Is your oral microbiome wrecking your endocrine health?

May 24, 2020

By Mark Burhenne, DDS

As a functional dentist, I’ve been coaching patients for years on the best ways to prevent and reverse oral disease. After all, the health of the mouth directly impacts and mirrors the health of your whole body!

In recent years, research on the oral microbiome has revealed just how important the optimal balance of bacteria is in your mouth. Not only can a dysbiosis of the oral microbiota lead to dental problems, like cavities and gum disease, but an imbalance of the oral microbiome is closely related to systemic diseases, too.

In particular, issues with oral bacteria can greatly impact the health of your endocrine system, from menopause to pregnancy outcomes to diabetes and beyond.

If you’re wondering why your endocrine health is still a problem, your oral microbiome might be the source of your concern. Let’s take a look.


What is the Oral Microbiome?

The oral microbiome (also called oral biome or oral microbiota) is basically what it sounds like: a community of bacteria that lives in your mouth. [1]

These bacteria live on all the surfaces within your oral cavity, like your teeth, gums, tongue, and the floor of your mouth.

Similar to the gut microbiome, the oral microbiome needs bacteria to be healthy. The microbial communities in the human mouth help to support the health of your mouth and entire body. Even “pathogenic” bacteria, known to cause disease, are generally present in certain amounts.

More than 700 species of bacteria have already been identified in the human oral microbiome. This collection of bacteria is second only to the gut microbiome for diversity and bacterial population. [2]

One major reason the oral microbiome is important is that it’s the largest “seeder” of bacteria to your gut—because you swallow 140 billion organisms per day! If your oral health is out of whack, it can affect your gut microbiome’s health, too. [3]

Why is this so important? Because if you want to live a healthy life and prevent or reverse disease, the root cause of your health problems must be addressed. For many people, this root cause lies with the oral microbiome… and they’re not even aware of it.

5 Ways Your Oral Health Affects Endocrine Health

It’s fairly well-established that your gut microbiome has an impact on endocrine health and disorders, like diabetes, adrenal fatigue or insufficiency, and even women’s health concerns. [4]

As it turns out, the same is true about your oral microbiome. A 2018 review of the current research explains how dysbiosis of the oral microbiome is related to: [5]

  • Diabetes
  • Adverse pregnancy outcomes (APOs)
  • Obesity
  • PCOS

And it doesn’t stop there …

1. Diabetes

The most well-known endocrine disorder, diabetes, is understood to be preventable in many cases. It’s a disease that has “multiple etiologies,” or a wide range of factors that are known to increase your risk. One of these etiologies is the oral microbiome.

The link between periodontitis (gum disease) and diabetes is pretty clear—if you have gum disease, you are far more likely to suffer from diabetes (and vice versa). [6]

Patients with both uncontrolled diabetes and chronic gum disease have significantly dysbiotic oral microbiomes. [7] This means they test for high levels of pathogenic bacteria but have fewer species and communities of “commensal” bacteria (sometimes called “healthy” bacteria).

2. Menopause

As you can imagine, the oral microbiome changes throughout menopause (just like your gut microbiota). Post-menopausal women are also at a greater risk of a number of issues related to bacterial communities, such as estrogen deficiency, periodontitis, and overall chronic inflammation.

Alterations in the oral microbiome during menopause aren’t consistent so far in the available research we can access. However, here’s what we do know:

  • Certain bacterial species, including dentium and A. geminatus, are found in higher concentrations in older women. [8] Both of these may be related to the chronic inflammation often seen in post-menopausal women as well as their increased risk for gum disease.
  • Dry mouth is more common during and after menopause. This decrease in saliva production is associated with issues such as bad breath, dental caries (cavities), oral thrush (Candida overgrowth), and generally declining oral health in older women. [9, 10]
  • Dysbiosis in the oral microbiome is associated with higher levels of gingivitis and full-blown periodontitis in postmenopausal women.
  • Menopausal women more frequently suffer from burning mouth syndrome compared to those in other stages of life. [11]


Polycystic ovary syndrome, or PCOS, is an endocrine disorder responsible for more cases of infertility than any other single cause. It’s already linked to dysbiosis in the gut microbiome. [12, 13]

A small 2016 pilot study found that women with PCOS had fewer strains of Actinobacteria, a commensal family of bacteria, than healthy controls. [14] While this isn’t conclusive proof of anything quite yet, it’s possible that oral health plays an important role in the progression of PCOS.

4. Obesity

Nearly 40 percent of Americans were obese between 2015-2016, according to the CDC. Obesity, like many other endocrine diseases, is multifactorial (not just one trigger is to blame).

A fascinating study in 2009 examined over 500 samples of oral bacteria in men and women, a little over half of whom were known to be obese. [15] One bacterial strain, in particular, Selemonas noxia, was found in significantly higher concentrations in the obese subjects.

In fact, 98.4 percent of the subjects with obesity could be identified on paper by the presence of that bacteria alone, which was not present at those levels in any of the healthy weight subjects.

5. Pregnancy & Delivery Complications

Known as Adverse Pregnancy Outcomes, APOs, issues with pregnancy and delivery may also have their roots in a dysbiotic oral microbiome.

When I work with women working to conceive, I stress the importance of addressing dysbiosis and any signs of gingivitis or gum disease before conception if possible.

Dysbiosis of the oral microbiome has been associated with:

  • Intra-amniotic infection/inflammation
  • Preterm birth
  • Miscarriage
  • Stillbirth

Is your oral microbiome dysbiotic?

There are a few tests that your dentist can administer to test your oral microbiome, but they’re not widely available yet.

The simplest way to identify a dysbiotic oral microbiome is to look for the signs:

  • Cavities
  • Bad breath
  • Chronic gingivitis
  • Gum disease

All of these are, for the most part, preventable. If you’re experiencing them, something is out of order with your oral microbiome.

Another major hint that you have a dysbiotic oral biome is your diet. High-sugar/high-carb diets are the hardest on your oral microbiome, so if you regularly eat sugary, starchy, processed, and/or acidic foods, chances are that you might need to address your oral health.

How to Improve Oral Microbiome Health

There are a few different processes involved in bumping up your oral microbiome health: disorganizing existing bacteria, supporting/increasing commensal bacteria, and avoiding bacteria-killing habits.

To DISORGANIZE your oral bacteria:

  • Floss every day.
  • Brush your teeth at least twice a day, and after foods or drinks full of sugar, acid, or processed chemicals. (BONUS tip: Toothpaste is not)
  • Scrape your tongue.

To INCREASE your commensal bacteria:

  • Add prebiotic foods to your diet, like bananas, onions, leeks, garlic, asparagus, and apples.
  • Try oral probiotics, chewable tablets that contain mouth-friendly commensal bacteria strains.
  • Start oil pulling with coconut oil.

To AVOID building up unhealthy oral bacteria or killing off the good stuff:

  • Throw away all conventional mouthwash — it acts as an antibiotic for your mouth! That can help on an incredibly rare occasion but isn’t appropriate for everyday use.
  • Stay away from processed, acidic, or sugary foods/drinks when you can.
  • Try mouth taping at night.
  • Get a professional cleaning at your dentist’s office every 6 months.


Mark Burhenne, DDS, knows that the mouth is the gateway to health in the rest of the body. He is a co-founder of and the author of the #1 bestseller, The 8-Hour Sleep Paradox, and is a practicing sleep medicine dentist in Sunnyvale, California. Dr. Burhenne has been practicing dentistry in the greater San Francisco area for over 30 years.

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