I talk a lot about protecting the oral microbiome. I also tell you to brush twice a day, floss, and remove plaque.
Those two pieces of advice can sound contradictory. If the bacteria in our mouths are important, why are we constantly trying to remove them?
The answer is that removing accumulated plaque is not the same thing as trying to eliminate the oral microbiome.
Within seconds of cleaning a tooth, saliva forms a thin, protective coating over the enamel called the pellicle. Bacteria attach to it and begin building communities surrounded by a matrix of complex sugars, proteins, fats, and DNA.
That is biofilm, and it is a normal part of the mouth.
Some of the organisms living there compete with potentially harmful microbes, interact with the immune system, influence acidity, and metabolize compounds in our food and saliva. Certain bacteria, especially on the tongue, convert nitrate from foods like leafy greens into nitrite. That nitrite can then contribute to nitric oxide production, which supports blood-vessel function and circulation.
So biofilm itself is not the problem. The better question is: what kind of biofilm is the environment in your mouth encouraging?
As biofilm grows, the conditions inside it change. Trouble begins when the environment starts favoring the bacteria and microbial activity associated with cavities or gum inflammation.
Around and beneath the gumline, accumulating plaque can trigger inflammation. That inflammation changes the local environment and nutrient supply, sometimes favoring bacteria that sustain even more inflammation. In susceptible people, that feedback loop can contribute to periodontal disease.
Cavities develop for a different reason. Bacteria in plaque ferment sugars and other carbohydrates into acids. Saliva helps neutralize those acids and gives enamel time to recover, but frequent snacking and sipping shorten that recovery time. Sucrose poses an extra problem because certain bacteria can use it not only to produce acid, but also to make extracellular sugars that help them stick to the tooth and strengthen the plaque matrix.
This is why I care as much about how often you eat sugar as how much you eat.
Saliva is part of this environment too. When saliva flow drops—from dry mouth, mouth breathing, medications, or dehydration—you lose some of the buffering and clearance that help keep the biofilm stable.
Brushing and flossing break up accumulating plaque without sterilizing the mouth. They change the environment where bacteria live and help prevent the conditions that favor cavities and gum disease.
There is another reason physical disruption matters: as biofilm matures, its matrix can make the organisms inside it harder for antimicrobials to reach. Rinsing with mouthwash is not a substitute for actually breaking up the biofilm.
For years, much of the messaging around oral care was built around a simple idea: plaque is bad, germs are bad, kill and disinfect.
The biology is far more interesting and complex than that.
The goal is still to brush, floss, and control plaque. But it is also to give your mouth time to recover between carbohydrate exposures, protect your saliva, and eat nitrate-rich foods like leafy greens that support microbial functions you actually want. It means being thoughtful about products designed primarily to kill bacteria rather than assuming that more antimicrobial activity means better oral health.
The future of oral care is not about getting better at killing bacteria. It is about getting better at shaping the environment they live in, because what those bacteria do does not stop at the gumline. They help protect our teeth and gums, participate in immune signaling, and even contribute to nitric oxide production that affects the rest of the body.
Until next week,
Dr. B
P.S. Many of you ask me what I use. Here is what’s in my bathroom cabinet:
7 things I do every day to protect my nitric oxide