome universe.

For instance, did you know you have an oral (mouth) microbiome? And that it is directly related to your digestive system and your risk of developing certain chronic diseases such as heart disease, hypertension, dementia, and digestive disorders?

We’ve known about this connection between the oral microbiome and chronic disease for quite some time. Yet it remains largely ignored throughout modern medicine (even in the integrative medicine space).

When was the last time you heard of a gastroenterologist or cardiologist looking into someone’s mouth or questioning their dental history? It just doesn’t typically happen during a regular 15-30 minute office visit (and in all fairness, most doctors don’t have the time or tools to deal with it.)

But we do have a growing body of evidence showing that oral health is directly connected to overall health.

In this article, we’ll explore:

  • My story of how a botched dental procedure led to health issues spiraling out of control
  • 13+ chronic diseases and other health issues associated with pathogens in the mouth
  • How your oral health increases your risk of disease and health issues
  • The nitric oxide link in the oral-health-heart connection
  • Signs and symptoms of poor oral microbiome health
  • 11 steps to better oral hygiene (what I’m now doing and using!)

How a Botched Dental Procedure Sent My Health Spiraling Out Of Control

I don’t want to spend too much time on this section (I’ve covered my healing journey in detail here).

However, I want to give some context about how I became so passionate about oral health.

About a decade ago, my health started spiraling out of control.

My digestion was a mess, my immune system became compromised, and I eventually began experiencing fertility issues, miscarriages, and pregnancy complications.

Even with my background in medicine and integrative health and plenty of assistance from various experts, it took me a while to pinpoint what triggered this.

I am sure now that bad dental work played a huge role in my health decline. Specifically, botched removal of two mercury amalgams which eventually led to oral infections (pulpitis), lots of antibiotics, and subsequent root canals.

Now, I want to be clear. In most cases, I’m still a huge advocate for removing mercury amalgams, especially for the chronically ill or those who wish to become pregnant.

However, at the time, I didn’t know how important it was to choose an excellent dentist, and especially a biological dentist who knew how to remove them safely.

Long story short, I eventually found a fantastic biological dentist who extracted both root canals and explored my wisdom tooth pockets, and years later I got zirconia implants.

These procedures took a long time and cost a lot of money, but it was all worth it because my health improved dramatically. There were many other issues I had to address, including mold exposure, but this helped remove one huge log from my health fire.

I share this story because undiscovered oral health issues often are at the crux of chronic disease or “mystery symptoms.”

Unfortunately, doctors and other healthcare providers are (typically) not trained to investigate this.

So, if you’ve “tried everything” and are still struggling with your health (like I was), I’d highly recommend finding an integrative physician (like me) and biological dentist who understands the implications of bad dental work.

We’ll talk more about that coming up.

More than 13 Chronic Diseases and Health Issues Associated With Poor Oral Microbiome Health

Most of us have heard about the link between gum disease and heart disease (a great motivator to floss daily!).

However, what’s lesser known (and what I wish I had known during my health crisis) is how pathogens in the mouth can increase your risk of a wide variety of health problems.

Some examples include: 1, 2, 3, 4

  • Arthritis
  • Cancer
  • Chronic inflammation
  • Chronic kidney disease
  • Dementia and Alzheimer’s
  • Diabetes
  • Erectile Dysfunction
  • Heart Disease
  • Hypertension
  • Obesity
  • Pregnancy complications including preterm birth, decreased birth weight, and even blood infection in the placenta or newborn.
  • Respiratory ailments such as pneumonia and chronic obstructive pulmonary disease
  • Stroke

How exactly can oral pathogens wreak so much havoc on the entire body? Let’s explore the science behind that now.

How Your Oral Health Increases Your Risk of Chronic Disease and Health Issues

Most of us wouldn’t consider the connection between our mouths and other organs and systems.

After all, we see a dentist for our teeth and a doctor for the rest of our body. Plus, very few health experts talk about the connection.

So here’s the deal.

The oral microbiome and gut microbiome are your body’s two largest microbial ecosystems, and science has shown they are intimately connected via the oral-gut microbiome axis.

This makes sense, given digestion begins in the mouth with the production of amylase in saliva, an enzyme that begins to break down starches.

Per a 2021 review entitled: “Oral–Gut Microbiome Axis in Gastrointestinal Disease and Cancer” published in the journal Cancers:5

“Recent studies have demonstrated that the oral-to-gut and gut-to-oral microbial transmission can regulate pathogenesis, indicating the presence of the oral–gut microbiome axis.

The researchers discuss how specific pathogens in the mouth have been shown to trickle into the gut microbiome and vice-versa, which can reshape the terrain of each ecosystem for better or worse.

So, if your oral health is good, it will positively impact your gut microbiome.

