How to restore your oral microbiome: Why your daily mouthwash is ruining your health
- Carmela Pengelly
- Jun 9
- 7 min read
If you use mouthwash regularly, you may be inadvertently compromising your dental, gut and overall health.
In this blog, I take a deep dive into the clinical realities of what mouthwash does, how to boost good bacteria in your mouth naturally, and how to protect the finely balanced ecosystems that exist in both your mouth and your gut.
I also detail easy, practical solutions for better dental health, which will benefit your entire well-being. 👉Skip to my 7 top tips for good dental health here.
👉Skip to the 3 best foods for healthy teeth and gums here.
👉Click on the link here if you would like to try my recipe for a gentle mouthwash that actually addresses the root causes of teeth and gum issues and helps you to restore and build your oral and gut health.
Is mouthwash healthy or unhealthy?
The short answer is that while mouthwashes kill bacteria and give you a temporary burst of minty freshness, they do so at a significant cost to your overall health.
What about zero-alcohol mouthwashes?
Even the zero-alcohol formulations are fundamentally flawed. As consumers, we have been conditioned to believe that as long as the bottle reads "alcohol-free," it is safe. However, in my view, this is little more than clever marketing, designed to keep us purchasing a product that actively disrupts our physiology.
Are natural mouthwashes healthier?
It is important to note that switching to a 'natural' or herbal mouthwash isn’t always a safe bet, either. Many commercial natural rinses rely heavily on highly concentrated, potent herbal antimicrobials like tea tree oil, or heavy doses of peppermint and thyme. While these natural mouthwashes work, nature does not always discriminate between beneficial and pathogenic bacteria. In concentrated amounts, these strong natural products act just like conventional chemical-based mouthwashes.
The "carpet bomb" effect: what is actually happening?
To understand why mouthwash is problematic, we have to look at the ingredients list. Commercial formulations rely on heavy-duty antimicrobials and detergents such as thymol, menthol, benzoic acid, and sodium lauryl sulfate (SLS).
Using a mouthwash daily could be likened to taking an antibiotic every single day. These ingredients are proven to kill bacteria that cause bad breath and gum disease. However, the downside is that they act as an antimicrobial carpet bomb, disrupting the diversity of your oral microbiome and reducing 'good' bacterial populations. The resulting imbalance is known as oral dysbiosis.
Why cardiologists warn against mouthwash: The nitric oxide connection
Because the mouth is the gateway to the rest of the body (via both the gut and the bloodstream), the consequences of oral dysbiosis are surprisingly far reaching.
1. Nitric oxide depletion (hypertension & insulin resistance)
Certain beneficial bacteria residing on the back of your tongue are responsible for converting inorganic nitrates from plant foods (like leafy greens) into nitrites. When swallowed, these nitrites are converted into nitric oxide, a crucial signaling molecule that relaxes blood vessels, lowers blood pressure, and regulates insulin sensitivity.
Studies have shown that frequent mouthwash use decreases the population of these vital bacteria. This depletion is linked with increased risk for hypertension, prediabetes, and type 2 diabetes.
2. Compromised nutrient absorption
Emerging research indicates that frequent mouthwash use can also lead to nutrient malabsorption. Nitric oxide is needed for healthy gut motility and adequate blood flow to the villi - the tiny, finger-like projections in your small intestine where nutrient absorption occurs. Without this vital blood circulation, your gut simply cannot absorb your food efficiently.
Filling the void
When bacterial numbers become depleted, this leaves a biological vacuum in which opportunistic bacteria start to overgrow. Often, these bacteria create inflammation leading to gum disease (gingivitis).
The oral-gut axis
We swallow an astonishing 1-1.5 litres of saliva a day and, with it we ingest about a billion bacteria. When your oral microbiome is in a state of dysbiosis, you end up swallowing highly unfavourable, inflammatory microbes. These migrate down the digestive tract, disrupting the gut microbiome and potentially contributing to leaky gut.
Additionally, you inevitably swallow residual amounts of the mouthwash itself during every rinse, directly irritating the gut lining and worsening gut dysbiosis.
Environment matters
Just like the gut, the oral microbiome requires a highly specific environment to thrive.
Beneficial, health-promoting bacteria require a low-acidity (neutral to slightly alkaline) environment. Many commercial mouthwashes (particularly those containing strong prescription agents like chlorhexidine) shift the mouth into an acidic state, which invites pathogenic microbes to breed while actively demineralising your tooth enamel.
7 easy ways to restore your microbiome
Here are my top 7 tips for restoring and maintaining a healthy oral microbiome.
1: Make your own natural, healthy mouthwash.Â
Instead of using harsh detergents like sodium lauryl sulfate (SLS) and often quite potent natural antimicrobials, like mint, swap to a gentle homemade rinse. 👉Click here for my mouthwash recipe.
2: Use natural toothpastes that contain baking soda and/or xylotol.
Baking soda acts as a natural alkaline buffer that immediately neutralises harmful mouth acids. By raising your oral pH, it actively stops calcium and phosphate from being leached out of your tooth enamel. Â
Simultaneously, xylitol safely starves out cavity-causing pathogens by mimicking a sugar source they can consume but cannot digest.
3: Boost saliva output.
