Every morning and night, billions of people around the world stand in front of their bathroom mirrors, toothbrush in hand, performing the same familiar ritual: brush, rinse, spit, repeat. Dentists remind us to floss, parents chase children to clean their teeth, and advertisements for toothpaste fill the airwaves. Yet what if one day, brushing and flossing became relics of the past—rituals we tell future generations about with nostalgia?
That may sound like science fiction, but at the University of California, Berkeley, chemical and biomolecular engineering professor Wenjun Zhang and her team are daring to imagine such a future. Their work is not about inventing a better toothbrush or stronger toothpaste. Instead, they are turning their attention inward, toward the microscopic world living inside our mouths—the oral microbiome. By learning to re-engineer the balance of bacteria, they hope to tip the scales in favor of health rather than disease.
The Hidden World in Our Mouths
Our mouths are far from sterile. They are home to hundreds of species of bacteria, each competing, cooperating, and coexisting in ways that scientists are only beginning to understand. Together, these microbes form communities called biofilms, which cling to the surfaces of our teeth. To most of us, biofilm is a nuisance we know as plaque, the sticky film dentists scrape off during cleanings. But to researchers, it is a complex and dynamic ecosystem.
Traditionally, dental science has focused on identifying the “bad guys”—bacteria such as Streptococcus mutans, notorious for producing acids that erode tooth enamel and lead to cavities. But Zhang’s research takes a more nuanced view. Not all bacteria of the same species are identical. Within each species are countless strains, some more harmful than others, some relatively harmless, and some even beneficial. This discovery complicates the old narrative of “good species” versus “bad species” and opens the door to a more sophisticated approach.
Beyond Species: A Genomic Treasure Hunt
Instead of grouping bacteria by name tags, Zhang and her team look at their genomes—the full set of DNA instructions inside each microbe. Using a metagenomic approach, they scan through vast databases of microbial DNA collected from human mouths, searching for clusters of genes associated with oral disease.
In their recent study, published in the Proceedings of the National Academy of Sciences, Zhang and her colleagues identified a gene cluster with striking potential. This cluster produces two specialized molecules: one that acts like glue, sticking bacterial cells together, and another that acts like a string, linking them into chains. Together, these molecules—playfully nicknamed mutanoclumpins—give bacteria the ability to form stronger, more resilient biofilms.
Turning Villains into Heroes
At first glance, the discovery seems like bad news. After all, stronger biofilms are harder to clean and more likely to lead to cavities. But Zhang sees possibility where others might see only problems.
If these gene clusters are present in some cavity-causing bacteria, why not transfer them to beneficial bacteria instead? By giving “good” microbes the tools to cling tightly to our teeth, researchers could allow them to establish strong, stable communities that crowd out their harmful rivals. Imagine a future where probiotics, not toothbrushes, defend our enamel.
One promising candidate is Streptococcus salivarius, a species often marketed as an oral probiotic. It is known for promoting oral health but lacks the ability to form durable biofilms. If engineered with mutanoclumpins, it might gain the strength to colonize teeth more effectively, holding the line against decay-promoting species.
The Power of Specialized Metabolism
The gene cluster Zhang’s team identified is part of what scientists call specialized metabolism. Unlike the basic pathways bacteria need to survive, specialized metabolic networks produce unique molecules that give microbes an edge in competitive environments.
In soil bacteria, such pathways have yielded a treasure trove of antibiotics, medicines that revolutionized human health. In the human microbiome, however, these networks remain largely uncharted. Zhang’s group is among the pioneers mapping this frontier, uncovering how microbial chemistry influences health and disease.
Graduate student McKenna Yao, who helped lead the study, explains that specialized metabolites act as weapons and tools in microbial battles. Some can kill competitors, others help bacteria capture scarce nutrients, and still others, like mutanoclumpins, help them build protective communities. These molecules are the strategies of survival in the microscopic world—and understanding them could transform how we think about disease prevention.
A New Way to Think About Cavities
For decades, preventing cavities has centered on mechanical removal of plaque and chemical control through fluoride and antiseptic rinses. While effective, these methods treat the symptom rather than the system. Zhang’s work suggests that cavities are not merely the result of “too much sugar” or “not enough brushing.” They are ecological imbalances in a complex microbial community.
By rebalancing that ecosystem—either by silencing harmful gene clusters or empowering beneficial ones—scientists may one day develop treatments that work with the microbiome rather than against it. Imagine swishing a probiotic mouth rinse that seeds your teeth with protective bacteria, replacing the nightly grind of brushing and flossing.
The Challenges Ahead
Of course, the road from laboratory discovery to everyday application is long. Before probiotics can replace toothbrushes, researchers must answer fundamental questions. Will engineered bacteria remain stable in the mouth over time? Could they have unintended effects on other microbes or even human health? How can we ensure they are safe and accessible for all?
Zhang herself acknowledges these challenges. Her team is still at the stage of mapping which gene clusters matter most, teasing apart how specific molecules influence oral ecosystems. But each discovery adds a piece to the puzzle. Just two years ago, her group identified a gene cluster that produces a previously unknown antibiotic within oral bacteria. Now, with mutanoclumpins, they have found another critical tool microbes use to shape their environment.
The Human Side of the Science
What makes Zhang’s vision compelling is not just the technical achievement but the human motivation behind it. Brushing and flossing, though simple, remain global public health challenges. Many children and adults lack access to dental care or develop cavities despite diligent hygiene. In parts of the world without clean water, toothpaste, or dental clinics, tooth decay is rampant and painful.
If oral probiotics could be developed into easy, affordable treatments, they might revolutionize dental health worldwide. They could spare countless people from the suffering of cavities, infections, and extractions. They could shift dentistry from a reactive practice—fixing problems after they occur—to a proactive one, nurturing the microbiome to prevent disease before it starts.
A Glimpse Into the Future
For now, toothbrushes and floss remain essential. Even Yao, one of the graduate students behind the discovery, cautions that “the best way you can remove the biofilm on your teeth is to brush.” Still, the team believes a better way may be on the horizon, one rooted in deeper understanding of microbial complexity.
The vision is bold: a future where oral care is not about scrubbing away plaque but about cultivating harmony among the microbes that share our mouths. A future where cavities are not an inevitable nuisance but a preventable imbalance. A future where the phrase “Don’t forget to brush your teeth” might fade into history, replaced by “Don’t forget to take your probiotics.”
Conclusion: Science That Touches Everyone
Not every breakthrough in microbiology feels personal. But this one does. It speaks to something we all experience daily: the effort to keep our teeth healthy. Whether we realize it or not, our mouths are ecosystems, and Zhang’s work reminds us that health is not a battle against nature but a partnership with it.
If her vision becomes reality, the next generation may inherit a world where tooth decay is no longer a childhood rite of passage, where dental visits bring checkups instead of drills, and where the toothbrush itself might become a relic of the past.
Until then, we brush. But we also dream—dream of a day when science turns one of life’s most tedious chores into something beautifully effortless.
More information: McKenna Loop Yao et al, Synergistic action of specialized metabolites from divergent biosynthesis in the human oral microbiome, Proceedings of the National Academy of Sciences (2025). DOI: 10.1073/pnas.2504492122