However, if your oral health is poor, those pathogens in the mouth can cause or contribute to gut dysbiosis. Likewise, if your gut health is poor, it can lead to “mystery” teeth and gum issues.

Could this solve the mystery of why some people are more prone to cavities and gum disease than others, even if they avoid sugar?

My conservative answer is more research is needed to make a definitive conclusion.

However, based on the existing evidence and my personal and clinical experience, I am quite confident that oral-to-gut and gut-to-oral pathways do play a key role in cavity and gum disease susceptibility.

The Nitric Oxide Link In The Oral-Health-Heart Connection

Nitic oxide production is an underappreciated function of the oral microbiome and plays a significant role in the oral-heart-health connection.

Here’s how this works.

Research has shown that certain oral bacteria contribute to nitric oxide production through a nitric oxide pathway in our mouth called the enterosalivary nitrate-nitrite-NO pathway.

This pathway is responsible for converting dietary sources of natural nitrates (typically from plants, not talking hot dogs or processed meats here) into usable nitric oxide via bacterial conversion.

Why does this matter?

It matters a LOT because suboptimal nitric oxide production is associated with an increased risk of heart disease—including hypertension and atherosclerosis. 6

Conversely, optimal nitric oxide production has been associated with a reduced risk of heart disease, better exercise endurance, and improved overall health. 7

This is important for everyone to understand, especially for older individuals, because nitric oxide production reduces with age. 

Therefore, having your oral microbiome in tip-top shape is a valid strategy for protecting your heart and longevity.

Signs and Symptoms of Poor Oral Microbiome Health

Sadly, many signs of poor oral microbiome health are considered “normal” and thus not properly addressed.

Here are some common signs and symptoms to watch out for:

  • Frequent cavities
  • Bad breath
  • Bleeding gums
  • Tonsil stones
  • Excessive plaque/tartar buildup
  • Chronic dental pain
  • Sensitivity to hot and cold

In my practice, we use a saliva test to measure specific pathogens in the mouth. This helps us pinpoint issues and prioritize an appropriate individual protocol.

So, how do you improve your oral microbiome to prevent disease and avoid dental issues? Follow these 11 steps.

11 Steps To Better Oral Microbiome Health (and why it matters)

#1: Use a tongue scraper daily

Tongue scraping only takes a few seconds a day and has been shown play a huge role in improving oral microbiome health. 8

I use drTungs tongue cleaner, but there are many different brands.

#2: Floss daily

The only caveat here is to avoid floss containing BPA and Teflon-based fluorinated chemicals (PFASs and PTFEs). Yes, sadly, this is a thing.

I’m a fan of drTungs Smart Floss, which is BPA, PTFE & PFAS Free. I also like the RiseWell floss that’s impregnated with hydroxyapatite, a safe and effective fluoride alternative.

#3: Avoid fluoride

Controversial opinion: Fluoride is a neurotoxin that should be avoided in water, toothpaste, floss, mouthwash, etc. I extensively cover this science in 10 Toxins To Avoid Before, During, And After Pregnancy.

However, it’s important to replace fluoride with something else that’s equally effective.

In truth, most natural toothpastes are no more effective than water. Which is why I always recommend hydroxyapatite!

Hydroxyapatite is a form of calcium similar to what your teeth are made of. It’s been studied in Japan for decades and has been shown as effective as fluoride for reducing cavities without the toxicity-factor. 9

Check out the International Academy of Oral Medicine and Toxicology’s (IAMOT) Fluoride Facts page for a holistic dental perspective on fluoride. Choosing a toothpaste free of chemicals like Sodium Lauryl Sulfate, triclosan, and plastic microbeads is also essential.

Some of my favorite clean toothpaste brands with hydroxyapatite are:

#4: Avoid antiseptic mouthwash

In general, antiseptics, antibacterials, etc., are contraindicated in cultivating a diverse and healthy oral microbiome.

Therefore, antiseptic mouthwash should not be an everyday thing unless you’ve recently had oral surgery or have an infection that warrants it.

Need more reason to quit? Using mouthwash regularly has even been shown to increase blood pressure. 10 11

One exception is RiseWell Mouthwash, which is alkaline and can help balance the mouth’s pH.

#5: Replace your toothbrush head every 1-3 months

Toothbrushes gather bacteria, so it’s best to replace them regularly. Also, consider where you’re storing your toothbrush (near the toilet?).

I prefer an electric toothbrush, which studies have shown might work a little better at reducing plaque and gingivitis. 12

There are even biodegradable toothbrush options, so don’t let a fear of waste keep you from switching out your toothbrush regularly.

#6: Eat a healthy diet, lower in sugars and refined carbs.

Eating this way benefits your gut microbiome, positively affecting your oral microbiome.

