What makes a good toothpaste? We put toothpaste in our mouths every day, but what is in there? Is it safe? Does it really improve our oral health? It may be surprising that not everything found in traditional toothpastes are safe for our mouths. Some toothpaste ingredients are toxic to the lining of our mouths.1 And since the oral microbiome- the bacteria living in our mouths- have only recently stepped into the spotlight, there are toothpaste ingredients that  harm these friendly bacteria.

Whether you’re looking for the best toothpaste for gum disease, bad breath, or cavities, read on to learn what ingredients to look for and what toothpaste ingredients to avoid. Both clinicians and consumers need the 411 on healthy, natural toothpastes that can build up a healthy oral microbiome and ward off cavities, gum disease, and bad breath.

Thank you to our sponsor, RiseWell, for making this blog possible.

RiseWell has an impressive line of non-toxic oral care products. They believe in clean ingredients that are evidence-based. I use them myself and have gifted them to my family members as a healthier alternative to traditional toothpastes.

Does Toothpaste Kill Good Bacteria?


 Yes, traditional toothpastes are antibiotics.


Before you gasp in dismay, this isn’t too shocking, right? For decades we have been taught that it is the evil bacteria in our mouths that cause cavities and gum disease. Why not use bacteria-killing agents in our mouths every single day? Indeed, because people don’t keep up with oral hygiene, antibiotic substances were added to help prevent oral dysbiosis.2 Toothpastes aren’t selective. They can harm the entire oral microbiome in the effort to kill the “bad guys.”3,4

But it’s the dawn of a new era. We are now acknowledging that the microbiome is much, much bigger than we once thought. It’s not just the pathogens we have to contend with. We have to contend with the entirety of the good and harmless bacteria, too. We have to consider that nourishing the good bacteria -not killing them- can protect us from the bad.

Just as we are doing in the gut microbiome, we need to move away from passing out antibiotics like candy. Killing is not the microbial strategy of the future. Because in the process, we kill the microbes that protect and defend us from disease. Antibiotic toothpastes (whether conventional or herbal) could be disrupting the healthy oral microbiome and encouraging oral dysbiosis.3

A number of substances are added to toothpastes to make them antibacterial. Crest toothpaste, Proctor & Gamble3 killed “bad” oral bacteria and Candida albicans but also killed beneficial mouth bacteria, such as Streptococcus salivarius and Lactobacillus salivarius. Colgate Total 12 White, Colgate & Palmolive, Co. killed all tested bacteria (Streptococcus mutans, Streptococcus sanguinis, and Enterococcus faecalis).5

Many of these agents found in traditional toothpastes do decrease plaque scores and help to reduce cavities. However, they may be too harsh and they may not be necessary for all people.

Antibiotic Ingredients in Traditional Toothpastes

  • Sodium fluoride3
  • Stannous chloride3
  • Sodium lauryl sulfate (SLS)5
  • Cocamidopropyl betaine5
  • Sodium lauroyl sarcosinate5
  • 0.2% chlorhexidine digluconate (a strong antibiotic usually found in mouthwash)
  • Cetylpyridinium chloride2
  • Triclosan2


Herbal or Natural Antimicrobial Toothpastes

There are antimicrobial natural toothpaste ingredients available too. Chamomile, echinacea, sage, myrrh, rhatany, and peppermint oil are natural antibacterial agents. Lime extract and fennel extracts have been used in toothpastes for their antibacterial and anti-Candida activity.2 Theobromine from cocoa beans and chitosan-containing toothpastes in one study were antimicrobial against three pathogens.5

Image by Daniel Albany from Pixabay

Use Antibiotic Toothpastes When You Have Oral Dysbiosis

Bacteria-killing toothpaste is best suited for someone who has signs of oral dysbiosis. That is, an imbalance of bacteria in the mouth that causes symptoms such as cavities, gingivitis, gum disease, bad breath, or root canal infections. By having these symptoms, it suggests that the oral microbiome is out of balance and could benefit from killing off certain opportunistic and pathogenic species in the mouth.

