Does mouthwash kill good bacteria?

Mouthwash can freshen your breath and fight germs. But it's fair to wonder if it's also wiping out bacteria your body actually needs. It works well at reducing harmful bacteria. But it has a downside. A review in the International Dental Journal says chlorhexidine may also lower helpful bacteria that play a role in heart health, not just the bacteria causing your dental problem. Because the rinse doesn't target only harmful germs, it can throw off the natural balance in your mouth; researchers call this shift dysbiosis.¹

The answer: it depends on the type of mouthwash you use. 

What you will learn in this article: 

• Alcohol-based and prescription rinses don't spare good bacteria. They clear helpful and harmful ones alike. 

• Some oral bacteria protect your heart and help control blood sugar. Losing them may have effects beyond your mouth. 

• Frequent antibacterial rinsing has been linked to a higher risk of pre-diabetes or diabetes in research. 

• Fluoride rinses can protect your teeth without the same broad bacterial wipeout. Your dental provider can help you pick the right one. 

Talk to your dental provider about your routine. You can schedule an appointment with an Aspen Dental provider to get personal guidance on which mouthwash, if any, fits your oral health goals. 

What does mouthwash actually do? 

Mouthwash kills bacteria. Some kinds target only germs linked to gum disease and bad breath. Others go further. They kill a wide range of bacteria, good and bad alike. 

Your mouth is home to hundreds of types of bacteria. Not all of them are harmful. Some actually protect your health. When a rinse kills those too, it can throw your mouth's balance off. 

Alcohol-based rinses and your oral bacteria 

Many over-the-counter rinses contain alcohol. A review in the International Dental Journal says alcohol may affect helpful bacteria as well as harmful ones. However, the authors found no studies that directly tested how alcohol-containing rinses change the whole oral microbiome.¹ 

This matters because your mouth needs a mix of bacteria to stay healthy. Wiping out too many good ones can leave room for less helpful bacteria to grow. 

What about chlorhexidine rinses? 

Chlorhexidine is a stronger, prescription-strength antibacterial rinse. Dentists often prescribe it after gum treatment or oral surgery. 

Why good bacteria matter beyond your mouth 

A study in the journal Nitric Oxide notes that earlier small trials found that using chlorhexidine twice a day lowered nitrate and nitrite levels in the body. The authors say this likely happened because the rinse reduced oral bacteria that help process nitrate. In the study’s own three-year results, mostly Hispanic adults ages 40 to 65 who were overweight or obese and used over-the-counter mouthwash at least twice a day had a higher risk of prediabetes or diabetes than less frequent users. The study found a link, not proof, that mouthwash caused the change. It also did not track the type of mouthwash or test whether changes to nitrate-processing bacteria caused the finding.²

So should you stop using mouthwash? 

Not necessarily. Mouthwash can still be a useful tool. The key is using the right kind, for the right reason, at the right frequency. 

Fluoride rinses, for example, help protect against cavities without the same broad antibacterial effect. They do not wipe out your microbiome the way alcohol or chlorhexidine rinses can. 

If you have been told to use chlorhexidine, follow your dental provider's instructions. It is typically prescribed for a short course, not long-term daily use. Your dental provider will guide you on when to start and stop. 

What to keep in mind 

Here are a few things worth knowing: 

• Alcohol may affect both helpful and harmful bacteria, but no mouth-rinsing study has tested how alcohol changes the whole oral microbiome.¹

• Chlorhexidine can reduce bacteria that help the body process nitrate. In one study of mostly Hispanic adults ages 40 to 65 who were overweight or obese, using over-the-counter mouthwash at least twice a day was linked to a higher three-year risk of prediabetes or diabetes.² 

 
Not every person needs a strong antibacterial rinse. If your main goal is fresher breath or cavity protection, ask your dental provider which type is the best fit for your goals. 

Does mouthwash kill good bacteria? FAQs 

With all this in mind, here are answers to the specific questions people usually have about their own routine. 

Is it safe to use mouthwash every day? 

It depends on the type. Fluoride rinses are generally used daily. Strong antibacterial rinses, like chlorhexidine, are typically meant for short-term use. Ask your dental provider what makes sense for you. 

Does mouthwash affect bacteria linked to blood sugar? 

Research suggests there may be a link, but it does not show that mouthwash causes blood sugar problems. The study discussed above found a higher risk with use at least twice a day, while less frequent use was not linked to higher risk. Talk to your dental provider if you have concerns about this. 

Should I use mouthwash before or after brushing? 

Timing matters. Many dental providers recommend rinsing after brushing so the mouthwash can act on a freshly cleaned surface. However, if you use a fluoride toothpaste, rinsing immediately after may wash away the concentrated fluoride before it has a chance to work. In that case, using mouthwash at a separate time — such as after lunch — may be a better fit. Ask your dental provider what timing works best for your routine. 

What type of mouthwash is least likely to harm good bacteria? 

Fluoride-based rinses do not carry the same broad antibacterial action as alcohol or chlorhexidine rinses. Your dental provider can help you choose based on your oral health history. 

Sources 

¹ National Institutes of Health, PubMed Central, International Dental Journal: "Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced?" https://pmc.ncbi.nlm.nih.gov/articles/PMC10690560/ 

² National Institutes of Health, PubMed Central, Nitric Oxide: "Over-the-counter mouthwash use and risk of pre-diabetes/diabetes." https://pmc.ncbi.nlm.nih.gov/articles/PMC6628144/