How Your Oral Biome Influences Your Overall Health

Inline_Oral_BiomeIn response to my post on oral health a few weeks ago, one reader offered a comment about the oral biome, and it’s a worthy follow-up, I’d say.

The human oral cavity is home to hundreds of microorganisms. Latest estimates place the number of bacterial species in your mouth at close to 700, with the odd fungus, protozoa and even virus thrown in for good measure. This oral microbiome isn’t a whole lot different than that of our gut, but where things get interesting is when we consider the diverse range of habitats within the mouth: teeth, tongue, cheeks, gums, tonsils. All provide different living conditions for those microorganisms that colonize them, but that diversity of habitats also encourages a diversity of species.

And it’s fair to say that human microbiological research as a whole began with the mouth. In 1683, Dutch businessman and self-taught scientist Antoni van Leeuwenhoek scraped off a bit of plaque from his teeth, slotted it under his home-made microscope, and was the first person ever to physically see his own bacteria. Suddenly, one’s body was no longer wholly one’s own.

Since then, the study of oral microbiology has waxed and waned, but in recent years the topic has been a hotbed of activity in the scientific sphere. While the health of your gut flora is important, it’s becoming increasingly apparent that so, too, is the health of your mouth flora.

What Is the Function of the Oral Microbiome?

By now, you’ve firmly wrapped your head around the importance of homeostasis. As hocus-pocus as it sounds, achieving equilibrium in the body is critical to maintaining robust health.

This Zen-like mantra applies whole-heartedly to the oral microbiome. In a healthy mouth, your microflora and their by-products play an essential role in the salivary immune system, bravely warding off pathogenic invasion down your throat and into your nether regions. These microscopic communities also aid in digestion, protect your teeth against acidic foods and substances, and process vitamins that are critical to our general health.

The little guys in your mouth can even play a role in odors. That glass of red smell a bit off? It could be that your oral community is haywire, rather than a crappy cork or a blast of sulfites.

And the party doesn’t end in your mouth. Research published a couple of years ago demonstrated that the small microbial population of the human lungs are populated, at least in large part, by the same microbiota occupying our mouth. It seems that the lungs, and presumably other parts of the body, “borrow” bacteria from the mouth to ensure they’re meeting their biological quota. Studies have even shown that the placental microbiome more closely resembles that of the mouth than any other part of the body. In this way, the mouth acts as a biodiversity reservoir for the rest of the body.

When Your Oral Environment Is “Off”

Back in 1929, an article published in the Journal of the American Dental Association entitled “Animal Parasites of the Mouth” first suggested that these might directly contribute to dental disease. Of those dental diseases, periodontal disease and gingivitis are the big players, and in fact contribute to the second most common human infection: dental cavities. (hint: the common cold is, not surprisingly, takes top billing).

Slowly, our understanding of the dynamics of oral disease is improving. After years of research, scientists can now use changes in the oral microbiome to predict the onset of dental cavities, months before those cavities become visible. Research has also shown that the development of oral microbiota is directly correlated to age, meaning the older one gets, the more diverse their oral microbiome should be. Those who develop cavities, however, invariably have a less mature (and hence less diverse) microbiome.

But that’s just the tip of the iceberg. Oral bacteria have now been implicated in a wide range of systemic diseases, including diabetes, rheumatoid arthritis, cardiovascular disease, colorectal cancer, and pancreatic cancer.

Take pancreatic cancer, for example. Research shows that those with significant counts of P. gingivalis and A. actinomycetemcomitans in the mouth have a higher risk of pancreatic cancer. A predominance of Fusobacteria and its genus Leptotrichia, on the other hand, is associated with a decreased risk of pancreatic cancer. It’s not coincidence.

And while the linkages between our oral microbiota and systemic disease may vary, there’s likely one thing they all have in common: our old nemesis—inflammation. Pathogenic species like P. gingivalis promote inflammation in the mouth, thereby contributing to oral disease, but they also exacerbate inflammation in the rest of the body. 

Other typical pathogenic bad boys, like Streptococcus mutans and Candida albicans, produce much the same inflammatory effect. And considering that oral strains have been found in other far off parts of the body, it’s not overly surprising.