Pathogenic bacteria in the mouth do not necessarily cause disease and therefore not everyone needs to use antibiotic toothpastes.3 In a study of 20 healthy people, average age 22 years old, many showed pathogens in the mouth and/or on their toothbrushes without any sign of oral dysbiosis.3 Historically, one species of bacteria has been given all of the blame for cavities: Streptococcus mutans. However, the relationship between Streptococcus mutans and cavities is not absolute. Some people may show high levels of Streptococcus mutans, but no cavities. Others may have cavities but there are no Streptococcus mutans bacteria present.6 It has since been discovered that cavities are caused by dysbiosis of multiple mouth bacteria, not just Streptococcus mutans.7

What this means is that there is a lot more at play in a healthy mouth than bad bugs. The strategy to kill bacteria is too one-sided. We need to balance out the other side of the equation for oral health. Build good bacteria to defend us from bad bugs. Boost the immune system and make good dietary choices to ward off dysbiosis. A healthy mouth (that eats a healthy diet) should not be using antibiotic toothpastes year-round just to maintain health.


Ingredients to Look for in Toothpastes

Typical ingredients in toothpaste are fluoride, abrasives, and detergents.1 Toothpaste is supposed to help remove debris and bacterial biofilms but it can also make toothbrushing more fun, freshen breath, and whiten teeth.

Brushing Away Mouth Bacteria

The most powerful effect of brushing teeth twice daily is to mechanically disturb bacterial biofilms on teeth and gums.8 Toothpaste is more of a bystander in this process. By gently scrubbing away bacterial communities, it prevents bacteria from building strong, potentially harmful empires. The same goes for bacteria on the tongue. By literally breaking up bacteria that are trying to band together, you can reduce cavities, gingivitis, and gum disease, and keep teeth stronger.9

Abrasive agents such as calcium carbonate (natural chalk) and clay are gentle and safe for tooth enamel. Hydroxyapatite toothpaste is gently abrasive and may be a good choice for sensitive teeth. Amorphous calcium phosphate is another abrasive that helps to remineralize teeth and prevent decay.8 Abrasives such as silica are commonly found in toothpaste and are thought to be nontoxic, stable, and harmless in the mouth.10

Toothpaste powders, even baking soda with salt, can be too abrasive if you brush too hard or if there is gum recession.8

Charcoal in toothpaste is marketed as a whitening agent due to its potential to clean teeth by adsorbing colored substances. But scientific proof that it whitens teeth effectively remains to be seen.7 It can be too abrasive on tooth enamel and harm teeth.11 Finely powdered charcoal in one study was said to be minimally abrasive and safe for enamel.7

Baking soda (sodium bicarbonate) has been used since the 1970s as part of the Dr. Paul Keyes technique of baking soda and hydrogen peroxide at-home dental care. Baking soda can reduce plaque and bleeding gums.12 It does not directly kill bacteria but acts as a cleansing agent. It can remove mucus and food particles. It shifts the pH in the mouth to be more alkaline or basic, which can promote strong teeth while discouraging certain acid-loving oral bacteria from growing. It may suppress the harmfulness of bacteria even when numbers are high in the mouth.13 And it has reduced Streptococcus sobrinus and Streptococcus mutans “bad oral bacteria” in animal studies.14

Minerals that Build Strong Teeth

Hydroxyapatite is the fundamental hard ingredient in teeth and bones, made from calcium, phosphorus, oxygen, and hydrogen. Available as a toothpaste ingredient, hydroxyapatite fights cavities on par with fluoride and has been suggested as an alternative to fluoride.15,16 This is a great agent to rebuild tooth structure (known as remineralization).17 It polishes stains off of teeth. Hydroxyapatite seems to prevent bacteria from attaching to teeth without killing them. There is still more to learn about hydroxyapatite and the oral microbiome, but since it is basically a safe material identical to bone, I don’t think of it as a threat to the friendly bacteria in the mouth.

Fluoride treatments strengthen and rebuild teeth. Calcium, found in the tooth’s hard hydroxyapatite material, can be swapped out for fluorine, which makes teeth more durable and less susceptible to cavities.18 The World Health Organization recommends brushing twice daily with fluoride toothpaste to prevent cavities. On the flip side, fluoride is toxic to all cell types,1 kills oral bacteria,3 can cause fluorosis or brown mottling of teeth, and may cause neurotoxicity.19 In one study, fluoride toothpastes seemed to encourage oral pathogens while fluoride with arginine decreased those, but enhanced other periopathogens.20

The topic is hotly debated so do your research, talk with your dentist, and use fluoride carefully. Consider hydroxyapatite if you want an alternative.

