Dr. James Belcher, December 2, 2025

Microbiome modulation instead of germ slashing: A new path to healthy teeth and gums

Many toothpastes and mouthwashes promise to "kill 99% of all bacteria." Sounds good—but it isn't necessarily true. Your mouth is an ecosystem, and killing everything also destroys what protects it. Learn here why selective blockage is the future of oral care.

Mikrobiom-Modulation statt Keim-Keule: Ein neuer Weg für gesunde Zähne und Zahnfleisch

What's behind it?

Microbiome modulation refers to an approach in oral care that doesn't "wipe out everything" but intervenes in a targeted way . Your mouth is home to over 700 different types of bacteria. Many of these are beneficial – they protect you from pathogens and strengthen your gums (Baker et al., 2024). 

Conventional products like strong mouthwashes kill all bacteria indiscriminately . This disrupts the balance – experts refer to this as dysbiosis . As a result, harmful germs can recolonize more quickly, increasing the risk of inflammation (Koromantzos et al., 2025). 

Why is it relevant?

A stable oral microbiome acts like a natural protective shield . If it becomes unbalanced, gingivitis and periodontitis can result. Studies show that these local inflammations may be linked to diseases such as diabetes, cardiovascular disease , and possibly also Alzheimer's disease (Hajishengalis et al., 2021). 

The future of dentistry therefore lies in combating pathogens such as Porphyromonas gingivalis to block them in a targeted manner – and simply let the good bacteria fulfill their protective function (Taudte et al. 2021; Eick et al., 2025). 


Infobox
Chlorhexidine , a commonly used antiseptic, can discolor teeth and alter taste perception – and also destroys many of your good bacteria (Worthington et al., 2017).  

Scientific background

PerioTrap researchers have developed a molecule called S-0636 that acts as a so-called pathoblocker . It does not kill P. gingivalis, but rather disables its disease-causing mechanisms – for example, the production of aggressive enzymes that attack tissue (Taudte et al., 2025).

This means: blockage of pathogenic germs and no harm to beneficial bacteria . In laboratory studies, biofilm mass could be reduced by up to 25% (Eick et al., 2025).

Practical tips for everyday life

  • ✓ Avoid using unnecessarily strong antiseptics in everyday life – they belong more in short-term therapy at the dentist. 
  • ✓ Look for mild and protective products that target specific blockages, promote the balance of your microbiome and protect your gums in the long term. 

At a glance

ⓘ “Everything-killing” approaches disrupt the oral microbiome.

ⓘ Selective blockade protects the good bacteria and only takes away the "weapons" of the harmful ones. 

Sources

  • Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The Oral Microbiome: Diversity, Biogeography and Human Health. Nature Reviews Microbiology. 2024.

  • Eick S, Taudte N, Ramsbeck D, Magdon A, Sculean A, Potempa J, Buchholz M. Effect of a bacterial glutaminyl cyclase inhibitor on multi-species biofilms. Frontiers in Oral Health. 2025;6:1716625. doi:10.3389/froh.2025.1716625.

  • Hajishengallis G, Chavakis T. Local and Systemic Mechanisms Linking Periodontal Disease and Inflammatory Comorbidities. Nature Reviews Immunology. 2021.

  • James P, Worthington HV, Parnell C, et al. Chlorhexidine Mouthrinse as an Adjunctive Treatment for Gingival Health. The Cochrane Database of Systematic Reviews. 2017.

  • Koromantzos PA, Bobetsis YA, Giota C, et al. Effect of Adjunctive Use of Commercial Daily Mouthwashes on Periodontal Health: An Umbrella Review. Journal of Clinical Periodontology. 2025. doi:10.1111/jcpe.70061.

  • Tartaglia GM, Kumar S, Fornari CD, Corti E, Connelly ST. Mouthwashes in the 21 Century: A Narrative Review About Active Molecules and Effectiveness on the Periodontal Outcomes. Expert Opinion on Drug Delivery. 2017;14(8):973–982. doi:10.1080/17425247.2017.1260118.

  • Taudte N, et al. Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis. J Biol Chem. 2021;296:100263.

  • Taudte N, et al. Novel small molecule targeting PgQC reduces Porphyromonas gingivalis virulence. bioRxiv. 2025.09.30.679452. doi:10.1101/2025.09.30.679452. This article is a preprint and has not been certified by peer review.

  • Zeng Y, Lin D, Chen A, Ning Y, Li X. Periodontal Treatment to Improve General Health and Manage Systemic Diseases. Advances in Experimental Medicine and Biology. 2025. 

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