Mouthwashes have long bragged about killing 99.9% of germs in your mouth, but Rutgers Health researchers suggest this scorched-earth approach may harm oral health by eliminating beneficial bacteria along with the bad.

A study in Frontiers in Oral Health from the Rutgers School of Dental Medicine found that a naturopathic mouthwash containing herbal ingredients could selectively target disease-causing bacteria while preserving the protective microbes that help maintain healthy gums and teeth.

“It’s a paradigm shift,” said Georgios Kotsakis, the dental school’s assistant dean for clinical research and senior author of the study. “We’re moving from eradicating all bacteria to focusing on selectivity. We want to keep the good bacteria alive while targeting the bad.”

The researchers tested a natural mouthwash called StellaLife VEGA Oral Care rinse against two conventional products: the prescription mouthwash chlorhexidine and Listerine Cool Mint.

They exposed various oral bacteria to each rinse and monitored their growth over several days.

The natural rinse significantly reduced populations of harmful bacteria such as Fusobacterium nucleatum and Porphyromonas gingivalis, while allowing beneficial species such as Streptococcus oralis and Veillonella parvula to survive.

Chlorhexidine and Listerine showed no such selectivity, eliminating beneficial and harmful bacteria alike. Chlorhexidine was particularly aggressive, reducing some beneficial bacteria populations by a million-fold.

“These good bacteria have important functions,” Kotsakis said. “They synergize with your tissues. They actually kill some of the bad bacteria themselves.”

Petri-dish results don’t necessarily translate to mouths full of teeth, saliva and dietary sugars, Kotsakis said. The study didn’t measure cavity formation or bleeding gums in people.

“Randomized clinical trials are the next step,” Kotsakis said.

The work fits an expanding effort to manage oral microbes rather than carpet-bomb them. Heavy use of strong antiseptic rinses has been linked to shifts that may raise blood pressure or blunt nitric oxide signaling. Scientists are also exploring oral probiotics—beneficial strains that could be swabbed on after a dental cleaning—to crowd out pathogens.

“If you’re brushing and flossing like a dentist—regularly and perfectly—you may not need a mouthwash, but in reality, even the best of us can miss some surfaces during cleaning at home,” Kotsakis said.

For those who use mouthwash, the goal should be reinforcing the mouth’s natural defenses, not destroying them, he said, adding that antiseptic mouthwash might be valuable for short-term use against specific oral disease but should not be used long-term.