Zinc is found in toothpastes and zinc is an essential mineral required for human health. Zinc citrate is used in natural toothpastes for bad breath. Zinc reduces bad breath by binding bad-smelling compounds made by bacteria in the mouth. Zinc lactate is an antibacterial agent and can harm the respiratory system. Doses of zinc lactate (0.1 -0.4%) in toothpaste could harm the mucosal lining.1  Zinc-hydroxyapatite effectively remineralized children’s teeth in a 1-year clinical study.17


Probiotic Toothpastes

Probiotic toothpaste ingredients can affect the oral microbiome, but not through killing mouth bacteria. They help crowd out pathogens. They make it hard for bad bacteria to bind to surfaces in the mouth. They interfere with the ways bacteria build a protective shield around themselves (known as a biofilm). They produce chemicals to repel bad bacteria, such as bacteriocin and hydrogen peroxide. Probiotic toothpastes can reduce inflamed gums and pathogenic bacteria in the mouth. However, probiotic toothpastes do not directly kill bacteria.5

Prebiotics for a Healthy Oral Microbiome

Prebiotics are substances that good bacteria use to live and grow. Often, prebiotics are nondigestible carbohydrates from the diet. For our purposes here, they are simple molecules such as arginine and nitrate.

Arginine is an essential amino acid with a role in blood pressure regulation and protein synthesis in the human body. Arginine in the mouth acts as a prebiotic. Bacteria transform arginine into ammonia, which makes the saliva more basic (non-acidic)20 and fights cavities.

Nitrate is a promising prebiotic for the oral microbiome. Nitrate encourages a healthier oral microbiome balance by helping good bugs grow and pushing out bad bacteria.21 We get 80% of nitrate from dietary vegetables and nitrate is high in lettuce and beetroot. Specifically, nitrate helps to increase Rothia and Neisseria species. It wards off periodontal pathogenic genera such as Porphyromonas, Fusobacterium, Prevotella, Leptotrichia and Alloprevotella. It reduces gingivitis and bad breath. It seems to prevent cavities by making the pH in the mouth more basic, producing ammonia, and burning up lactic acid.21

The human body cannot make nitrite. We depend on our oral bacteria to “eat” nitrate and produce nitrite so that we can make nitric oxide in the body. This is called the nitrate-nitrite-nitric oxide pathway. Nitric oxide is a vital substance for healthy blood pressure, cardiovascular health, and it even helps to defend the body by killing bacteria in the mouth and stomach.

Best Sweeteners for Toothpastes

Xylitol is a naturally occurring sugar alcohol found in plants such as in the Finnish birch tree. It is an anti-cavity agent, suppressing the growth of the bacteria implicated in cavities, Streptococcus mutans. Xylitol can also reverse cavities in children. While it reduces S. mutans, it doesn’t otherwise harm the normal oral bacteria.22 Xylitol starves out Candida species in the mouth, which makes it a good option for oral thrush. Xylitol makes it harder for Candida to bind to the mouth lining. Xylitol isn’t usually metabolized by lactobacillus bacteria, which helps to keep their numbers under control as well.23

Stevia is a sweetener from the plant Stevia rebaudiana, which may reduce plaque and inhibit lactobacilli bacteria. It seems to have a role in prevention of cavities. It is a good choice for sweetening toothpastes.


Enzymes to Protect the Oral Microbiome

Enzymes are one of the mouth’s primary defenses against pathogens. Toothpastes may contain lactoperoxidase, amyloglucosidase, or glucose oxidase enzymes. These enzymes can produce hydrogen peroxide and ward off bacteria, fungi, and viruses. Lactoperoxidase may simply keep bacteria under control, preventing streptococci and lactobacilli species from overgrowing.5 Bacteria in the mouth can make urease enzymes, which can produce ammonia, raising pH (promoting alkalinity), and reducing cavities.21

In one study, a toothpaste containing proteins and enzymes boosted salivary defenses and increased beneficial bacteria while decreasing periodontitis-related bacteria.24 In another study, a toothpaste containing enzymes did not have any antimicrobial activity on three pathogens.5


Antioxidants and Anti-inflammatory Plant Extracts for Oral Health

Plants can act as prebiotics for the oral microbiome as well as work to heal the mouth lining and calm inflammation. Aloe barbadensis is a calming, soothing medicinal plant often found in gut and oral health remedies. It has been shown to kill Streptococcus mutans, but not other pathogenic bacteria in the mouth.5 Green tea (Camilla sinensis) shows promise as a toothpaste ingredient for a healthy mouth. It reduces inflammation, is a potent antioxidant, and it restricts the growth of certain periodontal-related bacteria.25 Chamomile shows anti-inflammatory properties, as does myrrh extract, and mint extract.2


