How does toothpaste affect the good bacteria in your mouth?

The goal of brushing one’s teeth is to have fresh breath and prevent cavities. But the effect of toothpaste on the complex ecosystem of bacteria in our mouths — the oral microbiome — is often overlooked.

Recent research has highlighted just how crucial the oral microbiome is for our overall health. A well-balanced microbiome helps regulate harmful bacteria, aids digestion and protects the gums. But does toothpaste support this balance, or could it be disrupting it? And could the toothpaste of the future be designed to work with the oral microbiome rather than against it?

The mouth is one of the most densely populated microbial habitats in the body, home to more than 700 species of bacteria. These bacteria inhabit not only the surfaces of the teeth and gums in biofilm – a sticky, structured community that can be both beneficial and harmful – but also thrive in our saliva, contributing to the dynamic oral microbiome.

A healthy microbiome includes bacteria that help regulate pH levels (a measure of how acidic or alkaline a substance is), break down food and even produce natural antimicrobial compounds. But when the balance is disrupted — often due to diet, poor oral hygiene or certain medical conditions — harmful bacteria can take over. This imbalance, known as dysbiosis, is linked to tooth decay and gum disease.

What does toothpaste actually do?

The main function of toothpaste isn’t to kill bacteria outright but to disrupt the biofilm that allows harmful bacteria to thrive. Brushing mechanically removes this biofilm from teeth and gums, while abrasives in toothpaste help break it up further.

Many toothpastes also contain fluoride, which strengthens tooth enamel and helps prevent cavities. Interestingly, fluoride itself doesn’t kill bacteria, but it makes it harder for acid-producing bacteria like Streptococcus mutans, a key player in tooth decay, to cause damage.

Some toothpastes include antibacterial agents, such as triclosan (now banned in some countries due to safety concerns) or newer alternatives like stannous fluoride and zinc compounds. These ingredients target harmful bacteria, but there’s still debate about whether they also disrupt beneficial microbes in the process.

Despite toothpaste being a daily staple, research into its effects on the oral microbiome is still evolving. Some studies suggest that certain antibacterial agents reduce both harmful and beneficial bacteria, potentially changing the microbiome in ways we don’t yet fully understand. Others indicate that the microbiome recovers quite quickly after brushing, making any disruption temporary.

Scientists are now exploring whether future toothpaste formulations could take a more targeted approach, reducing harmful bacteria while preserving beneficial species. Some emerging research looks at probiotics and prebiotics — ingredients that could actively support a healthier oral microbiome rather than simply disrupting it.

Keeping the oral microbiome in balance isn’t just about avoiding cavities. There’s growing evidence linking gum disease to heart disease, diabetes and harms during pregnancy. Inflammation triggered by harmful oral bacteria can spread beyond the mouth, potentially contributing to long-term health problems.

Brushing with fluoride toothpaste twice a day and cleaning between the teeth helps reduce the bacterial load in the mouth, lowering the risk of both oral and systemic diseases.

Microbiome-friendly toothpaste?

As our understanding of the oral microbiome grows, toothpaste may evolve to become more selective in its action. Instead of broad-spectrum antibacterial agents, future formulations might include ingredients that support beneficial bacteria while keeping harmful species in check.

Some promising candidates include arginine, a naturally occurring amino acid that promotes the growth of beneficial bacteria, and plant-derived antimicrobials that disrupt harmful biofilms without killing good bacteria. However, research in this area is still in its early stages, and more evidence is needed to determine the long-term effects of these ingredients.

Toothpaste plays a key role in oral health by breaking up bacterial biofilm, reducing the risk of tooth decay and gum disease. While some ingredients may affect the oral microbiome, research suggests that brushing and flossing remain the most effective ways to maintain a healthy mouth.

Future toothpaste innovations may shift towards microbiome-friendly formulations but, for now, the best advice remains the same: brush twice a day with fluoride toothpaste, spit out the excess and clean between your teeth daily.

Nothing to disclose.

Albert Leung and Niamh Coffey do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.