Everyone wants a beautiful, bright smile. But at what cost? If you are wondering if teeth whitening products are safe for your oral microbiome, then read on. We will review what teeth whitening treatments can do to the bacteria in your mouth. We will discuss things you can do to improve your oral microbiome naturally even while cleaning stains off of your teeth or giving them a whitening treatment. While white, sparkly teeth are beautiful, even more beautiful is a healthy mouth. A healthy mouth paves the way for a beautiful, healthy body. We can thank our oral microbiomes for that.

If you are feeling like your smile is a bit dingy, maybe you are looking for tooth whitening treatments. Teeth can get yellow as we age. Foods and beverages can stain them. Teeth can change color due to internal damage.

The burning question for my friends and family was- what is the best teeth whitening treatment for the oral microbiome? But before we answer this question…

What Is the Oral Microbiome?

Over 20 billion bacteria live in your mouth, along with fungi, parasites, viruses, and bacteriophages. A diverse ecosystem in the mouth, it is known as the oral microbiome. This collection of microbes is mostly harmless or beneficial and is simply referred to as the “good bugs.” There are also “bad bugs” which are microbes that can cause disease when they get the opportunity.

With plenty of good bacteria taking up the available space in the mouth, you have a healthy mouth free of cavities, gum disease, root canal infections, bad breath, and more. Bad bugs can’t get a leg up and the microbiome is peaceful and harmonious. When the good bugs are killed off through antibiotics, a low-fiber diet, or an infection, bad bugs can rise to power, causing imbalance (or “dysbiosis”). Oral dysbiosis can show up as cavities, bleeding gums, root canal infections, bad breath, gum disease and more.

What are Teeth Whiteners?

Whiter and brighter smiles are in demand, especially since most people can get them at home now. But not all teeth whitening treatments are created equal, and some can cause harm. For a comprehensive review of tooth whitening treatments from a functional dentist, see Dr. Mark Burhenne’s 12 Best Ways to Whiten Teeth.

Some of the most popular teeth whitening ingredients are hydrogen peroxide and carbamide peroxide. They are used by dentists to whiten teeth and are found in at-home teeth bleaching kits.

Hydrogen peroxide is a natural agent that your body uses and that the microbiome uses. The question is: how strong a solution of hydrogen peroxide (H2O2) is safe for the oral microbiome? Dentists use much higher concentrations of hydrogen peroxide to whiten teeth. At-home treatments are less concentrated.

Teeth Whitening Agents Can Harm the Oral Microbiome

Hydrogen peroxide isn’t the greatest thing for your healthy oral microbiome. It’s a killer. The higher the concentration of hydrogen peroxide, the more likely that your good bacteria in the mouth will take a hit. Three percent hydrogen peroxide, found at the grocery store, is too high to use in the mouth without a healthcare practitioner’s oversight. Hydrogen peroxide can get into bacterial cells and damage their energy production machinery, harming DNA structure, and killing them.1 It a potent and biologically active substance. It causes oxidative damage to lipids, proteins, and nucleic acids.2

10% carbamide peroxide isn’t as strong as hydrogen peroxide and is the standard in dental clinics. Carbamide peroxide breaks down to urea and only 3% H202.1  It inhibits Streptococcus mutans and lactobacillus species in cell studies and in animal studies. Carbamide peroxide inhibited S. mutans, Streptococcus mitis, Streptococcus sanguis, Lactobacillus casei, and Lactobacillus acidophilus in vitro. It also killed oral microbiome biofilms more than 1% chlorhexidine (an antimicrobial used in mouthwash).3 It changes plaque (aka the microbiome) and salivary pH because it produces ammonia when it breaks down.1

Using hydrogen peroxide or carbamide peroxide can throw your oral microbiome out of balance, causing a condition known as black hairy tongue. Harmless, but annoying, it can give the tongue a furry appearance.

Hydrogen peroxide isn’t always friendly to your teeth, either. That’s why tooth whitening treatments can cause tooth sensitivity. They can deplete minerals from your teeth and make your enamel more rough.1 It’s because the whitening agent puts little microscopic nicks and dents in your tooth enamel. It can hurt if your enamel is already compromised. Hydrogen peroxide may also irritate your gums. Dr. Steven Lin, author of The Dental Diet, discourages people from using hydrogen peroxide mouthwash for these reasons.

Teeth Whitening Agents Can Treat Oral Dysbiosis

Image by Sabrina B. from Pixabay

There’s a flip side. Hydrogen peroxide has been known for quite some time to do good things when you’re dealing with oral dysbiosis. Oral dysbiosis is an imbalanced collection of mouth bacteria and microorganisms that cause unwanted symptoms in the mouth such as gum disease or cavities.