Saliva is your mouth’s natural defence system - it physically flushes away debris, buffers acids to keep pH more neutral, and delivers phosphate and the essential minerals, calcium, back into the teeth.
Staying hydrated is the key. Water is ideal, but you can also include herbal teas, while avoiding the more acidic ones, such as fruit teas. It's also very important to support your nervous system through daily stress management practices as chronic cortisol and adrenaline spikes can inhibit salivary production.
High salivary cortisol not only leaves your mouth parched and acidic, it also suppresses secretory IgA - an essential antibody in saliva that defends your teeth against decay-causing microbes.
4: Chew natural xylitol chewing gum after a meal.
Chewing natural xylitol gum after a meal delivers a powerful double-benefit: the physical act of chewing rapidly stimulates your mouth’s natural, mineral-rich saliva output to wash away debris and buffer acids, while the xylitol actively starves out residual plaque-forming bacteria.
5: Floss daily.Â
Commit to flossing once a day, preferably before bed, to prevent bacterial biofilms from forming overnight.
6: Use oral probiotics.Â
If you have a history of heavy mouthwash use or have poor dental health, you need to actively reseed the correct strains of bacteria.
Utilising a professional, practitioner-only oral probiotic—such as BioPractica ProDentis Oral - delivers targeted live bacteria to reverse oral dysbiosis.
Book a free discovery call with me here, to gain access to this product.
7: Gentle tongue scraping.Â
Use a pure copper or stainless steel tongue scraper every morning to mechanically remove dead cells and food debris without disrupting your beneficial microbiome.
What to eat to improve your oral health
Your daily dietary choices have a big influence on your oral ecosystem.
Minimise refined carbohydrates
Refined, processed carbohydrates, like crackers, white bread, and chips, tend to stick to your teeth, creating a breeding ground for bad bacteria.
Plus, a salivary enzyme, amylase, immediately breaks down these types of foods into simple sugars which creates acidity in the mouth.
What to Eat - the top 3 foods to restore your oral microbiome (and support overall health)
Crunchy plant foods.
Eating raw, crunchy vegetables like celery, carrots and apples helps to remove plaque, promotes healthy gum circulation and stimulates salivary output.
Leafy Greens.Â
Broccoli, sprouts, kale, and spinach are rich in nitrates, which the good bacteria in your mouth convert to nitrites - the nitrites are then utilised in the body to make nitric oxide, the all-important precursor for metabolic, cardiovascular, and blood sugar regulation.
Cheese.
The traditional cheese board at the end of a meal is very beneficial. Cheese rapidly neutralises dietary acids and helps to remineralise your teeth with bioavailable calcium and phosphate.
Find out exactly what bacteria are living in your mouth
At-home test kits are available that will give you a precise snapshot of your oral microbiome, using a saliva sample.
Since your oral and gut microbiomes are intrinsically linked, I recommend combining this test with a Microbiome Mapping stool test to identify where your gut flora may need rebalancing. Both of these test kits are available in our online dispensary.
Advanced Oral Microbiome Mapping TestUses PCR technology to identify your unique oral microbiome:
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Advanced Gut Microbiome Mapping TestUses PCR technology to identify your unique gut microbiomeplus detailed analysis of your overall gut health
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References
Abdelrahman, S. M., El Samak, M., El-Baz, L. M. F., Hanora, A. M. S., Satyal, P., & Dosoky, N. S. (2024). Effects of Mint Oils on the Human Oral Microbiome: A Pilot Study. Microorganisms, 12(8), 1538.
Aires, A., Barreto, A. S., & Semedo-Lemsaddek, T. (2020). Antimicrobial Effects of Essential Oils on Oral Microbiota Biofilms: The Toothbrush In Vitro Model. Antibiotics (Basel, Switzerland), 10(1), 21.
Bona, E., Cavarra, F., Caramaschi, A., Massa, N., Bazzano, C., Patini, R., Rocchetti, V., & Rimondini, L. (2025). Impact of an Essential-Oil-Based Oral Rinse on Oral and Gut Microbiota Diversity: A Pilot Study. Microbiology Research, 16(12), 251. https://doi.org/10.3390/microbiolres16120251
Brookes, Z., Teoh, L., Cieplik, F., & Kumar, P. (2023). Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced?. International dental journal, 73 Suppl 2(Suppl 2), S74–S81.
Joshipura, K., Muñoz-Torres, F., Fernández-Santiago, J., Patel, R. P., & Lopez-Candales, A. (2020). Over-the-counter mouthwash use, nitric oxide and hypertension risk. Blood pressure, 29(2), 103–112.Â
Tribble GD, Angelov N, Weltman R, Wang B-Y, Eswaran SV, Gay IC, Parthasarathy K, Dao D-HV, Richardson KN, Ismail NM, Sharina IG, Hyde ER, Ajami NJ, Petrosino JF and Bryan NS (2019) Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. Front. Cell. Infect. Microbiol. 9:39. doi: 10.3389/fcimb.2019.00039
Sindhusha, B.S., Srinivas, R., & Pachava, S. (2025). Does Mouthwash Use Increase Risk of Diabetes and Hypertension? A Systematic Review. Journal of Applied Dentistry and Oral Sciences, 11, 68 - 76.
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