How Alcohol-Based Mouthwashes Impact Your Oral Microbiome
Explore the oral microbiome's vital role in health and how alcohol-based mouthwashes can disrupt this delicate ecosystem.
Learn why a focus on maintaining microbial balance, rather than on simply disinfecting your mouth, supports both dental and overall wellness. Plus, discover gentler alternatives that preserve beneficial bacteria while promoting oral health.
When we think about oral health, brushing and flossing typically come to mind. However, beneath the surface lies a bustling ecosystem that plays a far greater role in our overall health than most people realize: the oral microbiome. This article explores what the oral microbiome is, examines the effects of alcohol-based mouthwashes on this delicate ecosystem, and touches on an effective alcohol-free alternative.

What is the Oral Microbiome?
The oral microbiome refers to the diverse community of microorganisms—bacteria, fungi, viruses, and protozoa—that live in our mouths. After the gut, it is the second-most diverse microbial community in the human body, housing more than 700 species of bacteria along with many other microbes¹⁻².
These microbes colonize different surfaces in the mouth, from the teeth and tongue to the cheeks, gums, and palate¹⁻². Together, they form a biofilm (commonly known as dental plaque), where microbes live in close association¹⁻².
Importantly, the oral microbiome is not just a collection of random microbes—it has coevolved with humans over millions of years, forming a finely balanced symbiotic relationship that supports health².
Why Does the Oral Microbiome Matter?
A healthy oral microbiome is essential for more than just fresh breath and cavity prevention. It helps to¹⁻³:
- Protect against pathogens by competing with harmful microbes for space and nutrients.
- Support the immune system and regulate inflammation.
- Aid in digestion by beginning the breakdown of food.
- Maintain systemic health, with growing evidence linking oral microbes to conditions such as cardiovascular disease, diabetes, and even certain cancers.
When the balance of the oral microbiome is disrupted (a condition known as dysbiosis) and harmful bacteria can flourish. This imbalance leads to common oral diseases such as caries, gingivitis, and periodontitis, while also contributing to systemic inflammation throughout the body¹⁻³.

Alcohol-Based Mouthwashes and the Oral Microbiome
Mouthwash is often marketed as a way for the average consumer to kill germs in one’s mouth and freshen their breath. Many of the most popular products rely on ethanol (alcohol) as a key ingredient. While effective as a disinfectant, alcohol-based mouthwashes may have unintended consequences for the oral microbiome. Let’s explore some of these below.
Potential Impacts of Alcohol-Based Mouthwash
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Disruption of Microbial Balance
Ethanol is a strong antimicrobial agent. While this can reduce harmful bacteria, it can also indiscriminately kill beneficial microbes that are crucial for maintaining oral health¹⁻³. Over time, this disruption may reduce microbial diversity, an important marker of a resilient and healthy microbiome².
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Alteration of Oral Environment
Similar to the unintended consequences of frequent use of alcohol-based hand sanitizing products on one’s hands, alcohol as an ingredient in mouthwashes can also cause a drying effect on oral tissues, reducing the protective role of saliva¹⁻³. Since saliva provides nutrients and antimicrobial proteins that help regulate microbial balance, reduced saliva flow can contribute to dysbiosis¹.
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Patient Tolerability and Risks
Some individuals experience a burning sensation or irritation when using alcohol-based rinses. Ethanol may also be unsuitable for people with oral mucosal injuries, those who are immunocompromised, recovering from alcoholism, or those with religious and cultural restrictions³.
The Case for Alcohol-Free Alternatives
Recent research has shown that alcohol-free mouthwashes can perform similarly to alcohol-based formulations in terms of preserving oral microbiome samples for study, without the drawbacks associated with ethanol¹⁻³. These products typically use alternative antimicrobial agents and are gentler on oral tissues while still helping to control plaque and gingivitis¹⁻³.

Striking the Right Balance: Considering A Hypochlorous Acid Based Mouth Rinse
Maintaining oral health is not exclusively about disinfecting the mouth. In fact, it’s about supporting balance within the oral microbiome¹⁻³. Choosing oral care products that preserve this balance can promote both oral and overall health.
One alcohol-free option to consider is a hypochlorous acid (HOCl) based oral rinse such as PureCleanse Oral™. It is a pure, stable super oxidizing saline oral rinsing solution for all ages, and features a non-toxic and easy-to-use formula, making it perfect for daily oral hygiene routines.
At Biomiq, we believe in science-driven solutions that respect the body’s natural ecosystems and use biomimicry to our collective advantage. We see the future of oral care not in wiping the slate clean, but in celebrating (and protecting) the complex ecosystem of beneficial microbes that promote oral health.
References
- Deo, P. N., & Deshmukh, R. (2019). Oral microbiome: Unveiling the fundamentals. Journal of oral and maxillofacial pathology, 23(1), 122-128.
- Kilian, M., Chapple, I. L. C., Hannig, M., Marsh, P. D., Meuric, V., Pedersen, A. M. L., ... & Zaura, E. (2016). The oral microbiome–an update for oral healthcare professionals. British dental journal, 221(10), 657-666.
- Yano, Y., Vogtmann, E., Shreves, A. H., Weinstein, S. J., Black, A., Diaz-Mayoral, N., ... & Abnet, C. C. (2023). Evaluation of alcohol-free mouthwash for studies of the oral microbiome. Plos one, 18(4), e0284956.