Dentists have reported that carbamide peroxide promotes gum health and decreases plaque and calculus (aka bacterial biofilms) on teeth since the 1970s.1 Peroxides have antibacterial and anti-cavity action in the mouth. Hydrogen peroxide might also fight oral dysbiosis by mechanically removing dead microbes from the tooth surface (debridement), and increasing oxygen to help heal gums. Some sources will say that teeth whitening keeps your mouth healthier or that it improves your mouth bacteria. What they mean is that by killing unfriendly bacteria, peroxides in teeth whitening products may be improving your oral health.

In one study, they showed that 6% hydrogen peroxide gel treatment at-home decreased Streptococcus mutans above and below the gumline, but 10% carbamide peroxide didn’t. Also known as Strep mutans, this bug is involved in cavities. Authors said that the teeth bleaching trays may have allowed more of the H202 to reach the bacteria above and below the gumline.

Under the supervision of a functional dentist or biological dentist, peroxide treatments may have a time and a place.

Some Studies Show No Change to Oral Bacteria After Whitening Treatments

Hydrogen peroxide and carbamide peroxide, common teeth whiteners, can kill friendly bacteria in the mouth. They can also kill unfriendly bacteria in the mouth. However, some studies have reported no lasting changes to the oral microbiome.1 This is pretty surprising.

After 30 days of at-home bleaching treatments, H202 6% did decrease S. mutans, but only temporarily. S. mutans was not permanently changed after using H202 or carbamide peroxide. The measurements were crude (colony-counting methods). They failed to show their PCR results and didn’t measure any other microbe except S. mutans.1 Other studies have shown little or no change in the population of cavity-causing bacteria when using bleaching agents over a very short period of time.1

One small study showed no change to the bacterial counts in saliva when using 37% carbamide peroxide treatment in the dental office followed by 10% carbamide peroxide in bleaching trays at night for three weeks.

There are a few possible explanations for why some studies don’t see lasting changes to the oral microbiota after bleaching:

  • Oral bacteria species can use up peroxide, so it disappears from the mouth more quickly
  • Oral bacteria species can resist peroxide or oxidative stress
  • Lactoperoxidase, an enzyme in the saliva, can transform peroxides so that they are not harmful to the microbiome1,2

How hydrogen peroxide works in the mouth is a complicated equation. While some studies show it doesn’t affect the oral microbiome, others show it does. I am skeptical that these studies that say there is no effect on the oral microbiome were equipped with the proper technology or looking at the right organisms or measuring them for the right length of time.

Oral Bacteria and Hydrogen Peroxide: A Two-Way Street

Some oral bacteria make hydrogen peroxide, which wards off oral pathogens, such as Strep mutans and Porphyromonas gingivalis.4 Oral bacteria that make hydrogen peroxide include S. sanguini, S. mitis. S. gordonii,and  S. oligofermentans. Oral bacteria Streptococcus oralis and S. uberis produce hydrogen peroxide and in vitro testing of these microbes as probiotics showed that they can whiten teeth.

Meanwhile, there are oral bacteria that can metabolize hydrogen peroxide, such as Neisseria sicca, Hemophilus segnis, Hemophilus parainfluenza, Actinomyces viscosus, and Staphylococcus epidermidis.2

Image by Gerd Altmann from Pixabay

Apply Teeth Whitening Agents to the Teeth Only

There are many different communities of bacteria in the mouth, which I discuss in my book, Heal Your Oral Microbiome. There are distinct oral bacteria that live below the gumline (subgingival), others that live above the gumline (on the teeth), some on the tongue, others in saliva, the throat, and the list goes on. When using teeth whiteners, one big advantage is that bleaching trays can deliver peroxides specifically to the teeth and not to the whole mouth. In contrast, an antibacterial mouthwash could have a wide effect in the mouth, killing bacteria throughout. If bleaching trays fit well, they can keep the peroxides on the teeth and hopefully very little on the gums, thereby sparing the rest of the good bacteria in the mouth. Indeed, one study stated that the peroxide treatment (delivered in bleaching trays) killed S. mutans at the gumline, but didn’t affect S. mutans in other areas of the mouth.1 We can presume that it didn’t kill friendly bacteria in other areas of the mouth, either.

A Healthy Mouth Is What Counts

Dentists often remark that their patients want whiter teeth but they aren’t very interested in their oral health. Let’s remember that white teeth are beautiful but they aren’t necessarily healthy. The real goal is a healthy mouth. Love your mouth. Make your mouth healthy. Focus on a healthy mouth, not just your pearly whites. Your heart, joints, metabolism, and brain will fare better if your mouth is healthy.

If you have a healthy oral microbiome, meaning no cavities, gum disease, root canal infections, bad breath, then you have a healthy oral microbiome already. You really don’t need to use peroxides in your mouth except to whiten teeth.

