Does Mouthwash Harm My Oral Microbiome?

Using mouthwash in our daily oral hygiene routine has become commonplace over the years to keep bad breath away. We add it to our teeth-brushing and flossing ritual to get rid of unwanted bacteria (and to keep that minty-fresh taste!). But now, we’re finding out that mouthwash gets rid of ALL bacteria – and some bacteria are good for us to keep (hello, microbiome). Here’s how mouthwash may harm your oral microbiome. 

What is the oral microbiome?

At any given time, there are over 700 species of bacteria, fungi and viruses living in your mouth. They’re in and around your teeth, gums, inner cheeks, tongue, and soft palate. This combination of microbes living in your oral cavity is your very own, personalized, oral microbiome. Scientists are just now starting to discover the fascinating connections between oral health and overall health, and how the oral microbiome plays a huge role in it all. 

What’s the purpose of the oral microbiome?

To keep your body healthy, your oral microbiome must remain balanced – meaning having a perfect level of both good and bacteria. When yours is balanced, you’ll be in good shape. When it isn’t, it can wreak havoc on your overall health. 

The balance (or imbalance) in your oral microbiome can affect your: 

  • Gastrointestinal Tract
  • Immune system
  • Cardiovascular health
  • Gut-brain health
  • Endocrine system
  • Natural nitric oxide production

When there is an imbalance in your microbiome, the harmful species can over-populate, possibly contributing to various chronic diseases – including gum disease. It’s now estimated that over 90% of all diseases have oral manifestations. One of the indications of an imbalance is bad breath (which usually sends us reaching for that mouthwash!).

Curious about your oral microbiome levels? You can test your own through your saliva! Bristle is a saliva-testing tool that can give us risk scores for decay, periodontal disease, and bad breath. It gives a breakdown of any bacterial species detected and how many of each there are! Learn more by downloading this comprehensive salivary oral microbiome testing brochure here.

Or, you can order a test for 15% off at with code BLOOM15.

Does mouthwash kill good bacteria?

Mouthwash kills good AND bad bacteria. It may seem like a good idea to get rid of the bacteria in the mouth, but by killing ALL of the bacteria, it throws off the balance in our oral microbiome.

That said, it’s a good idea to stay away from mouthwashes that kill 99% of all the bacteria. Here are some other common mouthwash ingredients that may harm your oral microbiome:  

  • Alcohol – Kills all bacteria, both good and bad.
  • Hydrogen peroxide – Kills all bacteria, both good and bad. It may also kill the cells inside your teeth.
  • Chlorhexidine – A broad-spectrum antimicrobial commonly found in mouthwashes. It may stain your teeth, increase calculus formations, and alter your taste perception.

A recent study showed only one week of mouthwash use alters the oral microbiome, lowering saliva pH, increasing acidity and heightening the risk of tooth damage.

Overall, environmental pH levels in the mouth dropped after one week of mouthwash use suggesting saliva had become more acidic. What this means for dental health is unclear but the researchers do note in the study that decreased saliva pH levels are linked with demineralization of tooth enamel and other dental problems. The study hypothesizes mouthwash use may be helpful in managing diseases such as gingivitis where saliva pH is more alkaline than normal.

Should I stop using mouthwash?

We’re just now beginning to discover details about the oral microbiome. At this time, it’s okay to use mouthwash, but ensure your use of it is limited. Keep up with your daily brushing and flossing, and maintain a healthy lifestyle. Those, along with regular dental visits, should keep your oral health in good check. 

If you have consistent bad breath even after consistent brushing and flossing (or mouthwash, for that matter), you may have another health condition at play, such as mouth breathing. Schedule an appointment with Dr. Elizabeth Turner here and she’ll help you find the root cause.

Interested in learning more about the oral microbiome? Check out our general dentistry services page here. 

About the Author

Dr. Elizabeth Turner is a whole-health, family dentist in Lakewood, CO who provides general, restorative, and cosmetic dental care. She focuses on the mouth-body connection and helps her patients smile confidently, breathe clearer, and live healthier lives. 

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