The Decline of the Modern Oral Microbiome

A study published in the Journal of Nature Genetics took an interesting look at our oral microbiome history over the millennia. Using calcified dental plaque on ancient teeth, they were able to produce a living oral record through the ages. The research showed that the two major shifts in oral microbiological biodiversity occurred first when we shifted from hunter-gathering to farming, and again when we started mass-producing flour and sugar during and after the Industrial Revolution.

It was at this point that our oral microbiomes became dominated by cariogenic bacteria, and it’s been a slippery slope ever since. As the research team concluded, “modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in postindustrial lifestyles.” 

On a lighter note, dental archaeology has revealed some seriously interesting details not only about our own ancestors, but about our close cousins the Neanderthals. DNA extracted from the teeth of five Neanderthals in northern Spain suggests that they may have been pursuing the odd “intimate liaison” with our own human ancestors. How’d they figure that one out? By identifying the presence of a microbe that causes gum disease in modern humans. Not only does this tell us that these folks enjoyed inter-species partnering from time to time, but more to the point, it indicates that many of the microbes in our current oral microbiome were already present at least 50,000 years ago, albeit in a more diverse fashion.

Which brings us around to something else of interest. Inter-species kisses aside, scientists have now shown that an average of 80 million bacteria are swapped between kissers, with those of the French kissing inclination are probably swapping a whole lot more than that. I’ll leave that for your consideration. 

It Comes Down to Balance

A traditional Western take on things is to create two mental bins: one for positive, and one for negative. Then, based on popular consensus, our minds thriftily compartmentalize the phenomena in our lives into one of the two bins. That thing is either good or bad – there’s no middle ground.

Primal thinking dictates a shift away from this black and white view of the world. We recognize that there’s rarely hard and fast “good and bad,” but more a sliding scale that becomes less desirable the further we move away from balance. When homeostasis is achieved, our health flourishes, while the opposite can be said for the outer fringes of that scale.

This, as it happens, is a great way to view the oral microbiome. Far from CW’s anti-microbial standpoint, I’ve already mentioned the diverse and critical roles that the microorganisms in our mouths play in our overall health. When the scale shifts, however, we see an overabundance of pathogenic bacteria, influential in both dental and systemic disease.

It’s that tilt of the scale that we want to avoid. And to avoid it, we need to understand just what’s going on in the microbial communities on our teeth, tongue, gums and cheeks.

Take plaque, for example. One study found that rather than just being composed of blobs of malicious organisms, plaque is actually a highly organized collection of both symbiotic and pathogenic bacteria and fungi that changes over time.

Layer upon layer of microorganisms attach themselves to the tooth, with each layer creating just the right conditions for the next species to move in and set up shop. It’s a very structured system of early colonizers, bacterial yeomen, and microbial aristocrats that are insulated by the vagaries of the mouth through their protective layers of insubordinates.

As with any ecological community, all the species have their place and (in the right amounts) ensure homeostasis is maintained within the mouth. It’s when the pathogenic species, like P. gingivalis, S. mutans and C. albicans, gain the upper hand that things start to go downhill. The key, then, is to encourage all species to live in relative harmony, like one big happy family.

Supporting a Healthy Oral Biome

On the one hand, we have many dentists advocating mechanical abrasion (aka brushing and flossing) as the only way to keep the pathogenic bacteria on your teeth and gums in check. On the other, there are those who recognize the amazingly beneficial role that certain microorganisms play in maintaining a healthy oral (and whole-body) environment. Those people recognize that brushing isn’t selective, and along with mouthwash and fluoride toothpastes, it’s wiping out ALL the bacteria, bad AND good. Kind of like antibiotics do elsewhere in the body.

Studies indicate that beneficial oral bacteria have a far harder time re-establishing themselves in the mouth after disturbance than do pathogenic bacteria. Think of the pathogenic types as weeds—they thrive on disturbance, and can easily out-compete the slower growing beneficial microorganisms under stressful conditions.

With this in mind, it seems prudent to advocate for less of a scorched earth style of oral hygiene and more of a supportive, equilibrium-restoring approach.