Plus, sugary foods have been shown to increase bad bacteria in the mouth, resulting in cavities. 13

#7: Don’t smoke

Smoking is terrible for your health, including your teeth, gums, and oral microbiome. It also increases your risk of a root canal (which you always want to avoid).14

#8: Enjoy foods rich in nitrates

Again, we’re not talking about nitrate preservatives used in processed meats… Instead, consume plenty of natural, plant-based sources of healthy nitrates found in plants, primarily vegetables.

Eating lots of veggies will help optimize nitric oxide production via the previously discussed enterosalivary nitrate-nitrite-NO pathway.

#9: Choose your dentist wisely

This is one of the single most important decisions you’ll make when it comes to your health and the health of your kiddos.

I only recommend seeing a holistic, biological, mercury-free dentist and getting your cleanings and checkups every six months (or more often).

These dentists are becoming easier to find. However, even if it means a drive, I think it’s worth it for the sake of your health (and if you don’t believe me, re-read my story).

To find a qualified dentist in your area, check out: Askthedentist.com and IAOMT.org.

#10: If you have root canals…

This is controversial, but many would argue that root canals are a source of chronic inflammation and dysbiosis in your mouth. They are best avoided (this doesn’t mean you should ignore an oral infection… it means ask your dentist about alternatives and do whatever you can to prevent problems in your mouth).

If you already have root canals and are suffering from chronic diseases, especially hypertension, a biological dentist or oral surgeon can use a 3D cone beam CT scan to evaluate these further.

Ultimately, root canals can be a massive stress on your body, and it’s often best to have them extracted. The timing of that is something you should discuss with your biological dentist and functional medicine physician.

Depending on the location, a biological dentist can do an extraction and eventual implants.

I’m not going to lie; this is complex, invasive, and expensive. Therefore, working with someone you trust who can give individualized advice and help you understand the risks vs. benefits is critical.15

#11: If you have silver fillings (amalgams), these contain mercury and should (almost) always be removed.

After years of sounding the alarm on silver fillings in the integrative health and holistic biological dental community, the FDA finally addressed this in a statement in Sept 2020:

“The U.S. Food and Drug Administration (FDA) is providing recommendations about the use of dental amalgam in certain groups of people who may be at greater risk to the potential adverse health effects of mercury exposure, to include:

  • Pregnant women and their developing fetuses;
  • Women who are planning to become pregnant;
  • Nursing women and their newborns and infants;
  • Children, especially those younger than six years of age;
  • People with pre-existing neurological disease;
  • People with impaired kidney function; and
  • People with known heightened sensitivity (allergy) to mercury or other components of dental amalgam.”

I’d take this a step further and recommend that no one be exposed to mercury daily from their fillings.

In my practice, I recommend having these removed safely with a mercury-safe dentist.

However, I do not recommend removal when pregnant or breastfeeding.

In the cases of root canals and silver fillings, it’s a risk-benefit conversation you should have with a dentist you trust.

Need Some Help Navigating Oral Health Issues Or Chronic Disease?

One of the biggest reasons patients chose our practice is because they weren’t getting results anywhere else.

Yes, we offer all the functional medicine consultations, lab work, nutrition counseling, and all the integrative health basics. But, our expertise expands far beyond the basics.

A deep understanding of the oral microbiome and how dentistry can cause chronic disease is a perfect example of this. As is our knowledge and approach to mold/mycotoxin exposure, preconception, autoimmunity, thyroid health, heavy metal toxicity, Candida, and so on.

If this sounds like what you’re looking for, and you’re located in Colorado, Michigan, or Texas, we’d love to connect! Click here to learn more about our services or here to apply to become a patient.


  1. https://pubmed.ncbi.nlm.nih.gov/28353075/
  2. https://pubmed.ncbi.nlm.nih.gov/28353075/
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8125773/
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672720/
  5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8125773/
  6. https://www.frontiersin.org/articles/10.3389/fcimb.2019.00039/full#h1
  7. https://www.sciencedirect.com/science/article/pii/S1089860322000544
  8. https://www.frontiersin.org/articles/10.3389/fcimb.2019.00039/full#h1
  9. https://www.biorxiv.org/content/10.1101/306423v1
  10. https://www.ncbi.nlm.nih.govpmc/articles/PMC7567004/#Abs1title
  11. https://www.nature.com/articles/s41598-020-61912-4
  12. https://www.cochrane.org/CD002281/ORAL_poweredelectric-toothbrushes-compared-to-manual-toothbrushes-for-maintaining-oral-health
  13. https://pubmed.ncbi.nlm.nih.gov/26261186/
  14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225991/
  15. https://www.frontiersin.org/articles/10.3389/froh.2021.672887/full

About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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