When it comes to H202 treatment, the best time to use it is when there is oral dysbiosis or a real infection that needs treatment or when you need to do a short-term whitening treatment. Work with your functional dentist to make sure you are using the right product at the right concentration. There are times when this may be a good idea. I gargled a diluted H202 solution when I had COVID as a way to lower the viral burden in my mouth. I knew it was probably affecting my oral microbiome, but the hit to my oral microbiota was worth it, given the risk of having a severe case of COVID.

What are the best teeth whitening treatments for the oral microbiome?

If teeth whitening with an at-home bleaching kit is something that makes you feel great, well, we all know beauty comes at a cost. Maybe you’re getting married or you’re graduating. Or maybe you’re feeling insecure and having a bright smile would make you feel more confident. You can still protect your friendly oral bacteria.

Here is what you can do to minimize the impact of peroxide teeth whiteners on your oral microbiome.

  • Apply teeth whiteners to teeth only, not your gums or the rest of your mouth. That way only the bacteria living on your teeth will be affected.
  • Get a whitening treatment by a dentist, who can keep the bleaching agent on your teeth only, and prevent it from touching your gums.
  • Always use bleaching trays to limit the exposure of your mouth to whitening agents.
  • Use the lowest concentration of peroxide needed to get the whitening effect you want for your teeth.
  • 10% carbamide peroxide whitening solution at-home whitening agents may be better for your mouth bacteria than 6% hydrogen peroxide. Carbamide peroxide is only 3% hydrogen peroxide when it breaks down.
  • Don’t whiten your teeth excessively, only to the minimum level that meets your satisfaction
  • Continue eating an oral-microbiome-enhancing diet, which is sugar-free, whole foods, plant-based and contains plenty of fiber.
  • Take oral probiotics or probiotic mouthwash to replenish oral bacteria.
  • Take oral prebiotics to feed a healthy oral microbiome.

Image by Free-Photos from Pixabay

Promote a Healthy Oral Microbiome with These Teeth Whitening Tips:

You don’t need to do teeth whitening treatments with hydrogen peroxide or carbamide peroxide to get beautiful, white teeth. In fact, there are some natural and microbiome-friendly teeth whiteners right at your fingertips.

  • Electric toothbrushes. These toothbrushes are better than manual toothbrushes at removing stains from teeth.
  • Hydroxyapatite toothpastes. This is a great agent to rebuild tooth structure, polish stains off of teeth, and it seems to prevent bacteria from attaching to teeth without killing them. It also brightens teeth from the inside out.
  • Baking soda toothpastes. These are the best for removing stains from yellowing teeth when compared to other toothpastes. Baking soda also removes plaque.
  • Oral probiotics. Certain probiotics may be able to promote teeth whitening naturally.
  • Brushing, flossing, and dental cleanings.

Other Things You Can Do To Get Whiter Teeth

  • Quit smoking and other tobacco products
  • Avoid these foods that stain teeth or rinse with water after consuming them:
    • Balsamic vinegar
    • Berries
    • Candy
    • Carbonated drinks
    • Citrus fruits
    • Coffee
    • Soy sauce
    • Tea
    • Tomato sauce
    • Wine

Oral Microbiota Bounce Back

The oral microbiome recovers. When you kill off your oral bacteria, they will eventually come back. We cannot live bacteria-free. So, when we use antibiotics or antibacterial mouthwash or hydrogen peroxide teeth whiteners, the microbiome will decrease. It will be changed temporarily. It might be changed permanently. But it always grows back. We know that it grows back pretty quickly even after it is killed. The concern is that it might grow back as an imbalanced, less healthy community of bugs. We could accidentally kill off beneficial species that cannot regrow.

Most of the studies mentioned in this article did not measure the microbiome with sophisticated technologies such as PCR or sequencing. They couldn’t detect subtle changes to the microbiome after teeth whitening treatment. They were more interested in Streptococcus mutans, a cavity-promoting bacterium, than the impact of tooth whiteners on the millions of other good bugs in the mouth. They only studied the effect of teeth whitening treatments on the oral microbiome for short periods. So, there is much more to learn about teeth whiteners and the oral microbiome.


  1. Briso A, Silva U, Souza M, Rahal V, Jardim Junior EG, Cintra L. A clinical, randomized study on the influence of dental whitening on Streptococcus mutans population. Aust Dent J. 2018;63(1):94-98.
  2. Franz-Montan M, Ramacciato JC, Rodrigues JA, Marchi GM, Rosalen PL, Groppo FC. The effect of combined bleaching techniques on oral microbiota. Indian journal of dental research : official publication of Indian Society for Dental Research. 2009;20(3):304-307.
  3. Yao CS, Waterfield JD, Shen Y, Haapasalo M, Macentee MI. In vitro antibacterial effect of carbamide peroxide on oral biofilm. Journal of oral microbiology. 2013;5.
  4. Abranches J, Zeng L, Kajfasz JK, et al. Biology of Oral Streptococci. Microbiology spectrum. 2018;6(5).

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.