If the study I mentioned earlier that examined the change in our dental health over time is anything to go by, turning back the clock and returning to a more Paleolithic (i.e. Primal) style of eating should encourage a more diverse oral microbiome. I also can’t help but think that opting for organic produce would help to re-introduce many symbiotic or commensal microorganisms to our mouths that would otherwise cease to exist on sprayed fruits and veggies. A little dirt in some cases might not be a bad choice either.

Beyond dietary variation, look to alkalizing, nutrient-rich, anti-inflammatory foods to support a healthy microbiome. Anecdotally at least, vitamin C intake appears to be positively correlated with a health oral microbiome, along with A, D, K2 and CoQ10.

Like our gut and other microbiomes of the body, the bacteria living within our mouths behave diurnally, which is to say they’re most active during the day and switch into “maintenance mode” during the night. But that diurnal pattern isn’t driven by light (it’s virtually always dark in there), but by our eating patterns. Since we don’t generally eat during the night, the bacteria in our mouths are rearing to go in the morning at breakfast time and begin to wind-down after dinner every evening.

With this in mind, eating regularity is key. Studies show that disruption to the normal circadian order of things via the likes of jet lag, can dramatically alter the composition of not only your gut microbiome, but your oral one as well. The result is dysbiosis, and, in the gut at least, scientists have found an increase in certain bacteria linked to obesity in people who have flown long distances and hence skipped a few time zones.

“Regularity” might simply mean confining all of your daily eating to certain hours of the day (i.e. an 8 a.m.-6 p.m. window—or shorter), or it could mean imposing Victorian-style meal times of breakfast at 8, lunch at 12 and dinner at 6. And for those frequent fliers who spend the odd day or three abroad, perhaps maintaining a regularity of eating that mimics your home time zone, regardless of what time of day it is at your destination, might be worth the hassle.

The same might apply to variable shift workers. With a notable lack of studies in this area, it’s up to you to experiment and see how your mouth responds.

And remember, saliva is your friend, so keep hydrated. More saliva will have a buffering effect on your teeth, and promote a healthier ratio of beneficial bacteria.


There’s not a lot here that will surprise you. Stress results in dysbiosis of the gut, and it does the same in the oral microbiome. While studies are notably lacking on the effect of stress on the human oral microbiome, work done on squirrels gives a good indication. Maintaining an oral bacterial equilibrium, which is critical to oral and systemic health, means keeping chronic stress to a minimum.

Then there’s smoking. Those nasty warning pictures on cigarette packaging really don’t exaggerate, and the detrimental effects of cigarettes have been shown to extend to the bacteria living in our mouths. More smoking means a greater frequency of pathogenic species.

Oral Treatments

We’ve now drifted into contentious waters. Conventional oral “hygiene” suggests cleanliness, but what is a clean tooth? There are plenty within alternative health spheres who believe that a certain amount of plaque is a good thing, provided it doesn’t get out of hand. OraWellness, who I mentioned a few weeks ago, is one of those groups. Yet, while it does make sense, I’ve struggled to find evidence to substantiate these claims. Who’s going to fund a study that advocates a shift away from toothpaste, toothbrushes, and the billions of dollars they haul in every year?

Once again, I find myself taking the middle ground. I brush, but not too hard, and I don’t stress if I miss a round from time to time. I stay away from fluoride, strong antibacterials, and conventional toothpaste in general. I continue to floss daily. And I’ll swish with salt water on a regular basis. It’s a simple strategy, but it works.

The takeaway here is likewise uncomplicated. Your oral health is what you make it. Diversifying your diet, eating Primally and regularly, minimizing stress, and adopting a more holistic oral care regime will go a long way towards sustaining oral and whole health. 

Thanks for reading, folks. Have you discovered anything about the oral microbiome or good oral care that I haven’t covered? Comments to add? Questions? Share them on the board, and have a good end to your week.


TAGS:  immune health

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending more than three decades educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates flavorful and delicious kitchen staples crafted with premium ingredients like avocado oil. With over 70 condiments, sauces, oils, and dressings in their lineup, Primal Kitchen makes it easy to prep mouthwatering meals that fit into your lifestyle.

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