Toothpaste Ingredients to Avoid

We can’t talk about the best ingredients for toothpaste without shining a light on the bad ingredients. If you have mouth ulcers that won’t heal or cavities or gum disease and you are doing everything right, then I would question if your toothpaste may be the problem. Some ugly ingredients have been used in toothpastes which are not so safe or healthy for the mouth. For example, SLS, cocamidopropyl betaine, and fluoride at commonly used concentrations are toxic to the mouth lining.1

In addition to avoiding unnecessary antibiotic ingredients, here are some other toothpaste ingredients8 to be on the lookout for:

  • Triclosan- antibiotic and antifungal, an endocrine-disrupting chemical.
  • Sodium lauryl sulfate (SLS)- foaming agent that can be very irritating, causing mouth sores, and cracking at corners of the lips.
  • Artificial sweeteners- may harm good bacteria metabolism and heart health.
  • Propylene glycol- plastic that may disturb hormone balance and irritate gums.
  • Titanium dioxide- gives a white appearance and can be carcinogenic and neurotoxic.
  • Fluoride1 (controversial, discussed earlier)
  • Parabens- may disturb hormone balance.

See more toothpaste ingredients to avoid here.

Build a Healthy Oral Microbiome with Toothbrushing, Toothpaste, and Lifestyle Changes

There’s more than meets the eye when it comes to your toothpaste. Here are my tips for picking the best toothpaste for your unique oral microbiome.

Read the ingredients and choose wisely. Don’t just buy any toothpaste off the shelf if you’re working on your oral health or your oral microbiome. I recommend RiseWell’s high-quality, non-toxic toothpastes with hydroxyapatite to clean and protect teeth.

The best toothpaste ingredients for the oral microbiome. These natural toothpaste ingredients are neutral or beneficial for mouth bacteria- not harmful:

  • Gentle abrasives such as calcium carbonate, clay, silica
  • Hydroxyapatite
  • Baking soda
  • Xylitol
  • Stevia
  • Prebiotics such as arginine and nitrate
  • Probiotics
  • Enzymes
  • Zinc citrate
  • Anti-inflammatory and antioxidant plants generally regarded as safe

Antibiotic toothpastes are not for everyone all the time. They should be used strategically. Work with your functional dentist or biological dentist to figure out if you need an antibacterial/antifungal toothpaste. If you have oral dysbiosis with cavities, bleeding gums, gum disease, and more, then fluoride-containing, antibacterial toothpastes make sense. Follow up with testing and with dental check-ups to see when you can switch to a health-maintenance toothpaste.

If you have generally good oral health and you’re eating a very healthy diet, then consider a non-toxic toothpaste that does not have antibiotic activity. Follow up with your dentist and test your oral microbiome to make sure it’s going well.

If you have mouth ulcers, mouth irritation, mouth burning, or other symptoms, it could be toxins from your toothpaste harming your mouth lining. Other possible causes are vitamin deficiencies or food sensitivities.

Eat a whole foods diet of vegetables, fruits, meats, nuts, and seeds with plenty of fiber to build a healthy oral microbiome and ward off oral pathogens. Toothpaste cannot fix a poor diet.

Break up bacterial biofilms regularly with toothbrushing, flossing, and regular dental cleanings. If you have dysbiosis, consider breaking up bacterial biofilms more frequently through the day with the GIFTS method (Gum and tooth rubbing with Index Finger and Tongue cleaning and water Swishing).9

Breathe through your nose. If you are mouth-breathing, it can undermine your other oral health efforts.


The Best Toothpaste for a Healthy Mouth

Not all toothpastes are created equal. They can contain toxic ingredients and some ingredients are intended to kill microbes in the mouth, possibly harming friendly mouth bacteria in the process. We are entering a new paradigm of thinking about the human-microbial superorganism, where nourishing and enhancing health-promoting microbes may be our best defense against the harmful ones. Killing microbes all the time could be undermining our best efforts for a healthy mouth. The best toothpaste ingredients are harmless to the oral microbiome but also improve oral health. Follow the recommendations mentioned here to build a healthy oral microbiome as a way to fight cavities, gum disease, and bad breath.

RiseWell is an oral hygiene brand that was developed by dentists and leading experts to create safe oral care that is clinically proven to work. Unlike many natural toothpastes, we didn’t just remove the toxic ingredients found in traditional toothpastes, we swapped in 100% safe and natural alternatives that clean and protect just as effectively. We use only the best ingredients, no matter the cost, to bring 100% clean, naturally effective oral care to you and your family. Our products will not only keep you safe and healthy, but they will also spark joy and ignite happiness, so you can start every day well.


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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.